61 - SPIN - JRP Full Proposal Incl Projects 1-5

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APPLICATION FORM FULL PROPOSALS JOINT RESEARCH PROJECTS SPIN 2012-2016
FILE NUMBER: 61-SPIN-JRP FULL
Part I:
Joint Research Projects
1. Title of the Joint Research Programme
Incentives driving the transmission of Highly Pathogenic Avian Influenza virus H5N1 in the
Indonesian poultry chain
2. Applicants
a. Main applicant in the Netherlands

Prof. J.A. Stegeman, DVM, PhD, Dip ECVPH
Faculty of Veterinary Medicine
Utrecht University (UU)
Yalelaan 7
3584 CL Utrecht
+31 30 253 1091 (phone)
+31 30 252 1887 (fax)
j.a.stegeman@uu.nl
Male
b. Co-applicant in Indonesia
Prof. Dr. Retno Damayanti Soeyoedono
Bogor Agricultural University
Agatus Campus IPB Darmaga (IPB)
16680 Bogor
Indonesia
+ 62 8129554242 (HP)
retnodmail@yahoo.com
Female
c. Additional project partners in The Netherlands (minimum of one)
Dr. G. Koch (Virologist)

Central Veterinary Institute of Wageningen UR
Department of Virology
Postbox 65
8200 AB Lelystad
Guus.Koch@wur.nl
+31 320 238800 (phone)
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Dr. H. Hogeveen (Animal Health Economist)

Business Economics Group
Wageningen University
Hollandseweg 1
6706 KN Wageningen
henk.hogeveen@wur.nl
+ 31 317-485335 (phone)
Dr. D. Klinkenberg
Yalelaan 7
3584 CL Utrecht
+31 30 253 1248 (phone)
+31 30 252 1887 (fax)
d.klinkenberg@uu.nl
Male
d. Additional project partners in Indonesia (minimum of one)
Dr. Michael Haryadi Wibowo,

Department of Microbiology,
Faculty of Veterinary Medicine,
Gadjah Mada University,
Yogyakarta,
Indonesia
+ 62 274 560862 (phone)
+ 62 274 560861 (fax)
bowomikro@yahoo.com
Male
Prof. David H. Muljono

Eijkman Institute for molecular biology
JL. Diponegoro 69
Jakarta 10430
Indonesia
+62 21 3148695 (phone)
+62 21 3917131 (fax)
davidhm@eijkman.go.id
Male
Dr. drh. Denny Widaya Lukman, MSi (Dr.med vet, MSc, DVM)
Department of Infectious Diseases and Veterinary Public Health
Faculty of Veterinary Madicine
Bogor Agricultural University (IPB)
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Jl. Agatis Kampus IPB Darmaga

Bogor 16680
Indonesia
Phone/Fax : +62-251-8625588
HP : +62-8153803047
email address : dennylukman@hotmail.com
Dr. drh. Yusuf Ridwan, MSi ( Dr, MSc, DVM)
Bogor 16680
Indonesia
Phone : +62-251-8627272
Fax : +62-251-8629466
HP : +62-81213544179
email address : yusufridwan67@yahoo.com
Male
Dr. Ir. Etih Sudarnika, MSi (Dr, MSc, Ir)

Bogor 16680
Indonesia
Phone/Fax : +62-251-8628811
HP : +62-8128322058
email address : etih23@yahoo.com / etih@ipb.ac.id
Female
Dr. drh. Sri Murtini, MSi (Dr, MSc, DVM)

Bogor 16680
Indonesia
Phone/Fax : +62-251-8265876
HP : +62-81384473515
email address : smurtinifs@yahoo.com
Female
Prof.Dr. Ir. Arief Daryanto, M.Ec

Department of Economics
Faculty of Economics and Management
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Bogor 16680
Indonesia
Phone/Fax : +62-251-8626602
HP : +62-8129997947
email address : adaryant@indo.net.id / adaryant@mb.ipb.ac.id
Male
Research Proposal
3. Summary of the Joint Research Project Proposal (Max. 800 words) Word count: 612
Highly Pathogenic Avian Influenza virus (HPAIv) is endemic in Indonesian poultry and individual
cases of (fatal) infections in humans are reported regularly. The biggest threat of the virus, however,
is its capability to re-assort with other Influenza viruses creating the potential for an Influenza
pandemic in humans. In recent years several attempts have been initiated to eliminate HPAIv from
the Indonesian poultry population. Despite these efforts the poultry sector is still confronted with
outbreaks and, more importantly, fatal cases in humans still occur. Moreover, the disease is moving
further eastwards. Although effective vaccines are available, implementation of vaccination
programmes has not resulted in elimination of HPAIv. Moreover, eradication by culling infected
flocks, which appeared successful in e.g. Thailand, has not been implemented in Indonesia. In
addition, cooperation between veterinary authorities and poultry industry in the control of HPAI is
suboptimal in Indonesia.
To improve the HPAI situation control measures that fit the Indonesian situations have to be
developed. For that purpose it is essential to understand 1) the (importance of) transmission routes
of HPAIv within and between the various sectors of the poultry husbandry and 2) the incentives in
the poultry chain that act as driving forces for the contacts between the different parts of that chain.
If this would be known, it can be examined how changes in incentives can affect the contacts within
the poultry chain and, consequently, the transmission of HPAIv.
In this project first a detailed description of the poultry husbandry in Indonesia will be made,
distinguished in broiler type chickens, layer type chickens, ducks and backyard poultry. Next, for
each of these poultry chains the existing contacts between farms within the chain, but also with
farms of other poultry chains will be identified and quantified (frequency at which the contacts
occur) in afield study. Based on this information a mathematical model will be developed describing
the contact structure of the Indonesian poultry husbandry and the transmission within this contact
structure. To establish relevant transmission routes between various parts of the poultry chain a
phylogenetic analysis of HPAIv isolates that have been collected in the past 5 years at several
locations on West-Java will be performed. This molecular epidemiological work will be extended
using isolates collected in a field study in the same area that will be used to establish the contact
structure of the Indonesian poultry husbandry. In addition to this information, literature and expert
knowledge will be used to parameterize the model. The mathematical model will be (in part)
validated using prevalences of infection observed in other field studies.
On the basis of this model, a value chain analysis of Indonesian poultry production will be
performed. It has been used successfully to identify the extent in which animal diseases influence
actors in the chain elsewhere. Here, relationships, characteristics and dynamics that take place
among different actors will be systematically summarized. Next, stochastic simulation models will
be created for the main actors in which the economic effect of measures can be evaluated, including
changes of the contacts between farms and improved bio-security. Moreover, the effect of changes
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in value (money and commodity) exchange in the poultry chain on the contact structure can be
investigated. To estimate the reaction of the chain as a whole upon implementation of measures to
improve control of HPAIv, agent-based modelling will be applied in which the agents represent
various actors in the Indonesian poultry chain. Finally, the JRP addresses the question which
organisational forms of the Indonesian poultry supply chain and government intervention provide
the most efficient way of coordination under the conditions of food safety and security. Principal-
agent theory and cost-benefit analysis are used for supply chain optimisation under different
scenarios.
4. Detailed description of the Priority Programme (Max. 2500 words)Word count: 2498
a. Scientific Background (shared research question(s) or mutual research theme, problem

definition)
Highly Pathogenic Avian Influenza virus (HPAIv) is endemic in Indonesian poultry and (fatal) cases
of infections in humans are reported regularly. The biggest threat of the virus, however, is its
capability to re-assort with other Influenza viruses creating the potential for a pandemic in humans.
In recent years several attempts have been initiated to eliminate HPAIv from Indonesia. Despite
these efforts the poultry sector is still confronted with outbreaks. Moreover, the disease is moving
eastwards. Although effective vaccines are available (Bouma et al., 2009, Poetri et al., 2009)
vaccination has not resulted in elimination of HPAIv. Moreover, eradication by culling infected
flocks, which appeared successful in e.g. Thailand (Tiensin et al, 2005), has not been implemented in
Indonesia. In addition, cooperation between veterinary authorities and poultry industry in the
control HPAI is suboptimal.
b. Objective(s)
To improve the HPAI situation control measures that fit the Indonesian situations have to be
developed. For that purpose it is essential to understand 1) the (importance of) transmission routes
of HPAIv within and between the various poultry production chains (broilers, layers, ducks and
backyard poultry) and 2) the incentives in the poultry chains that act as driving forces for the
contacts between the different parts of that chain. Next, it can be examined how changes in
incentives and changes in the structure of the poultry husbandry can affect the contacts within and
between the poultry chains and, consequently, the transmission of HPAIv.
c. Workplan (approach, methods, deliverables, management)
Approach
A detailed description of the poultry sectors in Indonesia will be made. Next, for each poultry sector
the existing contacts between farms within that sector and to other sectors will be identified and
quantified. Based on this information a mathematical model will be developed describing the
contact structure of the Indonesian poultry husbandry and the transmission rate of HPAIv within
this contact structure will be estimated. To establish relevant transmission routes between various
parts of the poultry chain a phylogenetic analysis of HPAIv isolates that have been collected in the
past 5 years and isolates that will be collected in the field study of this project will be done. In
addition to this information, literature and expert knowledge will be used to parameterize the
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model. The mathematical model will be (in part) validated using prevalences of infection observed
in the field (including previous work).
On the basis of this model, a value chain analysis of Indonesian poultry production will be
performed. It has been used successfully to identify the extent in which animal diseases influence
actors in the chain elsewhere. Here, relationships, characteristics and dynamics that take place
among different actors will be systematically summarized. Next, stochastic simulation models will
be created for the main actors in which the economic effect of measures can be evaluated, including
changes of the contacts between farms and improved bio-security. Moreover, the effect of changes
in value (money and commodity) exchange in the poultry chain on the contact structure can be
investigated. To estimate the reaction of the chain as a whole upon implementation of measures to
improve control of HPAIv, agent-based modelling will be applied in which the agents represent
various actors in the Indonesian poultry chain.
Methods
Contact structure
Literature review and elicitation of expert knowledge will be used to identify the contact types that
could potentially transfer HPAIv. According to poultry type, four production chains will be
distinguished: broilers, layers, ducks and backyard chicken. Local poultry experts will be
interviewed to obtain a comprehensive list of contacts to and from each of the farm types in a
poultry production chain. Contacts may be associated with the transport of live birds, persons,
materials, feed, etc. Next, literature will be reviewed regarding information on the potential of these
contacts to transmit infectious poultry diseases. Finally, these results will be used to develop a
structured questionnaire to collect data on the rate of contacts between poultry farms in West-Java.
This questionnaire will be validated in a pilot study. Next, an area in West-Java/Banten will be
designated. Poultry farms in the area will be visited and classified according to their poultry type.
The location of the farm will be recorded in a Geographical Information System and herd
characteristics such as type of poultry, number of birds, biosecurity level, etc. will be recorded. Next,
farmers will be interviewed to obtain an overview of incoming and outgoing contacts according to
the structured questionnaire made under a; type of contact (for example live birds, feed trucks,
technical personel, manure disposal, etc), where do they come from (poultry farm yes/no, type of
poultry, poultry sector). A logbook will be provided to the farmers to record the contacts. Poultry
collector houses/live bird markets will also be included in the study, although they may be outside
the chosen area. From the interviews and the log books the contact rate can be estimated and risk
factors associated with the contact rate can be estimated, such as biosecurity level and poultry type.
Using the data collected in the field a model will be constructed describing both the contact and
spatial network of the Indonesian poultry population.
Molecular Epidemiology
HPAIv samples collected in the framework of the Indonesian Dutch partnership will be available
for the project. The sample bank includes samples collected at poultry collector houses from
incoming poultry. The databank of the samples comprises epidemiological data such as origin of the
poultry type, geographical location of the farm of origin and date of collection. The samples are
available for full genome sequencing. Sequences will be compared by up-to-date phylogenetic
analytic techniques to assess genetic variation. Next analyses will be performed to determine
whether genotypes cluster according geographically and or according to poultry type.
An area of West-Java will be designated (same area as in project 1). Poultry farms in the area will be
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visited and classified according to their poultry type (broiler, layer, duck, back yard) and sector
(biosecurity I, II, III, IV). The location of the farm will be pointed in a Geographical Information
System and herd characteristics such as type of poultry, number of birds, biosecurity level, etc. will
be recorded. Farmers will be asked to notify IPB (the PhD student) in case the birds show signs of
systemic or respiratory disease or increased mortality. Upon notification samples will be collected
from 10 birds in the acute phase of disease (those showing typical signs) and recently deceased
birds will be submitted for necropsy. Samples will be pooled and tested for the presence of AIv by
RT-PCR. Clinical samples positive for AIv will be stored at -80 0C. Farms within a 3 km radius of the
infected farm and farms with known dangerous contacts will be visited asking for the presence of
disease. In case disease is reported, samples will be collected in a similar way as described above.
Samples will be collected for a period of one to one and a half year depending on the number of
positive farms.
Whole genomes of isolates will be sequenced and the genetic diversity will be analysed to create
phylogenetic trees of the viruses (as in Bataille et al., 2011). Next, genetic data will be combined
with epidemiologic data to refine the tree of transmission events (as in Ypma et al., 2012).
Value chain analysis

The basis for our work will be the development of a quantitative value chain simulation model. In
this model, relationships, characteristics and dynamics that take place among actors in the
Indonesian poultry chain will be systematically summarized (Kaplinsky and Morris, 2001) and a
quantitative poultry value chain simulation model will be developed for West Java. Input for this
value chain will be based on (scientific) literature, available reports and databases and interviews
with key persons in the Javan poultry chain. The quantitative value chain will be developed as a
simulation model as is done recently for the Dutch poultry chain in relation to the use of antibiotics
(Muljono et al., 2012). This simulation model enables the calculation of the effects of changes of, for
instance, production efficiency because of a reduced disease burden. Stochastic Monte Carlo
simulation models will be developed with specific emphasis on estimating the economic effects of
occurrence of viral diseases. Using these models, the expected costs of these diseases can be
estimated. Input for the models will be based on the developed value chain, scientific literature on
the pathogenesis of the diseases under study, local reports on occurrence of these diseases (if
available) and interviews with veterinary experts on these diseases (expertise). The developed
stochastic simulation models will be used to estimate the expected (economic) effect of
implementation of preventive measures.
As a next step the intentions and motivations of stakeholders to implement preventive measures
will be studied. A questionnaire, based on the Theory of Planned Behaviour (Azjen, 1991) will be
constructed. The questionnaire will be carried out for 100 stakeholders, divided over the four
different groups of stakeholders (companies, breeder farms, commercial farms, backyard farms) by
individual interviews. Data will be analysed to quantify the importance of factors with regard to the
motivation of farmers to change their behaviour and their attitude towards the disease and
behaviour to improve the disease status (e.g., Ellis-Iversen et al., 2010).
Finally for the most important groups of farmers (actors) identified in the poultry value chain,
agent-based models will be created, where a farmer is an agent acting in interaction with other
actors in the system. By applying agent-based modelling, the actions and interactions of farmers,
given certain disease prevention policies, can be modelled and the effects of the individual
behaviour on the total farm system can be estimated. This type of multi-agent models have been
applied to model the spread of disease (e.g., Kim et al, 2010), but hardly to model the behaviour of
farmers (e.g., Valeeva and Verwaart, 2011). The parameters to be used in the agent-based models
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will be derived from the economic analysis as well as the questionnaires on motivation and
behaviour of poultry farmers with regard to prevention of viral poultry diseases and the
information on contact structure and spread of HPAI as is studied in elsewhere in the JRP.
Restructuring Indonesian Poultry production

Based on economic theory and an existing conceptual framework (Teulings et al., 2003), the public
interests in Indonesia with regard to the poultry production chain will be inventoried. Based on
economic theory, the framework first addresses the definition of a public interest. Next, the
framework also considers the how to? question: if there is a public interest, which role should the
government play in protecting it? Specifically, the government has three reasons to intervene: In
case of unequally distributed positive effects of a change, in case of complex external effects with
free-riders and in case that the distribution of income is not politically acceptable. By means of a
participatory workshop in co-operation with FAO, including officials from various governmental
levels and stakeholders from the poultry production chain, the conditions for an improved poultry
production chain will be determined.
Based on the quantitative value chain simulation model developed in project 4, the economic
efficiency of production (added value) as well as the risks for spread of AI (based on results from
projects 1 and 2) of the current structure of the poultry production chain in West Java will be
determined. With participation of stakeholders, several elements for alternative structures (e.g.,
fixed farmer-trader relations, limited number of farmers per trader, larger farm size, changed
payment systems, etc.) will be defined. For all these different elements, the effect on economic
efficiency, spread of AI, food security and other conditions that were found to be important during
subproject 1 will be estimated.
Using these estimations calculated several hybrid forms of supply chain organisation will be
developed. Minimal conditions that need to be met according to the information derived during
subproject 1 (e.g., for number of jobs, price of meat or availability of poultry given a growing
population) will be modelled as constraints. Using these constraint models and principal-agent
theory (e.g. Schneeweiss, 2003), first- and second-best solutions for the poultry sector in West Java
can be derived, based on different costs of input factors (feed, barns, veterinary services) and
scenarios (e.g. different growth scenarios of the population) under maximisation of the added value
and minimisation of the risk of AI outbreaks. The difference in risk of AI outbreaks and added value
of the optimal structure will be compared with the added value and risk of AI outbreaks under the
current structure to estimate the value of the improved structure of the poultry production chain.
When an improved (optimal) new structure of the poultry production chain in West Java has been
developed, an analysis will be made whether this new structure can be implemented in West Java
without governmental intervention. In order to do so, again a participatory workshop will be
organised. During this workshop, knowledge will be elicited whether stakeholders will benefit from
a change in structure. As a consequence of external effects (free-riders) as well as stakeholders who
might not benefit from a change in structure of the poultry production chain, it is expected that
governmental intervention is necessary. This intervention brings problems and poses new
dilemmas.
If the government wants to remain flexible in its steering, it will enter into principal/agent
relationships. In case of a specific relationship instead of competition, the activities to be co-
ordinated and those that can be segregated must be determined. The government must also choose
between output and input steering. The answers to questions with regard to these dilemmas will
assist in selecting the intervention instruments to be used: 1. regulation and legislation; 2.
outsourcing of public tasks; 3. public organisation. The choice of one of these forms of intervention
depends on the costs and benefits, which will be estimated, presented to and discussed with the
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government and other stakeholders.
Deliverables
- 4 PhD Theses (3 GLS Utrecht University, 1 Wageningen School of Social Sciences)
- 20 papers in international peer reviewed journals
- Epidemiological Model describing the spread of HPAIv among poultry in West-Java/Banten
- Agent-based model to simulate the effect of stimulation of interventions over the full poultry
chain in West Java
- Proposal for restructuring the poultry husbandry in Indonesia
Management
PhD students will start preparing their work in The Netherlands. Next they will perform their
fieldwork in Indonesia. Data analysis and writing of the PhD theses will be done in The Netherlands.
The postdoc will spend half of his/her time in Indonesia and half of his/her time in The Netherlands
to ensure sufficient integration with the work of projects 1 and 2.
d. Scientific Relevance (including relevance of anticipated results)

The combination of mathematical modelling, molecular epidemiology and social sciences is an
innovative approach. Results will give us new insights in the transmission of HPAIv in Indonesia
and provide new ideas how to intervene in the transmission. These include the effect of changes in
the poultry husbandry driven by economic forces or government interventions.
5. Projects within the programme (include project title and reference number, names of Project
Leaders and abstracts) (Max. 400 words per project) Word count: 1571
Project 61-SPIN-JRP - 1 Unravelling the contacts within and between Indonesian poultry
sectors
Project Leaders : Prof. J.A. Stegeman and Dr. Y. Ridwan
Highly Pathogenic Avian Influenza virus (HPAIv) H5N1 is endemic in Indonesian poultry and the
disease causes considerable economic losses to poultry keepers. Besides the economic damage,
however, the virus is important from the perspective of public health. Effective control of HPAIv
H5N1 in the poultry population is pivotal to reduce the risks posed to humans.
Control programmes based on vaccination or stamping out are either not effective or not feasible in
the Indonesian situation. In order to develop more effective control programs it is crucial to
understand the transmission network, e.g. the quantitative contribution of the relevant
transmission routes of HPAIv within and between the sectors of the poultry husbandry. Once this is
known, one can examine the effect of interventions in simulation studies. As a first step to gain such
understanding in this project the contact structure of the Indonesian poultry husbandry is
quantified.
Local poultry experts will be interviewed to obtain a comprehensive list of contacts to and from
each of the farm types (broilers, layers, ducks and backyard) in a poultry production chain. Next,
literature will be reviewed regarding information on the potential of these contacts to transmit
infectious poultry diseases. These results will be used to develop a structured questionnaire and a
logbook to collect data on the rate of contacts between poultry farms in West-Java.
An area in West-Java/Banten will be designated and relevant contact information will be collected
from farms in this area by interview and log book. Poultry collector houses/live bird markets will
also be included in the study, although they may be outside the chosen area. In addition the contact
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pattern of persons visiting farms (for example feed suppliers, veterinarians, etc) will also be
examined. Analysis of these data will reveal the rate of contacts that could potentially transfer HPAIv
1) between farms within the same poultry production chain (broilers, layers, ducks, backyard), 2)
between farms in different poultry production chains and 3) to and within poultry collector houses
and live bid markets is estimated. Next the effect of various factors, such as poultry type or poultry
sector (biosecurity level I, II, III and IV) will be estimated. Finally, a contact network will be created
including both the contact and spatial components of the Indonesian poultry population.
Project SPIN-61-JRP-2 Unraveling transmission of Highly Pathogenic Avian Influenza virus

using molecular epidemiology
Project Leaders: Dr. G. Koch, Dr. M. Wibowo, Dr. S. Murtini
Highly Pathogenic Avian Influenza virus (HPAIv) H5N1 was first detected in 2003 and since that
year became endemic in Indonesian poultry. The disease causes considerable economic losses to the
poultry industry in particular to the small holders. Besides the economic impact, the virus also
caused 183 human cases of infection of which 156 had a fatal course (WHO March 1, 2012). Effective
control of HPAIv H5N1 in the poultry population is pivotal to reduce the risks posed to humans.
Control programmes based on vaccination or stamping out are either not effective or not feasible in
transmission routes of HPAIv within and between the sectors of the poultry husbandry.
Once this is known, one can examine the effect of interventions in simulation studies. As a first step
to gain such understanding in this project the contact structure of the Indonesian poultry
husbandry is quantified.
In project 1 an area in West-Java/Banten programme will be chosen in which epidemiological data
related to contacts between the different components of the poultry chain. In the same area, a
syndromic surveillance programme will be started. In the programme farmers are requested to
submit samples in case clinical signs such increased mortality, drop in (egg) production or reduced
water and food consumption is observed. The samples will be tested for AI in a RT-PCR. Those that
collect samples will be at the footprint of those that collect the epidemiological data in project 1. To
increase willingness to participate the resulting PCR data will be stored anonymously in a database
although geographical location of the farm concerned has to be stored for later analysis. In case of a
positive PCR the neighbouring and contact farms will be visited to evaluate the production numbers
in those farms and collect samples if findings indicate possible AI infection. Poultry collector
houses/live bird markets will also be included in the surveillance, although they may be outside the
chosen area. Positive samples will be processed for whole influenza genome sequencing. The
sequence data will be used in phylogenetics to produce a genetic transmission network.
Project SPIN-61-JRP-3 Epidemiological model for Highly Pathogenic Avian Influenza virus
transmission in Indonesia
Project Leaders : Dr. D. Klinkenberg and Dr. E. Sudarnika
disease causes considerable economic losses to poultry keepers of both professional and back yard
farms. Besides the economic damage, however, the virus is important from the perspective of public
health. Effective control of HPAIv H5N1 in the poultry population is pivotal to reduce the risks posed
to humans.
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In this project we will develop an epidemiological model describing the transmission of HPAIv in
the Indonesian poultry husbandry. For that purpose the contact network from project 1 and the
transmission parameters collected in project 2 will be combined. The resulting model can be used to
investigate the effect of changes in contact structure on the transmission of HPAIv.
First, an epidemiological model will be developed that includes the contacts within a poultry
production chain and the interactions that exist with other poultry chains. The poultry production
chains of interest here are those of broilers, layers, ducks and backyard chickens. Besides contacts
within and between these chains, the spatial network of these farms will be included in the model.
Next, the contact rate as established in project 1 will be incorporated into the model as well as the
transmission parameters generated in project 2.
Once the model has been parameterized, it will be (partly) validated using available datasets. Next,
different scenarios will be tested in order to examine the effect of differences in contact rate at the
transmission of HPAIv in Indonesian poultry. In addition the transmission parameters in the model
can also be varied in order to estimate the effect of intervention measures like vaccination or
cleaning and disinfection.
The model will provide insight in the highly complex transmission dynamics within the Indonesian
poultry industry.
Project 4 Economic benefits of a reduction of viral poultry diseases

Project Leaders : Dr. H. Hogeveen and Dr. A. Daryanto
Programmes to reduce the level of infection of HPAI in Indonesia are not always successful. Lack of
(proven) economic efficiency of preventive measures explain part of this lack of success. Another
part might be explained by the fact that farmers, especially smaller family farms, might be driven by
other motivators than only economics. In order to correctly estimate the economic effects of
interventions, more viral poultry diseases than only HPAI should be taken into account, e.g. New
Castle Disease and infectious bursal disease. An important part of our in the research approach
towards improved health and safety in Indonesia is the explicit incorporation of economics and
farmer behaviour. By studying the economics of combined prevention of viral poultry diseases in
West Java as well as the motivators for uptake of preventive measures for the different actors in the
Javan poultry value chain, policy making towards an improved and safer Javan poultry chain can be
supported. The proposed research consists of 5 parts. The first subproject aims at the development
of a quantitative value chain simulation model, using existing knowlege about the poultry value
chain in West Java. In the second subproject Monte Carlo simulation models will be developed to
estimate the costs of viral poultry diseases for different stakeholders in the West Javan poultry
chain. These models are based on existing knowledge of the pathogenesis of viral poultry diseases
and existing expertise on the economic effects of these diseases. The developed models will be
applied to estimate the costs and benefits of interventions. In order to be able to predict the
behaviour of stakeholders, in subproject 3 the motivation of stakeholders in West Java to implement
interventions will be studied, based on the Theory of Planned Behaviour and a questionnaire. All
information will be synthesized in an agent-based model (subproject 4) to simulate the effect of
stimulation of interventions over the full poultry chain in West Java.
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Project SPIN-61-JRP-5 Restructuring the poultry supply chain in West Java

Project Leaders: Dr. H. Hogeveen and Dr. D. Lukman
As a consequence of its vulnerability to avian influenza (AI) the poultry husbandry in Indonesia
should be re-organised so as to optimise the disease prevention efficiency of the chain under the
condition of food security for the population. Since the external effects that are caused by the
current method of poultry production and marketing, are complex, government intervention is
needed. The project addresses the question which organisational forms of the Indonesian poultry
supply chain and government intervention provide the most efficient way of coordination under the
conditions of food safety and security. Principal-agent theory and cost-benefit analysis are used for
supply chain optimisation under different scenarios.
6. Relevant publications by members of the research group(s) (as defined under 2)

(a limit of 25 publications applies for each research group member referred to. Only list those
publications most pertinent to this application.
International (refereed) journals
J.A. Stegeman
Spekreijse, D., Bouma, A., Koch, G., Stegeman, J.A.
Quantification of dust-borne transmission of highly pathogenic avian influenza virus between
chickens. Influenza and other Respiratory diseases (IF 3,812), in press.
Gonzales, GL., Elbers, A.R.W., Koch, G., De Wit, J.J., and Stegeman, J.A.
Rate of introduction of a low pathogenic avian influenza virus infection in different poultry
production sectors in The Netherlands. Influenza and other Respiratory diseases (IF 3,812), in
press.
Ypma, R.J.F., Bataille, A.M.A., Stegeman, A., Koch, G., Wallinga, J., and Van Ballegooijen, W.M., 2011.
Unraveling transmission trees of infectious diseases by combining genetic and epidemiological
data. Proceedings of the Royal Society B., 279, 444-450. (IF 5,064)
Te Beest, D.E., Stegeman, J.A., Mulder, Y.M., Van Boven, M., and Koopmans, M.P.G., 2011.
Exposure of uninfected poultry farms to HPAI (H7N7) virus by professionals during outbreak
control activities. Zoonoses and Public Health, 58, 493-9. (IF 2,220)
Comin, A., Klinkenberg, D., Marangon, S., Toffan, A., and Stegeman, A., 2011.
Transmission dynamics of low pathogenicity Avian Influenza infections in turkey flocks. Plos
one, 6, e26935. (IF 4,411)
Page 12 of 117
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Jonges, M., Bataille, A., Enserink, R.M., Meijer, A., Fouchier, R., Stegeman A., Koch, G., Koopmans
M., 2011. Comparative analysis of avian influenza virus diversity during a highly pathogenic
avian influenza virus (H7N7) outbreak. J. Virology, 85, 10598-10604. (IF 5,189)
Te Beest, D.E., Hagenaars, T., Stegeman, A., Koopmans, M.P., and Van Boven, M., 2011.
Risk based culling for highly infectious livestock diseases. Vet Res 42, 81. (IF 3,765)
Bataille, A., Van der Meer, F., Stegeman, A., and Koch, G., 2011.
Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza
epidemic. PLOS pathogens 7, e1002094. (IF 9,079)
Airborne transmission of a highly pathogenic avian influenza virus strain H5N1 between groups
of chickens quantified in an experimental setting. Veterinary Microbiology, 152, 88-95. (IF 3,256)
Poetri, O., Bouma, A., Claassen, I., Koch, G., Soejoedono, R., Stegeman, J.A., and Van Boven, M., 2011. A
single vaccination of commercial broilers does not reduce transmission of H5N1 highly
pathogenic avian influenza. Veterinary Research, 42: 74. (IF 3,765)
Fasina, F.O., Rivas, A.L. Bisschop, S.P., Stegeman, J.A., and Hernandez, J.A., 2011.
Identification of risk factors associated with highly pathogenic avian influenza H5N1 virus
infection in poultry farms in Nigeria during the epidemic of 2006-2007. Preventive Veterinary
Medicine, 98, 2004-8. (IF 2,07)
Te Beest, D.E., Van Boven, M., Bos, M.E.H., Stegeman, A., and Koopmans, M. 2010.
Effectiveness of personal protective equipment and Oseltamivir prophylaxis during Avian
Influenza A (H7N7) epidemic, The Netherlands, 2003. Emerging Infectious Diseases, 16, 1562-8.
(IF 6,859)
Bos, M.E.H., Te Beest, D.E., Van Boven, M., Robert-Du Ry van Beest Holle, M., Meijer, A., Bosman, A.,
Mulder, Y., Koopmans, M.P.G., and Stegeman, A., 2010. High probability of Avian Influenza virus
(H7N7) transmission from poultry to humans active in disease control on infected farms. Journal
of Infectious Diseases 201, 1390-1396. (IF 6,288)
Gonzales, J.L., Elbers, A.R.W., Bouma, A., Koch, G., De Wit, J.J., and Stegeman, J.A., 2010.
Low-pathogenic notifiable Avian Influenza serosurveillance and the risk of infection in poultry A
critical review of the European Union active surveillance programme (2005-2007). Influenza and
other respiratory viruses 4, 91-99. (IF 3,812)
Van der Goot, J.A., Engel, B., Van de Water, S.G., Buist, W., De Jong, MC., Koch, G., Van Boven , M.,
and Stegeman A., 2010. Validation of diagnostic tests for detection of avian influenza in
vaccinated chickens using Bayesian analysis. Vaccine, 281, 1771-7. (IF 3,572)
Tiensin, T., Ahmed, S.S., Rojahnastien, S., Songserm, T., Ratanakom, P., Chaichoun, K., Kalpravidh,
K., Wongkasemijt, K., Patchimasiri, S., Chanachai, K., Thanapongtam, W., Chotinan, S., Stegeman, A.,
and Nielen, M., 2009. Ecologic risk factor investigationof clusters of avian influenza (H5N1) virus
infection in Thailand. Journal of Infectious Diseases, 199, 1734-43. (IF 6,288)
Poetri, O.N., Bouma, A., Murtini, S., Claassen, I., Koch, G., Soejoedono, S., Stegeman, J.A., and Van
Boven, M., 2009.An inactivated H5N2 vaccine reduces transmission of highly pathogenic avian
influenza H5N1 virus in native chickens. Vaccine, 27, 2864-69. (IF 3,572)
Bavinck, V., Bouma, A., Van Boven, M., Bos, M.E.H., Stassen, E., and Stegeman, J.A., 2009.
Page 13 of 117
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The role of backyard poultry flocks in the epidemic of highly pathogenic avian influenza (H7N7)
in The Netherlands in 2003. Preventive Veterinary Medicine, 88, 278-85. (IF 2,07)
Bouma, A., Teguh Muljono, A., Jatikusuma, A., Nell, A.J., Mujiartiningsih, S., Dhamaryinthi, I., Sawitri
Siregar, E., Claasen, I., Koch, G., Stegeman J.A., 2008. Field trial for assessment o Avian Influenza
vaccination effectiveness in Indonesia. Rev. Scientif. Tech. OIE, 27, 633-642. (IF 1,609)
Van der Goot, J., van Boven, M., Stegeman, A., van de Water, S.J., De Jong, M.C.M., and Koch, G.,
2008. Transmission of highly pathogenic avian influenza H5N1 virus in Pekin ducks is
significantly reduced by a genetically distant H5N2 vaccine. Virology, 382, 91-97. (IF 3,305)
Tiensin, T, Nielen, M, Vernooij, H, Songserm, T, Kalpravidh, W, Chotiprasatintara, S., Chaisingh, A.,
Wongkasemjit, S., Chanachai, K., Thanapongtham, W., Srisuvan, T, and Stegeman, A., 2007.
Transmission of the highly pathogenic avian influenza H5N1 virus within flocks during the 2004
epidemic in Thailand. Journal of Infectious Diseases, 196, 1679-84. (IF 6,288)
Bos, M.E., van Boven, M., Nielen, M., Bouma, A., Elbers, A.R.W., Nodelijk, G., Koch, G., Stegeman,
J.A.,and De Jong, M.C.M., 2007. Estimating the day of highly pathogenic avian influenza (H7N7)
virus introduction into a poultry flock based on mortality data. Veterinary Research, 38, 493-504.
(IF 3,765)
Tiensin, T., Chaitaweesup, P., Songserm, T., Chaising, A., Hoonsuwan, W., Buranathai, C.,
Parakamawongsa, T., Premashtira, S., Amonsin, A., Gilbert, M., Nielen, M., and Stegeman, J.A., 2005.
Highly pathogenic Avian Influenza H5N1, Thailand, 2004. Emerging Infectious Diseases, 11, 1664-
1672. (IF 6,859)
Thomas, M.E., Bouma, A., Ekker, H.M., Fonken, A.J.M., Stegeman, J.A., and Nielen, M., 2005.
Risk factors for the introduction of highly pathogenic Avian Influenza virus into poultry farms
during the epidemic in the Netherlands in 2003. Preventive Veterinary Medicine 69, 1-11. (IF
2,07)
Stegeman, J.A., Bouma, A., Elbers, A.R.W., De Jong, M.C.M., Nodelijk, G., De Klerk, F., Koch, G., and
Van Boven, M., 2004. The avian influenza A virus (H7N7) epidemic in The Netherlands. Course of
the epidemic and effectiveness of control measures. Journal of Infectious Diseases, 190:
G. Koch
Bataille A, van der Meer F, Stegeman A, Koch G (2011)
Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian
Influenza Epidemic. PLoS Pathog 7(6): e1002094. doi:10.1371/journal.ppat.1002094 (IF 9,079)
Ypma RJ, Bataille AM, Stegeman A, Koch G, Wallinga J, van Ballegooijen WM.
Unravelling transmission trees of infectious diseases by combining genetic and epidemiological
data. Proc Biol Sci. 2012 Feb 7;279(1728):444-50. Epub 2011 Jul 6. (IF 5,064)
Jonges M, Bataille A, Enserink R, Meijer A, Fouchier RA, Stegeman A, Koch G, Koopmans M.
Comparative analysis of avian influenza virus diversity in poultry and humans during a highly
pathogenic avian influenza A (H7N7) virus outbreak. J Virol. 2011 85(20):10598-604. (IF 5,189)
Gonzales JL, Elbers AR, Bouma A, Koch G, de Wit JJ, Stegeman JA
Transmission characteristics of low pathogenic avian influenza virus of H7N7 and H5N7
subtypes in layer chickens. Veterinary Microbiology 2012;155(2-4):207-13. (IF 3,256)
Poetri O., Bouma A., Claassen, I., Koch, G., Soejoedono, R., Stegeman, A., Van Boven (2011).
A single vaccination of commercial broilers does not reduce transmission of H5N1 higly
pathogenic avian influenza. Veterinary Research 42(1) .
Poetri O. N., Bouma, A., Murtini S., Claassen I., Koch, G., Soejoedono R.D., Stegeman, J. A.,
Van Boven, M. (2009). An inactivated H5N2 vaccine reduces transmission of highly pathogenic
H5N1 avian influenza virus among native chickens. Vaccine 27(21): 2864-2869 (IF 3,572)
Page 14 of 117
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Spekreijse D., Bouma A., Koch, G., Stegeman, J. A. (2011).

Airborne transmission of a highly pathogenic avian influenza virus strain H5N1 between groups
of chickens quantified in an experimental setting. Veterinary Microbiology 152(1-2): 88-95. (IF
3,256)
Spekreijse D., Bouma A., Stegeman J. A., Koch G., de Jong, M. C. (2011).
The effect of inoculation dose of a highly pathogenic avian influenza virus strain H5N1 on the
infectiousness of chickens. Veterinary Microbiology 147(1-2):59-66. (IF 3,256)
Dundon WG, Heidari A, Fusaro A, Monne I, Beato MS, Cattoli G, Koch G, Starick E, Brown IH, Aldous
EW, Briand FX, Le Gall-Recule G, Jestin V, Jrgensen PH, Berg M, Zohari S, Metreveli G, Munir M,
Sta hl K, Albina E, Hammoumi S, Gil P, de Almeida RS, Smietanka K, Doman ska-Blicharz K, Minta Z,
Van Borm S, van den Berg T, Martin AM, Barbieri I, Capua I;
Genetic data from avian influenza and avian paramyxoviruses generated by the European
network of excellence (EPIZONE) between 2006 and 2011--review and recommendations for
surveillance. EPIZONE Network of Excellence Molecular Epidemiology of AI; APMV working
group. Veterinary Microbiology 2012 Jan 27;154(3-4):209-21 (IF 3,256)
Loeffen WL, Stockhofe N, Weesendorp E, van Zoelen-Bos D, Heutink R, Quak S, Goovaerts D, Heldens
JG, Maas R, Moormann RJ, Koch G Efficacy of a pandemic (H1N1) 2009 virus vaccine in pigs
against the pandemic influenza virus is superior to commercially available swine influenza
vaccines. Veterinary Microbiology 2011, 152(3-4):304-14 (IF 3,256)
Loeffen WL, de Vries RP, Stockhofe N, van Zoelen-Bos D, Maas R, Koch G, Moormann RJ, Rottier PJ, de
Haan CA. Vaccination with a soluble recombinant hemagglutinin trimer protects pigs against a
challenge with pandemic (H1N1) 2009 influenza virus. Vaccine. 2011 29:1545-50. (IF 3,572)
Gonzales JL, Elbers AR, Bouma A, Koch G, de Wit JJ, Stegeman JA.
Low-pathogenic notifiable avian influenza serosurveillance and the risk of infection in poultry - a
critical review of the European Union active surveillance programme (2005-2007). Influenza
Other Respiratory Viruses. 2010 Mar;4(2):91-9. (IF 3,812)
van der Goot JA, Engel B, van de Water SG, Buist W, de Jong MC, Koch G, van Boven M, Stegeman A.
Validation of diagnostic tests for detection of avian influenza in vaccinated chickens using
Bayesian analysis. Vaccine. 2010 28(7):1771-7. (IF 3,572)
Van Reeth K, Brown IH, Du rrwald R, Foni E, Labarque G, Lenihan P, Maldonado J, Markowska-Daniel
I, Pensaert M, Pospisil Z, Koch G. Seroprevalence of H1N1, H3N2 and H1N2 influenza viruses in
pigs in seven European countries in 2002-2003. Influenza Other Respiratory Viruses. 2008
May;2(3):99-105. (IF 3,812),
Bouma A, Claassen I, Natih K, Klinkenberg D, Donnelly CA, Koch G, van Boven M.
Estimation of transmission parameters of H5N1 avian influenza virus in chickens. PLoS
Pathogens 2009 Jan;5(1):e1000281. (IF 9,079)
Bos ME, Nielen M, Koch G, Bouma A, De Jong MC, Stegeman A.
Back-calculation method shows that within-flock transmission of highly pathogenic avian
influenza (H7N7) virus in the Netherlands is not influenced by housing risk factors. Preventive
Veterinary Medicine 2009 ;88(4):278-85. (IF 2,07)
Bos ME, Nielen M, Koch G, Stegeman A, De Jong MC.
Effect of H7N1 vaccination on highly pathogenic avian influenza H7N7 virus transmission in
turkeys. Vaccine. 2008; 26(50):6322-8. (IF 3,572)
van der Goot JA, van Boven M, Koch G, de Jong MC.
Variable effect of vaccination against highly pathogenic avian influenza (H7N7) virus on disease
and transmission in pheasants and teals. Vaccine. 2007;25(49):8318-25. (IF 3,572)
Page 15 of 117
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Maas R, Tacken M, Ruuls L, Koch G, van Rooij E, Stockhofe-Zurwieden N.

Avian influenza (H5N1) susceptibility and receptors in dogs. Emerging Infectious Disease. 2007
(8):1219-21. (IF: 6,859)
Bos ME, Van Boven M, Nielen M, Bouma A, Elbers AR, Nodelijk G, Koch G, Stegeman A, De Jong MC.
Estimating the day of highly pathogenic avian influenza (H7N7) virus introduction into a poultry
flock based on mortality data. Veterinary Research 2007 38(3):493-504. (IF 3,765)
van der Goot JA, Koch G, de Jong MC, van Boven M.
Quantification of the effect of vaccination on transmission of avian influenza (H7N7) in chickens.
Proceedings National Academy of Science U S A. 2005;102(50):18141-6. (IF 9.771)
Stegeman A, Bouma A, Elbers AR, de Jong MC, Nodelijk G, de Klerk F, Koch G, van Boven M
Avian influenza A virus (H7N7) epidemic in The Netherlands in 2003: course of the epidemic and
effectiveness of control measures. Journal of Infectious disease 2004;190(12):2088-95. (IF 6,288)
Fouchier RA, Schneeberger PM, Rozendaal FW, Broekman JM, Kemink SA, Munster V, Kuiken
Rimmelzwaan GF, Schutten M, Van Doornum GJ, Koch G, Bosman A, Koopmans M, Osterhaus AD.
Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute
respiratory distress syndrome. Proceedings National Academy of Science U S A.
2004;101(5):1356-61. (IF 9.771)
van der Goot JA, de Jong MC, Koch G, Van Boven M.
Comparison of the transmission characteristics of low and high pathogenicity avian influenza A
virus (H5N2). Epidemiology and Infections. 2003;131(2):1003-13. (IF 2.257)
Siregar, E., Claasen, I., Koch, G., Stegeman J.A., 2008.
Field trial for assessment o Avian Influenza vaccination effectiveness in Indonesia. Review
Scientific. Technology OIE, 27, 633-642. (IF 1,609)
Van der Goot, J., van Boven, M., Stegeman, A., van de Water, S.J., De Jong, M.C.M., and Koch, G.
2008. Transmission of highly pathogenic avian influenza H5N1 virus in Pekin ducks is
D. Klinkenberg
Severins, M., Klinkenberg, D., Heesterbeek, H., 2012.
How selection forces dictate the variant surface antigens used by malaria parasites. Journal of the
Royal Society Interface 9, 246-260. (IF 4,259)
Galsworthy S.J., Ten Bosch Q.A., Hoye B.J., Heesterbeek J.A.P., Klaassen M., Klinkenberg D., 2011.
Effects of infection-induced migration delays on the epidemiology of avian influenza in wild
mallard populations. PLoS ONE 6: e26118. (IF 4,411)
Klinkenberg, D., Nishiura, H., 2011.
The correlation between infectivity and incubation period of measles, estimated from
households with two cases. Journal of Theoretical Biology 284, 52-60. (IF 2,371)
Fraser, C., Cummings, D.A.T., Klinkenberg, D., Burke, D.S., Ferguson, N.M., 2011.
Influenza transmission in households during the 1918 pandemic. American Journal of
Epidemiology 174, 505-514. (IF 5,745)
Klinkenberg, D., Thomas, M.E., Calvo, A.F.F., Bouma, A., 2011.
Salmonella Enteritidis surveillance by egg immunology: impact of the sampling scheme on the
release of contaminated table eggs. Risk Analysis 31, 1260-1270. (IF 2,344)
Courcoul, A., Hogerwerf, L., Klinkenberg, D., Nielen, M., Vergu, E., Beaudeau, F., 2011.
Modelling effectiveness of herd level vaccination against Q fever in dairy cattle. Veterinary
Research 42, 68. (IF 3,765)
Page 16 of 117
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Thomas, M.E., Bouma, A., Klinkenberg, D., 2011.

A comparison of transmission characteristics of Salmonella enterica serovar Enteritidis between
pair-housed and group-housed laying hens Veterinary Research 42, 40. (IF 3,765)
Hollingsworth, T.D., Klinkenberg, D., Heesterbeek, H., Anderson, R.M., 2011.
Mitigation strategies for pandemic influenza A: balancing conflicting policy objectives. PLoS
Computational Biology 7, e1001076. (IF 5,515)
Velkers, F.C., Swinkels, W.J., Rebel, J.M., Bouma, A., Daemen, A.J., Klinkenberg, D., Boersma, W.J.,
Stegeman, J.A., De Jong, M.C.M., Heesterbeek, J.A.P., 2010. Effect of Eimeria acervulina infection
history on the immune response and transmission in broilers. Veterinary Parasitology 173, 184-
192. (IF 2,458)
Thomas, M.E., Klinkenberg, D., Ejeta, G., Van Knapen, F., Bergwerff, A.A., Stegeman, J.A., Bouma, A.,
2009. Quantification of horizontal transmission of Salmonella enterica serovar enteritidis
bacteria in pair-housed groups of laying hens. Applied and Environmental Microbiology 75,
6361-6366. (IF3,778)
Nishiura, H., Klinkenberg, D., Roberts, M., Heesterbeek, J.A.P., 2009.
Early epidemiological assessment of the virulence of emerging infectious diseases: A case study
of an influenza pandemic. PLoS ONE 4, e6852. (IF 4,411)
Van Gerwe, T., Miflin, J.K., Templeton, J.M., Bouma, A., Wagenaar, J.A., Jacobs-Reitsma, W.F.,
Stegeman, A., Klinkenberg, D., 2009.
Quantifying transmission of campylobacter jejuni in commercial broiler flocks. Applied and
Environmental Microbiology 75, 625-628. (IF 3,778)
Bouma, A., Claassen, I., Natih, K., Klinkenberg, D., Donnelly, C.A., Koch, G., Van Boven, M., 2009.
Pathogens 5, e1000281. (IF 9,079)
van Boven, M., Klinkenberg, D., Pen, I., Weissing, F.J., Heesterbeek, H., 2008.
Self-interest versus group-interest in antiviral control. PLoS ONE 3, e1558. (IF 4,411)
Effects of heterogeneity in infection-exposure history and immunity on the dynamics of a
protozoan parasite. Journal of the Royal Society Interface 4, 841-849. (IF 4,259)
van Boven, M., Koopmans, M., Du Ry van Beest Holle, M., Meijer, A., Klinkenberg, D., Donnelly, C.A.,
Heesterbeek, H.J., 2007. Detecting emerging transmissibility of avian influenza virus in human
households. PLoS Computational Biology 3, e145. (IF 5,515)
Klinkenberg, D., Heesterbeek, J.A.P., 2007.
A model for the dynamics of a protozoan parasite within and between successive host
populations. Parasitology 134, 949-958. (IF 2,53)
Klinkenberg, D., Fraser, C., Heesterbeek, H., 2006.

The effectiveness of contact tracing in emerging epidemics. PLoS ONE 1, e12. (IF 4,411)
A simple model for the within-host dynamics of aprotozoan parasite. Proceedings of the Royal
Society B: Biological Sciences 272, 593-600. (IF5,064)
Klinkenberg, D., Nielen, M., Mourits, M.C.M., De Jong, M.C.M., 2005.
The effectiveness of classical swine fever surveillance programmes in the Netherlands. Preventive
Veterinary Medicine 67, 1937. (IF 2,07)
Klinkenberg, D., Everts-Van Der Wind, A., Graat, E.A.M., De Jong, M.C.M., 2003.
Quantification of the effect of control strategies on classical swine fever epidemics. Mathematical
Biosciences 186,145-173. (IF 1,593)
Klinkenberg, D., De Bree, J., Laevens, H., De Jong, M.C.M., 2002.
Page 17 of 117
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Within- and between-pen transmission of Classical Swine Fever Virus: A new method to estimate
the basic reproduction ratio from transmission experiments. Epidemiology and Infection 128,
293-299. (IF 2,257)
Mangen, M.J., Jalvingh, A.W., Nielen, M., Mourits, M.C.M., Klinkenberg, D., Dijkhuizen, A.A., 2001.
Spatial and stochastic simulation to compare two emergency-vaccination strategies with a
marker vaccine in the 1997/1998 Dutch Classical Swine Fever epidemic. Preventive Veterinary
Medicine 48, 177-200. (IF 2,07)
H. Hogeveen
Currently, H. Hogeveen has published a total of 77 papers in ISI journals, of which 69 (90%) are
published in the 25% highest impact journals within their categories. His h-factor is 16. The list
underneath is a selection of these publications, that are most relevant for this research proposal.
The average impact factors of the journals of this list is 2.07. All but one of these papers are
published in the 25% highest impact journals within their categories. Thirteen of the 17 listed
papers are in the 10% highest impact journals within their categories.

Vosough Ahmadi, B., A.G.J. Velthuis, H. Hogeveen and R.B.M. Huirne (2006).
Simulating E. coli O157 transmission to assess effectiveness of slaughterhouse inverventions.
Preventive Veterinary Medicine, 77 (1): 15-30.
Valeeva, N.I., T.J.G.M. Lam and H. Hogeveen (2007).
Motivation of dairy farmers to improve mastitis management. Journal of Dairy Science, 90: 4466-
4477.
Vosough Ahmadi, B., K. Frankena, J. Turner, A.G.J. Velthuis, H. Hogeveen and R.B.M. Huirne (2007).
Effectiveness of interventions in reducing the prevalence of E.coli O157:H7 in lactating cows in
Dutch dairy herds. Veterinary Research, 38: 755-771.
Steeneveld, W. H. Hogeveen and J.M. Swinkels. 2007.
Stochastic modelling to assess economic effects of chronic subclinical mastitis caused by
Streptococcus uberis. Journal of Dairy Research 74: 459-467.
Huijps, K., S. de Vliegher, T.J.G.M. Lam and H. Hogeveen (2009).
Cost estimation of heifer mastitis by stochastic modelling. Veterinary Microbiology, 134: 121-
127.
Benedictus, A., H. Hogeveen and B.R. Berends (2009).
The price of the precautionary principle: cost-effectiveness of BSE intervention strategies in the
Netherlands. Preventive Veterinary Medicine, 89:212-222.
Halasa, T., H. Hogeveen, M. Nielen and R.B.M. Huirne (2009).
Bio-economic modelling of mastitis. Livestock Science, 124: 295-305.
Huijps, K., H. Hogeveen, T.J.G.M. Lam and R.B.M. Huirne (2009).

Preferences of cost factors for mastitis management among Dutch dairy farmers using Adaptive
Conjoint Analysis. Preventive Veterinary Medicine, 92: 351-359.
Ellis-Iversen, J., A.J. Cook, E. Watson, M. Nielen, L. Larkin, M. Wooldridge and H. Hogeveen (2010).
Perceptions, circumstances and motivators that influence implementation of zoonotic control
programs. Preventive Veterinary Medicine, 93: 276-285.
Huijps, K., H. Hogeveen, T.J.G.M. Lam and A.J.G.M. Oude Lansink (2010).
Efficiency of management measures to improve the mastitis situation on farm level. Journal of
Dairy Science, 93:115-124.
Page 18 of 117
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Bruijnis, M.R.N., H. Hogeveen and E.N. Stassen (2010).

Assessing the economic consequences of foot disorders in dairy cattle using a dynamic stochastic
simulation model. Journal of Dairy Science, 93: 2419-2432.
Inchaisri, C., R. Jorritsma, P.L.A.M. Vos, G.C. van der Weijden and H. Hogeveen (2010).
Economic consequences of reproductive performance in dairy cattle. Theriogenology, 74: 835-
846.
Huijps, K., H. Hogeveen, G. Antonides, N. Valeeva, T.J.G.M. Lam and A.G.J.M. Oude Lansink (2010).
Sub-optimal decision making of dairy farmers with respect to mastitis management. European
Review of Agricultural Economics. 37: 553-568.
Lam, T.J.G.M., J. Jansen, B.H.P. van den Borne, R.J. Renes and H. Hogeveen (2011).
What veterinarians need to know about communication to optimise their role as advisors on
udder health in dairy herds. New Zealand Veterinary Journal, 59:8-15.
Analysis of the economically optimal voluntary waiting period. Journal of Dairy Science 94: 3811-
3824.
Charlier, J. M. van der Voort, H. Hogeveen and J. Vercruysse (2012).
ParaCalc - a novel tool to evaluate the economic importance of worm infections on the dairy.
Veterinary Parasitology 184: 204-211.
Derks, M., L.M.A. van de Ven, T. van Werven, W.D.J. Kremer and H. Hogeveen (2012).
The perception of veterinary herd health management by Dutch dairy farmers and its current
status in the Netherlands: an outline. Preventive Veterinary Medicine, in press.
R. Soejoedono
He F, Soejoedono RD, Murtini S, Goutama M and Kwang J. 2010.
Complementary monoclonal antibody-based dot ELISA for universal detection of H5 avian
influenza virus. BMC Microbiology 2010, 10:330 (IF 2,96)
pathogenic avianinfluenza. Veterinary Research 42(1) . (IF 3,765)
Poetri O. N., Bouma, A., Murtini S., Claassen I., Koch, G., Soejoedono R.D., Stegeman, J. A., Van Boven,
M. (2009).
An inactivated H5N2 vaccine reduces transmission of highly pathogenic H5N1 avian influenza
virus among native chickens. Vaccine 27(21): 2864-2869 (IF 3,572)
S. Murtini
Boven, M., 2009.
An inactivated H5N2 vaccine reduces transmission of highly pathogenic avian
Murwani R, Murtini S. 2009.

Effect of chlortetracycline additive in broiler fed local diets on antibody titers to NDV vaccine.
International Journal of Poultry Science 8 (8): 755-759.
Murtini S, Murwani R, F. Satrija, E Handaryani, 2010.
Anti Mareks Disease Virus Activity of Scurrula oortiana ( Tea Mistletoe) Stem Extract in
Embryonated Chicken Eggs. International Journal of Poultry Science 9 (9): 879-885.
Page 19 of 117
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A. Daryanto
Rochman, TR, Gumbira Said E, Daryanto A and Nuryantoro N (2011),

Analysis of National Agricultural Industry Competitiveness in Nanotechnology Development
Perspective Using SWOT-AHP Methods, International Journal of Business and Management, 6(8),
235-244.
D. Muljono
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Comparation of Several Newcastle Disease Vaccination Programs on the Native Chicken. Journal
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Comparison of Antibody Titer in Broiler Chicken Vaccinated at 7 and 14 Days Old with Avian
Influenza H5N2 Subtype Heterologous Vaccine, Journal of Sain Veteriner, Faculty of Veterinary
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Wibowo MH, and Wahyuni AETH. 2008.

Pathogenicity Study of Escherichia coli Isolated from Poultry on Broiler Chicken at 15-days of
Age. Journal Veteriner, Faculty of Veterinary Medicine, Udayana University, Bali, Indonesia. 9 (2):
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Isolation and Serological Identification of Avian Influenza Virus from Poultry Sample Obtained
from Jogjakarta Special Territory and Central Java. Journal of Sain Veteriner, Faculty of Veterinary
Asmara W, Wibowo MH, and Tabbu CR. 2005.
Hemagglutinin H5 Subtype Identification of Avian Influenza Virus, Isolated from Various Species
of Birds Using RT-PCR. Journal of Sain Veteriner, Faculty of Veterinary Medicine, Gadjah Mada
University. 23 (1): 42-46.
S. Murtini
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Penetapan rute dan dosis inokulasi pada telur ayam berembrio sebagai media uji khasiat ekstrak
benalu teh (Scurrula oortiana). Jurnal Ilmu Ternak dan Veteriner 11 (2): 137-143. ISSN : 0853-
7380
Murtini S, R. Murwani, F. Satrija, E. Handharyani. 2006.
Efek imunomodulasi ekstrak benalu teh (Scurrula oortiana) pada telur ayam berembrio. Jurnal
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Wibawan TWI, Murtini S, Soejoedono RD, Mahardika IGNK. 2009.
Pasif. Jurnal Veteriner 10(3): 118-124. ISSN : 1411-8327
Angi AH, Wibawan TWI, Murtini S. 2009.
Keampuan Netralisasi Antibodi Spesifik Avian Influenza H5 terhadap Beberapa Virus H5N1
Isolat Lapang. Forum Pascasarjana IPB 32(1): 55-66. ISSN : 0126-1886
E. Sudarnika
Sudarnika E, Sudarwanto M, Saefuddin A, Cahyaningsih U, Hadi UK, Kusriastuti R, Eng JV, Zhang D
Hawley WA. 2011.
Malaria incidence rate of heat assisted regeneration long lasting insecticidal
nets area and control. Jurnal Veteriner 12 (1): 40 49.
Sugiharti D. Purnamawati, A dan Sudarnika, E. 2009.
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Kondisi Biosekuriti pada Tempat Penjualan Unggas Hidup di Pasar Tradisional Kabupataean
Tasikmalaya dan Risikonya terhadappenyebaran Avian Influenza. Buletin Laboratorium
Veteriner Balai Besar Veteriner Wates Jogjakarta 9(3): 17-27.
Purnamawati, A dan Sudarnika, E. 2009.
Kajian Vaksinasi Avian Influenza pada Ayam Buras Milik Rakyat di Kabupaten Tasik Malaya, Jawa
Barat. Buletin Laboratorium Veteriner Balai Besar Veteriner Wates Jogjakarta 9(1): 28-34.
Sudarnika, E., Zahid, A., Basri, C. and Saefuddin A. 2008.

The Use Of Logistic Regression Model To Identify The Risk Factor Of H5n1 Avian Influenza Virus
Of Native Chicken In Sumatera And Kalimantan Island, Indonesia. Mathematics Journal
Universiti Teknologi Malaysia. Special Edition Part II: 519-524.
Saefuddin A., Sudarnika E. 2008.
The Role of Statistics in Biological and Medical Sciences in Developing Countries. Mathematics
Journal Universiti Teknologi Malaysia. Special Edition Part II: 379-384.
Sudarwanto M, Sudarnika E. 2008.
Association between pH and Somatic Cell Count in Milk as Parameter of Subclinic Mastitis.
Journal of Animal Science and Technology 31(2):107-113.
Sudarnika, E. 2002.
The Application of Random Effects Regression Model for Meta-analysis on Estimating the
Efficacy of Newcastle Disease Vaccine in Native Chicken. Forum Statistika dan Komputasi Special
edition:172-178.
Sudarnika, E. 2001.
Description of Small Holder Native Chicken farm in Four District in West Java.
Media Peternakan Special edition. Bogor.
Koesharto, F.X., Soviana,S. Dan Sudarnika, E. 2000.
Population Fluctuation of Splangia endius Parasitoide (Hymoptera: Pteromalidae) from fly
(Diptera: Muscidae) on Chicken Farm in Bogor Distric. Media Veteriner 7:1-4.
Dr. A. Daryanto
Ananto N, Daryanto A, Marimin, and Eriyatno (2011).
Model Kebijakan Integrasi Perencanaan Pembangunan Sektor Pertanian: Studi Kasus
Swasembada Daging Sapi (Integrated Planning Policy Model for Agricultural Sector: Case Study
for Self Sufficiency in Beef). Jurnal Perencanaan Pembangunan Edisi 3 Tahun 2011, Bappenas,
Jakarta
Indahsari GK, Daryanto A, Gumbira-Said E, and Wibowo R (2011).
Indonesia's Bioethanol Industry Diamond Porter Model. Jurnal Analisis Kebijakan Pertanian.
Saptana, Daryanto A, Suwarsinah, HK, and Kuntjoro SU (2011).
Analisis Efisiensi Produksi Komoditas Cabai Merah Besar dan Cabai Merah Keriting di Provinsi
Jawa Tengah: Pendekatan Fungsi Produksi Frontier Stokastik, Jurnal Sosial Ekonomi Pertanian
Indonesia 1 (1) : 24-31.
Liwang, T, Daryanto A, Gumbira-Said E, and Nuryartono N (2011).
Analisis Perilaku Konsumen Benih Kelapa Sawit di Indonesia (Consumer Behaviour Analysis of
Palm Oil Seed in Indonesia). Jurnal Penelitian Ilmu-Ilmu Sosial 12 (1) :114-127
Daryanto A and Saptana (2011),
Dampak Kebijakan Pemerintah DKI di Bidang Perunggasan Terhadap Ketersediaan Ayam di DKI
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Jakarta (The Impact of DKI Province Policy of Broiler Industry on the Avalaibility of Chicken).
Jurnal Analisis Kebijakan Pertanian 9 (3) : 219-236, Bogor.
Virgantari F, Daryanto A, Harianto, and Kuntjoro SU (2011).
Analisis Permintaan Ikan di Indonesia: Pendekatan Model Quadratic Almost Ideal Demand
System (QUAIDS) (Demand Analysis for Fish in Indonesia: QUAIDS Approach). Jurnal Sosial
Ekonomi Kelautan dan Perikanan 6 (2) : 191-203.
Strategi Manajemen Resiko Petani Cabai Merah Pada Lahan Sawah Dataran Rendah Jawa Tengah
(Risk Management Strategy of Low Land Red Chilli Farmers in the Central Java Province). Jurnal
Manajemen dan Agribisnis 7 (2): 115-131.
Saputra H, Daryanto A, and Hendrawan DS (2009).

Strategi Pengembangan Ternak Sapi Potong Berwawasan Agribisnis di Provinsi Aceh
(Development Strategy of Beef Cattle Based on Agribusiness Approach in the Aceh Province).
Jurnal Manajemen dan Agribisnis 6 (2): 152-162.
Priyarsono DS, Daryanto A, and Kalangi LS (2008).
Peranan Investasi Di Sektor Pertanian dan Agroindustri Dalam Penyerapan Tenaga Kerja dan
Distribusi Pendapatan: Pendekatan Sistem Neraca Sosial Ekonomi (The Role of Investment in the
Agricultural and Agribusiness Sectors on the Labour Absorption and Income Distribution). SOCA
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Priyarsono DS, Daryanto A and Herliana L (2004).
Dapatkah Pertanian menjadi Mesin Pertumbuhan Ekonomi Indonesia: Analisis Sistem Neraca
Sosial Ekonomi (Can Agriculture as an Engine of Growth in the Indonesian Economy: Social
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Daryanto, A (2000),
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Simmons, P and Daryanto, A (1999), Indonesian Agribusiness in the Aftermath of the East Asian
Economic Crisis, Agrimedia 5 (3), 38-43
D. Lukman
Suardana I W., Sumiarto B., and Lukman D.W. 2007.
Isolasi dan identifikasi Escherichia coli O157:H7 pada daging sapi di kabupaten Badung Provinsi
Bali. Jurnal Veteriner 8 (1): 16 23.
Nugroho W.S, Sudarwanto M, Lukman DW, Naim R, Setyaningsih S, Hassan AA, Usleber E. 2008.
Deteksi Mycobacterium avium subspecies Paratuberculosis pada susu formula lanjutan di Bogor.
Jurnal Teknologi dan Industri Pangan 19:19-24.
Nugroho W.S, Sudarwanto M, Lukman DW, Naim R, Hassan AA, Usleber E. 2008.
Detection of Mycobacterium avium subspecies paratuberculosis in formula milk from Bogor
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Ajzen, I. 1991.
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antibiotics. In preparation
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virus in native chickens. Vaccine, 27, 2864-69. (IF 3,572)
Schneeweiss, C. (2003),
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Added Value and Cooperation
8. Added value of the integrated approach (including scientific disciplines involved)

(Max. 500 words) Word count: 190
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The combination of the projects of this JRP is essential for the overall result. The contact structure
study (project 1) and the study on molecular epidemiology (project 2) provide the cornerstones for
the epidemiological model developed by the postdoc (project 3) to describe the transmission of
HPAIv in the Indonesian poultry husbandry. Next this model will be combined with the value chain
(project 4) and poultry sector models (project 5) to provide insight in the influence of incentives in
the poultry chain that drive the transmission of HPAIv. So, although each of the projects is
scientifically interesting and will provide valuable results on its own, only by the integrated
approach the final objectives of the JRP can be obtained. In this JRP epidemiology, molecular
virology and economics are combined. The added value of that combination of disciplines is that the
epidemiological model is substantiated with the virus transmission pathways as identified by
molecular virology and the economical modelling uses the epidemiological model. The latter implies
that the effect of economics and incentives on the transmission of the virus can be studied in detail.
Without integration this would not be possible.
9. Relevance of the programme for development issues in Indonesia

a. Societal relevance;
The poultry sector is important for the development of rural areas in Indonesia. Moreover, poultry is
the main source of animal protein for humans in Indonesia. Results of this JRP will support
programmes for food safety and food security in Indonesia. In addition, this JRP is also relevant for
the veterinary infrastructure in Indonesia. Approximately 70% of the veterinarians in Indonesia are
working in the poultry sector and they can use the information gathered in this JRP to improve their
services, especially because the results will be specific for the Indonesian situation. In addition,
information regarding the contact structure, intervention measures and incentives will not just be
applicable to HPAIv, but also to other (zoonotic) poultry pathogens and so increase the profitability
of poultry production. Consequently, it could increase the incomes of poultry keepers and would
also help in increasing food safety. Further, the results can help improving public health, because if
the spread of HPAI in poultry is reduced, exposure of humans to HPAIv will be reduced as well.
Improvements in the poultry sector will generate additional value in other parts of Indonesian
economy due to multiplier effects.
b. Scientific capacity / institution building;
In this JRP 3 Indonesian veterinarians and 1 Indonesion agricultural economist will be trained to
the PhD level, increasing the capacity of veterinary scientists in Java. Moreover,
the collaboration of the different institutes within this project will help further build the
infrastructure for veterinary sciences in Indonesia. In this project Indonesian researchers will
improve their skills in writing papers for international peer reviewed journals. IPB is in the process
of initiating a zoonoses centre in Bogor and this JRP will be very helpful during the start up of that
centre. There is no doubt that zoonoses are very important in Indonesia (besides HPAI, there is
rabies, brucellosis, tuberculosis and many more), so more knowledge and a better understanding
of zoonoses in the Indonesian context will be very useful for the coutry in facing these problems. In
this respect also the collaboration with the Eijkman Institute is important.
In Indonesia (but thishas improved in The Netherlands only after the Q-Fever epidemic
institutions working on infections in animals are working separately from those working on
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infections in humans. However, for the control of zoonotic agents like HPAIv collaboration between
veterinary and medical field is essential; One Health approach. Working together in a project will
help closing this gap.
c. Dissemination and knowledge sharing;

The results of this project will be published in international double peer reviewed journals and
presented at (inter)national conferences. In addition the results will be published in Indonesian
journals and they will be shared with technicians and poultry veterinarians during workshops to
be organised at the end of the JRP. During the project knowledge on epidemiology, molecular
virology and economics will be shared between Dutch and Indonesian researchers. Moreover, at
the end of the JRP a workshop will be organized to present and discuss the final results with
Indonesian stakeholders.
10. Embedding and additional support (science policy and activities of participating research
groups)
Highly Pathogenic Avian Influenza in poultry has been a research topic for both Utrecht University
and Central Veterinary Institute for the past decade, as shown by many publications in international
double peer reviewed journals. Moreover, Utrecht University and Wageningen University have
participated in many (inter)national research projects on HPAI. Current focus is in particular on
better understanding of the spread of HPAIv between poultry flocks, which is strongly related to the
topic of this JRP. In addition, Utrecht University has also studied HPAI in tropical areas, Thailand in
particular. This JRP can benefit from that experience. In addition, the Dutch government is planning
activities in Vietnam to help HPAI control there and CVI and Utrecht University will be involved. The
Business Economics group of Wageningen University has a long and outstanding record in the field
of Animal Health Economics and is closely collaborating with Utrecht University.
IPB has worked on Avian Influenza since 2004 and since 2006 there has been collaboration on this
topic between the Dutch research institutes and IPB. It is emphasized that the project will fit well
within IPBs initiative to establish a zoonoses centre. Eijkman Institute has been involved in the
diagnosis and research of human AI cases. Since 2005 there has been a collaboration between the
Dutch and Indonesian government on the development of control strategies againt HPaIv. The
research groups from Lelystad, Utrecht and Bogor in this JRP have been involved in this activity.
11. International co-operation and network building (Max. 2000 words)

Word count: 1062
a. Report on joint programme development
After the positive evaluation of our letter of intent a mission to Indonesia was organized to
elaborate SPIN proposal 61-SPIN-JRP. A trip was planned by Ivo Claassen (CVI/WUR), Guus Koch
(CVI/WUR), Robert Paling (BIC/UU), Arjan Stegeman (DGL/UU) and Henk Hogeveen (WU) from 4-9
February 2012, during which a workshop was organized at IPB, Bogor to discuss and elaborate
project ideas. The workshop was attended by the following Indonesian participants: Prof. Dr. drh.
Retno D. Soejoedono, Dr. drh. Denny Widaya Lukman, Dr. drh. Yusuf Ridwan, Dr. Ir. Etih Sudarnika, Dr.
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drh. Sri Murtini, Dr. drh. Michael Haryadi Wibowo (Gadja Mada), Prof. Dr. drh. I Wayan Teguh
Wibawan, drh. Chaerul Basri, Drh. Abdul Zahid Ilyas, Dr. Ir. I Made Artika (Eijkman), Dr. drh Srihadi
Agungpriyono, Drh. Agus Setiyono, Drh. Fadjar Satrija, Drh. Rahmat Hidayat, Drh. Okti Nadia Poetri.
During a meeting with Dr. Ir Arief Daryanto, MEc and Dr. Desianto Budi Utomo, PhD, involvement of
the Economics Faculty of IPB and PC (Poultry integration company) was discussed. It was agreed
that it would be important to include CP in the project as well, because it would give us a view of the
contact structure within a poultry integration.
In addition to the development of the JRP it was agreed that all candidates need to be of high quality
given the demands of the PhD system at Utrecht University (at the time of submission of the thesis 3
papers must have been accepted by high ranking peer reviewed journals) and Wageningen
University.
During a visit to Ir J. F. Rummenie of the Agricultural office, Dutch Embassy (Feb 8th ,2012) we
explained our proposal and according to Rummenie, the project would fit excellent within his ideas
and plans of improving the structure of poultry husbandry in Indonesia. If these plans would start,
the JRP could well benefit from it and vice versa.
In addition, Professor Muljono, Dr. Artika and Dr. Basuki of the Eijkman Institute in Jakarta were
visited. During this visit we discussed the possibilities of cooperation of the Eijkman Institute in the
molecular work in project 2. It is difficult for the Eijkman Institute to culture animal viruses because
of the hygiene protocols in place. However, sequencing directly from clinical swabs is possible. We
agreed to send a few papers on the molecular work we did in The Netherlands to prof. Muljono
(prof. Muljono was interested upon receipt of these manuscripts) and professor Muljono would
discuss within the institute whether cooperation would be possible. We also met Dr. Prof. Mazurki,
the director of the Eijkman Institute.
Also the FAO office in Jakarta was visited to discuss possibilities for collaboration and data sharing.
The meeting was attended by Jim McGrane (team leader AI Indonesia ), Luuk Schoonman
(veterinary epidemiologist and senior technical advisor), and Mia Kim (molecular virologist, FAO
Rome). FAO supported the development of the JRP as outlined. FAO indicated that they are very
willing to cooperate with the Dutch team and IPB on this topic. Data sharing was not seen as a major
problem but FAO indicated that the Government of Indonesia, department of Agriculture should be
involved.
The Campaign Management Unit (CMU-UPPAI) at the ministry of Agriculture, Jakarta

was visited and the JRP was discussed with Pak Mohammed Azhar (Coordinator CMU) and Pak
Ison Idris (epidemiologist, disease surveillance). CMU indicated that they would like to be informed
and possibly involved. Also they inquired about the possibility to propose PhD candidates for the
KNAW proposals. It was made clear during the presentations that the project proposals did not
include the development and/or implementation of intervention methods but rather could be used
for supporting government policies on disease control and restructuring of poultry industry.
As follow up of the mission it was agreed that the Dutch researchers would produce a full draft of
the proposal by the beginning of March. This was send to the Indonesia project leaders and the
Eijkman Institute for comments and these comments were incorporated in the proposals.
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Finally, Dr. Ir. Arief Daryanto (IPB School of Management) has visited Utrecht and Wageningen from
March 9-14 to work in co-operation with Henk Hogeveen (WU), Ivo Claassen (CVI/WUR) and Erno
Kuiper (WU) on the finalization of the setup of projects 4 and 5.
b. Level of co-operation
The existing scientific network between the Dutch partners and IPB will be strengthened and
extended with Gadja Mada University in Yogjakarta. It is foreseen that four Indonesians will pursue
their MSc into a PhD tract during this project. Each of them will have at least one Dutch and one
Indonesian supervisor who will co-author the publications in the theses. The aim is to have groups
of scientists in Indonesia and The Netherlands that continue to work on the epidemiology and
economics of infectious diseases in the future. In this cooperation the Indonesian partners bring
their unique data and expertise, essential to understand the population dynamics of HPAIv; the
Dutch partners can bring in knowledge of mathematical modeling, molecular techniques and
economics methodologies.
c. Prior scientific collaboration between the research groups

This project will pursue on research done as part of the Indonesian Dutch partnership on control
of HPAI in Indonesia (2005-2011). Research in this partnership was focused on studying the
effectiveness of vaccination on the transmission of HPAIv. Results demonstrated that vaccination
can be effective, but successful application in the field appeared difficult. A memorandum of
understanding has been signed between UU and IPB, and 4 Indonesians have been trained to MSc
level and one of them will finalize her PhD thesis next year. This prior scientific collaboration is very
beneficial for this JRP, because of the mutual trust between the partners that has already been
established and, moreover, all kinds of problems in starting projects like this have already been
dealt with in the partnership. One of the participants in the JRP (Dr. I Claassen, CVI) has lived in
Indonesia and acted as coordinator for the Indonesion-Dutch Parnership for the past 5 years.
d. Linkages with other national, regional and international research initiatives or research
groups Both Utrecht University and Central Veterinary Institute cooperate with RIVM (Dutch Public
Health Institut) on HPAIv. Long standing international collaborations have been achieved with IZSV
in Padova Italy and VLA-AH in the UK. In the field of Animal Health Economics there are many links
with other researchers in the field of Animal Health Economcis (e.g. at the Royal Veterinary College
in London, the Scottish Agricultural College, Arhus University as well as numerous contacts with
veterinary faculties all over the world. The Business Economics Group is a very international group
with PhD students from 16 different countries In addition, Utrecht University has also studied HPAI
in tropical areas, Thailand in particular (Drs. Songserm of Kasetsart University and Tiensin of
Department of Livestock Development). This JRP can benefit from that experience. In addition, the
Dutch government is planning activities in Vietnam to help HPAI control there and CVI and Utrecht
University will be involved.
12. Stakeholder participation (communication and dissemination)

Participation of the stakeholders is necessary to generate the input for spjects 1, 3 and 4 specifically,
and to evaluate the proposals that will be tested under project 5. Stakeholders that are involved in
poultry production and marketing are many ie. Large integrated industry, feed suppliers, breeders
that supply DOC (Day Old Chicks), Broiler and layer farmers, poultry shop owners, veterinary
pharmaceutical industry, traders, transporters, slaughterers, wet markets and consumers. On the
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side of the government at central level and at decentralized (provincial and district level) veterinary
services and universities (veterinary and animal husbandry faculties) and research institutes are
connected with poultry industry. Also several NGO representing producers (GAPPI, FMPI, GPMT,
GPPU, PINSAR, GOPAN), the veterinary association, and consumers organizations. Several of these
stakeholders will be involved in the projects. Collaboration with these stakeholders has been
established during earlier projects by Dutch and Indonesian project partners.
Stakeholders will participate both as a source of valuable information necessary to accomplish the
project and also as the persons that can bring the results of the project into policy/practice.
Indonesian Government, Netherlands Embassy, FAO, and CP (Poultry company) will participate in
the project as stakeholders. Initially they will help developing questionnaires and gathering
essential information on Indonesian poultry husbandry. This information will be collected by
personal interviews and workshops in Indonesia. See individual projects for details. During the time
of the JRP, the stakeholders will be invited for meetings when Dutch project leaders visit Indonesia
to discuss the progress of the JRP and ask suggestions for improvements. A mid-term workshop
involving most stakeholders will be planned to and the results of this workshop will be used to fne
tune the projects design and needed. At the end of the JRP the results will be disseminated by
workshops with stakeholders.
13. Joint activities (Max. 1000 words) Word count: 167

A joint kick off meeting will be held in Indonesia once the JRP researchers have been contracted.
The research of projects 1 and 2 involves joint activities in the field, because the same area is used
for data collection. Activities regarding the preparation of the fieldwork will be combined to
increase efficiency. Moreover, the postdoc of project 3 will spend 1 year in Indonesia being involved
in this work and to make sure that the developed model will mimick the situation in the field as
good as possible. For that reasonhe/she works closely together with the PhD students of projects 1
and 2. In addition, the postdoc will also cooperate with PhD student of project 4 to have the model
of project 4 incorporated in the value chain model.
During the stay of the PhD students in the Netherlands bi-monthly meetings will be organized to
discuss the progress of the projects. At the end of the JRPa joint symposium will be organized in
Indonesia to present the outcomes of the JRP.
Management and Administration
14. Information on the managing capacities of the Programme Coordinator

(Max. 250 words) Word count:
Professor Stegeman is professor of Farm Animal Health at Utrecht University. He has been a project
leader for many research projects (international as well as national) at Utrecht University and
before that at the Central Veterinary Institute. Moreover, he is programme leader of the research
programme Advances in Veterinary Medicine of the Faculty of Veterinary Medicine. In addition he
was head of the department of Farm Animal Health from 2004 2011. In the past 6 years 33 PhD
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students have graduated under his supervision. Prof. Stegeman is supported by the management
capacity of the Office for Internation Cooperation of the Faculty of Veterinary Medicine of UU. This
office, headed by Dr. R.W. Paling, has extensive management and financal management experience
with internationally funded project for university collaboration. Including a research project with
the Faculty of Veterinary Medicine of IPB (Asia link project 2004-2007)
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Duration and Planning
15. Time table of the programme and Milestones
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Funds required
16. Summary of Total JRP Costs and Personnel
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17. Financial contribution from (an)other source(s) (inside or outside the Netherlands or
Indonesia) and own contribution
: 212.602 From: Utrecht University
0,1 fte for daily advisorship of 2 PhD students (projects 1 and 4) by Prof. J.A. Stegeman, Dr. D.
Klinkenberg, Dr. A. Bouma and Dr H. Hogeveen
0.025 fte for secondary advisorship (promotorship) by prof J.A. Stegeman for project 2 and
postdoc guidance of prof J.A. Stegeman for project 3.
Gross salary costs, no overhead
Purpose:
Supervisor JRP
Supervision projects 1 + 3, thesis supervisor (promotor) PhD students project 1, 2 and 4
: 22.000 From: CVI Lelystad (add specification)
Purpose (e.g. specific activity or project number)

Supervision of project 2 (4 hours/week by Dr. G. Koch, gross salary costs, no overhead)
: 139,400 From: Wageningen University
For advisorship of a PhD fellow an associated professor (co-promotor; hourly tariff for Ministry of EL&I
136) will spend 0.1 fte in daily advisorship during 5 years. A full professor (promotor; hourly tariff for
Ministry of EL&I 153) will spend 0.025 fte (for 5 years) in advisorship.
Purpose:
Supervisor JRP
Supervision PhD student project 5
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Checklist
Number Check
Signature Main Applicant ...
Signature Co-applicant ...
Signatures Project Leaders from the Netherlands ...
Signatures Indonesian Project Leaders ...
Guarantee of institutional commitment ...
signed by institute director or Dean
Specifications of additional research activities ...
Guarantees of financing from other sources / matching funds ...
Other relevant details ...
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REFERENCE NUMBER: 61-SPIN-JRP-1
1. Project title
Unraveling the contact structure within Indonesian Poultry Husbandry
2. Research Group
a. Project Leader in the Netherlands

Yalelaan 7
3584 CL Utrecht
+31 30 253 1091 (phone)
+31 30 252 1887 (fax)
j.a.stegeman@uu.nl
Male
b. Project Leader in Indonesia

Dr. drh. Yusuf Ridwan, MSI (Dr., MSc, DVM)
Bogor 16680
Tel.: +62 251 8627272
Fax: +62 812 13544179
E-mail: yusufridwan67@yahoo.com
Male
c. Proposed Researcher:
X SPIN PhD fellow for 18 months (MSc course)
X DIKTI PhD fellow
d. Other participants
Dr. Desianto Budi Utomo
Pt. Charoen Pokphand Indonesia
Jl. Ancol Viii No. 1
Jakarta 14430
Tel.: +62 21 691 9999
Fax: +62 21 692 7518
E-mail: desianto@cpjf.co.id
Male
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Dr. I. Claassen
Postbox 65
8200 AB Lelystad
i.claassen@wur.nl
+ 31 320 238800
Research Proposal
3. Summary of the Project Proposal (Max. 400 words) Word count: 379
disease causes considerable economic losses to poultry keepers. Besides the economic damage,
however, the virus is important from the perspective of public health. Effective control of HPAIv
H5N1 in the poultry population is pivotal to reduce the risks posed to humans.
Control programs based on vaccination or stamping out are either not effective or not feasible in
transmission routes of HPAIv within and between the sectors of the poultry husbandry. Once this
is known, one can examine the effect of interventions in simulation studies. As a first step to gain
such understanding in this project the contact structure of the Indonesian poultry husbandry is
quantified.
Local poultry experts will be interviewed to obtain a comprehensive list of contacts to and from
each of the farm types (broilers, layers, ducks and backyard) in a poultry production chain. Next,
literature will be reviewed regarding information on the potential of these contacts to transmit
infectious poultry diseases. These results will be used to develop a structured questionnaire and a
logbook to collect data on the rate of contacts between poultry farms in West-Java.
An area in West-Java/Banten will be designated and relevant contact information will be collected
from farms in this area by interview and log book. Poultry collector houses/live bird markets will
also be included in the study, although they may be outside the chosen area. In addition the contact
pattern of persons visiting farms (for example feed suppliers, veterinarians, etc) will also be
examined. Analysis of these data will reveal the rate of contacts that could potentially transfer
HPAIv 1) between farms within the same poultry production chain (broilers, layers, ducks,
backyard), 2) between farms in different poultry production chains and 3) to and within poultry
collector houses and live bird markets is estimated. Next the effect of various factors, such as
poultry type or poultry sector (biosecurity level I, II, III and IV) on the contact rate will be
estimated. Finally, a contact network will be created including both the contact and spatial
components of the Indonesian poultry population.
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4. Detailed description of the Project (Max. 2000 words) Word count: 1186
a. Scientific Background
farms (Anonymous, 2012a). Besides the economic damage, however, the virus is important from
the perspective of public health. Indonesia is the country that has reported the highest number of
fatal human cases of HPAIv H5N1 infections; also in the year 2012 new cases have been reported
(Anonymous, 2012b). Nevertheless, the biggest threat of the virus to public health is its capability
to re-assort with other Influenza viruses creating the potential for a pandemic in humans (Peiris et
al., 2007). Effective control of HPAIv H5N1 in the poultry population is pivotal to reduce the risks
posed to humans.
Several attempts have been initiated to control the spread of HPAIv H5N1 in Indonesian poultry,
but despite these efforts the poultry sector is still confronted with outbreaks. Although effective
vaccines are available (Poetri, et al., 2009; Bouma A, et al., 2009), vaccination has not resulted in
elimination of HPAIv from Indonesian poultry. Moreover, eradication of the virus by culling
infected flocks and flocks considered at risk for infection, which appeared successful in e.g.
Thailand (Tiensin, et al., 2005), has not been implemented in Indonesia. Such an approach is very
costly, because money to compensate farmers for their losses is essential for its success (Lubroth J,
2007). In addition, cooperation between veterinary authorities and poultry industry in the control
of HPAI is suboptimal in Indonesia.
Poultry production in Indonesia is oriented at national consumption, not at export. However,

poultry is the most important source of animal protein in Indonesia. Consequently, many people
are dependent on poultry for their income or food, which has been compromised by HPAI H5N1
outbreaks. Within the Indonesian poultry production chain most emphasis is on the production of
broilers (meat type chickens). At slaughter weight, most of them are transported to poultry
collector houses or live bird markets; only a limited proportion is slaughtered in abattoirs. Laying
hens are the second important poultry type, followed by ducks. The majority of the birds is kept on
relatively small farms, because until recently the Indonesian government promoted small scale
poultry farming. In addition to professional poultry farming, back yard poultry is widespread in
Indonesia. With respect to their biosecurity level, poultry farms can be distinguished in 4 sectors.
Level 1 has a very high level of biosecurity, whereas level 4 is back yard farming with very limited
biosecurity.
Having seen in the past years that control programmes based on vaccination or stamping out
either are not effective or not feasible in the Indonesian situation the question can be raised
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whether effective control programmes can be developed that better fit the Indonesian situation. In
order to develop such programs it is crucial to understand the transmission network, e.g. the
quantitative contribution of the relevant transmission routes of HPAIv within and between the
sectors of the poultry husbandry. Once this is known, one can test the effect of interventions in
simulation studies. Although several studies have been performed in the past years to identify risk
factors(Hogerwerf L, et al., ; 2010; Loth L, et al., 2011 ; Yupiana Y, et al., 2010), these studies do not
provide detailed knowledge for understanding the HPAIv transmission in the poultry chain. As a
first step to gain such understanding it is essential to have a clear insight in the contact structure
of the Indonesian poultry husbandry.
b. Specific Objective(s)
Gain insight in the contact structure of the Indonesian poultry husbandry, more specifically,
1) Estimate the rate of contacts that could potentially transfer HPAIv 1) between farms within the
same poultry production chain (broilers, layers, ducks, backyard), 2) between farms in different
poultry production chains and 3) to and within poultry collector houses and live bid markets.
2) Estimate the differences in contact rates between the various poultry sectors (I, II, III and IV).
3) Create a network describing the relevant contacts in the Indonesian poultry production chain.
c. Workplan
Objective 1. Estimate the rate of contacts that could potentially transfer HPAIv 1) between farms
within the same poultry production chain (broilers, layers, ducks, backyard), 2) between farms in
different poultry production chains and 3) to and within poultry collector houses and live bid
markets.
a. Literature review and elicitation of expert knowledge to identify the contact types that could
potentially transfer HPAIv.
According to poultry type, four production chains will be distinguished: broilers, layers, ducks and
backyard chicken. Local poultry experts will be interviewed to obtain a comprehensive list of
contacts to and from each of the farm types in a poultry production chain. Contacts may be
associated with the transport of live birds, persons, materials, feed, as well as other relevant
contacts. Next, literature will be reviewed regarding information on the potential of these contacts
to transmit infectious poultry diseases. Finally, these results will be used to develop a structured
questionnaire to collect data on the rate of contacts between poultry farms in West-Java. This
questionnaire will be validated in a pilot study.
b. Collecting contact information in a field study

An area in West-Java/Banten will be designated. The advantage of this area is that in a previous
project all poultry farms have already been localized. Poultry farms in the area will be visited and
classified according to their poultry type. The location of the farm will be recorded in a
Geographical Information System and herd characteristics such as type of poultry, number of
birds, biosecurity level, etc. will be recorded. Next, farmers will be interviewed to obtain an
overview of incoming and outgoing contacts according to the structured questionnaire made
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under a; type of contact (for example live birds, feed trucks, technical personel, manure disposal,
etc), where do they come from (poultry farm yes/no, type of poultry, poultry sector). Next, farms
will be given a logbook to record the contacts. Poultry collector houses/live bird markets will also
be included in the study, although they may be outside the chosen area. From the interviews and
the logbooks the contact rate can be estimated.
2) Estimate the differences in contact rates between the various poultry sectors (I, II, III and IV).
From the interviews and the logbooks risk factors associated with the contact rate can be
estimated, such as biosecurity level and poultry type.
3) Create a network describing the relevant contacts in the Indonesian poultry production chain.
Using the data collected in the field a mathematical model will be constructed describing both the
contact and spatial network of the Indonesian poultry population (this part is together with
project 3).
d. Scientific Relevance
This project will give us detailed insight in the contact structure of the poultry industry. Such
information is now lacking and as a consequence it is now impossible to understand the
transmission of HPAI H5N1 in Indonesian poultry at a level that is sufficient to propose promising
intervention programmes. A model combining both the contact network and the spatial network
describing the transmission of HPAIv is new and very helpful in studying/generating hypotheses
regarding HPAIv H5N1 transmission in Indonesia.
5. Participation in a graduate School ('onderzoeksschool'):
Graduate School of Life Sciences of Utrecht University
6. Scientific performance of members of the research group(s)

Spekreijse, D., Bouma, A., Koch, G., Stegeman, J.A. Quantification of dust-borne transmission of
highly pathogenic avian influenza virus between chickens. Influenza and other Respiratory
diseases (IF 3,812), in press.
Gonzales, GL., Elbers, A.R.W., Koch, G., De Wit, J.J., and Stegeman, J.A. Rate of introduction of a low
pathogenic avian influenza virus infection in different poultry production sectors in The
Netherlands. Influenza and other Respiratory diseases (IF 3,812), in press.
Te Beest, D.E., Stegeman, J.A., Mulder, Y.M., Van Boven, M., and Koopmans, M.P.G., 2011. Exposure of
uninfected poultry farms to HPAI (H7N7) virus by professionals during outbreak control
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activities. Zoonoses and Public Health, 58, 493-9. (IF 2,220)

Comin, A., Klinkenberg, D., Marangon, S., Toffan, A., and Stegeman, A., 2011. Transmission dynamics
of low pathogenicity Avian Influenza infections in turkey flocks. Plos one, 6, e26935. (IF 4,411)
Jonges, M., Bataille, A., Enserink, R.M., Meijer, A., Fouchier, R., Stegeman A., Koch, G., Koopmans M.,
2011. Comparative analysis of avian influenza virus diversity during a highly pathogenic avian
influenza virus (H7N7) outbreak. J. Virology, 85, 10598-10604. (IF 5,189)
Te Beest, D.E., Hagenaars, T., Stegeman, A., Koopmans, M.P., and Van Boven, M., 2011. Risk based
culling for highly infectious livestock diseases. Vet Res 42, 81. (IF 3,765)
Bataille, A., Van der Meer, F., Stegeman, A., and Koch, G., 2011. Evolutionary analysis of inter-farm
transmission dynamics in a highly pathogenic avian influenza epidemic. PLOS pathogens 7,
e1002094. (IF 9,079)
Spekreijse, D., Bouma, A., Koch, G., Stegeman, J.A. Airborne transmission of a highly pathogenic
avian influenza virus strain H5N1 between groups of chickens quantified in an experimental
setting. Veterinary Microbiology, 152, 88-95. (IF 3,256)
Poetri, O., Bouma, A., Claassen, I., Koch, G., Soejoedono, R., Stegeman, J.A., and Van Boven, M., 2011.
A single vaccination of commercial broilers does not reduce transmission of H5N1 highly
Fasina, F.O., Rivas, A.L. Bisschop, S.P., Stegeman, J.A., and Hernandez, J.A., 2011. Identification of risk
factors associated with highly pathogenic avian influenza H5N1 virus infection in poultry farms
in Nigeria during the epidemic of 2006-2007. Preventive Veterinary Medicine, 98, 2004-8. (IF
2,07)
Te Beest, D.E., Van Boven, M., Bos, M.E.H., Stegeman, A., and Koopmans, M. 2010. Effectiveness of
personal protective equipment and Oseltamivir prophylaxis during Avian Influenza A (H7N7)
epidemic, The Netherlands, 2003. Emerging Infectious Diseases, 16, 1562-8. (IF 6,859)
Mulder, Y., Koopmans, M.P.G., and Stegeman, A., 2010. High probability of Avian Influenza virus
(H7N7) transmission from poultry to humans active in disease control on infected farms.
Journal of Infectious Diseases 201, 1390-1396. (IF 6,288)
Gonzales, J.L., Elbers, A.R.W., Bouma, A., Koch, G., De Wit, J.J., and Stegeman, J.A., 2010. Low-
pathogenic notifiable Avian Influenza serosurveillance and the risk of infection in poultry A
and other respiratory viruses 4, 91-99. (IF 3,812)
Van der Goot, J.A., Engel, B., Van de Water, S.G., Buist, W., De Jong, MC., Koch, G., Van Boven , M., and
Stegeman A., 2010. Validation of diagnostic tests for detection of avian influenza in vaccinated
chickens using Bayesian analysis. Vaccine, 281, 1771-7. (IF 3,572)
Tiensin, T., Ahmed, S.S., Rojahnastien, S., Songserm, T., Ratanakom, P., Chaichoun, K., Kalpravidh, K.,
Wongkasemijt, K., Patchimasiri, S., Chanachai, K., Thanapongtam, W., Chotinan, S., Stegeman, A.,
and Nielen, M., 2009. Ecologic risk factor investigationof clusters of avian influenza (H5N1)
virus infection in Thailand. Journal of Infectious Diseases, 199, 1734-43. (IF 6,288)
Boven, M., 2009. An inactivated H5N2 vaccine reduces transmission of highly pathogenic avian
Bavinck, V., Bouma, A., Van Boven, M., Bos, M.E.H., Stassen, E., and Stegeman, J.A., 2009. The role of
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backyard poultry flocks in the epidemic of highly pathogenic avian influenza (H7N7) in The
Netherlands in 2003. Preventive Veterinary Medicine, 88, 278-85.
Siregar, E., Claasen, I., Koch, G., Stegeman J.A., 2008. Field trial for assessment o Avian Influenza
vaccination effectiveness in Indonesia. Rev. Scientif. Tech. OIE, 27, 633-642. (IF 1,609)
Van der Goot, J., van Boven, M., Stegeman, A., van de Water, S.J., De Jong, M.C.M.,and Koch, G., 2008.
Transmission of highly pathogenic avian influenza H5N1 virus in Pekin ducks is significantly
reduced by a genetically distant H5N2 vaccine. Virology, 382, 91-97. (IF 3,305)

Transmission of the highly pathogenic avian influenza H5N1 virus within flocks during the
2004 epidemic in Thailand. Journal of Infectious Diseases, 196, 1679-84. (IF 6,288)
Bos, M.E., van Boven, M., Nielen, M., Bouma, A., Elbers, A.R.W., Nodelijk, G., Koch, G., Stegeman, J.A.,
and De Jong, M.C.M., 2007. Estimating the day of highly pathogenic avian influenza (H7N7)
virus introduction into a poultry flock based on mortality data. Veterinary Research, 38, 493-
504. (IF 3,765)
Highly pathogenic Avian Influenza H5N1, Thailand, 2004. Emerging Infectious Diseases, 11,
1664-1672. (IF 6,859)
Thomas, M.E., Bouma, A., Ekker, H.M., Fonken, A.J.M., Stegeman, J.A., and Nielen, M., 2005. Risk
factors for the introduction of highly pathogenic Avian Influenza virus into poultry farms
2,07)
Stegeman, J.A., Bouma, A., Elbers, A.R.W., De Jong, M.C.M., Nodelijk, G., De Klerk, F., Koch, G., and Van
Boven, M., 2004. The avian influenza A virus (H7N7) epidemic in The Netherlands. Course of
the epidemic and effectiveness of control measures. Journal of Infectious Diseases, 190: 2088-
2095. (IF 6,288)
Bouma, A., Claassen, I., Natih, K., Klinkenberg, D., Donnely, C.A., Koch, G., and Van Boven, M., 2009.
Estimation of transmission parameers of H5N1 avian influenza virus in chickens. PLoS
Pathogens e1000281. (IF 9,079)
National (refereed) journals

Ridwan, Y., S. Kusumamihardja, P. Dorny, J. Vercruyse. 1996.
The Epidemiology of Gastrointestinal Nematodes of Sheep in West Java Indonesia. Hemera
Zoa , 78 (1) : 8-11
Tiuria, R., F.Athaillah. B.P. Priosoeryanto, S. Satrija, E.B. Retnani dan Y. Ridwan. 2000.
Pengaruh infeksi Cacing Ascaridia galli terhadap Respon Sel Goblet dan Sel mast pada usus
ayam petelur. Majalah Parasitologi Indonesia, 13 (1 2)
Ahmad, R.Z., Satrija, F., Y. Ridwan, M. Larsen. 2001.
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Isolasi dan Identifikasi Kandidat Kapang Nematofagus Arthrobotrys oligospora, Kapang

Endoparasit, dan Onacosporium gephyropagum, dari Beberapa Lokasi di Daerah Bogor. Jurnal
Mikologi Kedokteran Indonesia, 2 (1) : 140-145
Ridwan Y, F Satrija. L.K. Darusman, E. Handaryani.2006.
Chemical compound and anthelmintic activity of painted nettle leaves extract againts chicken
tapeworm (articel in Indonesia). J.IL. Pert. Indon. 11 (2):1-6
Ridwan Y, J.Q. Ayunina. 2007.
Fitochemical and biological activity of Painted nettle varieties againts chicken tapeworm in
vitro (articel in Indonesia). J. Prot. 14(1):23-28.
Candra AA, Y. Ridwan, E.B. Retnani. 2008.
Potency of Mimosa pudica L. root extract as atnthelmintic against Hymenolepis nana in mice
(article in Indonesia). Media Peternakan, 31 (1): 29-35.
In vitro anticestoda activity of leaves extract of Coleus blumei Bent against Hymenolepis
microstoma : observation using SEM (articel in Indonesia). Media Kedokteran Hewan, 25 (2) :
126-133.
Efectivity of anticestoda of Coleus blumei Bent extract against Hymenolepis microstoma in
mice. Media Peternakan, 33 (1): 6-11..
Suharti S,KG Wiryawan, R Tiuria, Y Ridwan, S Fitriana, N Sumarni. 2010.
Efectivity of Jatropha curcass Linn leaves as anthelmintic to Ascaridia galli and to local chicken
performa, Media Peternakan, 33 (2): 108-114.
Satrija F. Y. Ridwan. EB. Retnani.
Eficacy of Piperazin Dihidroklorida against Toxocara vitulorum in buffalo calves. Jurnal
veteriner 12 (2):77-82
Books or contributions to books
Stegeman, J.A. Epidemiology of livestock diseases. In: Yields of farmed species: constraints and
opportunities in the 21st century. (eds. Wiseman, J., and Sylvester Bradley, R). Nottingham
University Press, Nottingham, UK, 2005, 403-416.
Bouma, A., and Stegeman, J.A., 2005. Vaccination of poultry against avian influenza:
epidemiological rules of thumb and experimental quantification of the effectiveness of
vaccination. In: Avian Influenza, Prevention and Control (eds. R.S. Schrijver and G. Koch),
Springer, Dordrecht, The Netherlands, 85-92.
7. Literature references (Max. 1 page)
Anonymous, 2012a. Avian influenza situation in indonesia update . http://www.oie.int/animal-

health-in-the-world/update-on-avian-influenza/2011
Anonymous, 2012b. Health in the world/ update on avian influenza. 2012.

http://www.who.int/csr/don/2012_01_19/en/index.html
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Bouma A, Claassen I, Natih K, Klinkenberg D, C.A., Donnelly CA, Koch G, FAU, van Boven M,
Estimation of transmission parameters of H5N1 avian influenza virus in chickens. - PLoS
Pathog.2009 Jan;5(1):e100028.
Hogerwerf L, R.G., Wallace RG, D., Ottaviani D, J., Slingenbergh J, D., Prosser D, Bergmann L, M.,
Gilbert M, 2010. Persistence of highly pathogenic avian influenza H5N1 virus defined by agro-
ecological niche. - Ecohealth., 7, 213-25.
Loth L, Gilbert M, Wu J, Czarnecki C, M., Hidayat M, Xiao X, 2011. Identifying risk factors of highly
pathogenic avian influenza (H5N1 subtype) in indonesia. - Prev Vet Med. 102, 50-8.
Lubroth J, 2007. Control strategies for highly pathogenic avian influenza: A global perspective. -
Dev Biol (Basel) 30, 13-21.
Peiris JS, de Jong MD, Guan Y, 2007. Avian influenza virus (H5N1): A threat to human health. - Clin
Microbiol Rev. 20, 243-67.
Poetri, O.N., Bouma, A., Murtini, S., Claassen, I., Koch, G., Soejoedono, R.D., Stegeman, J.A., van Boven,
M., 2009. An inactivated H5N2 vaccine reduces transmission of highly pathogenic H5N1 avian
influenza virus among native chickens. Vaccine 27, 2864-2869.
Tiensin, T., Chaitaweesub, P., Songserm, T., Chalsingh, A., Hoonsuwan, W., Buranathai, C.,
Parakamawongsa, T., Premashthira, S., Amonsin, A., Gilbert, M., Nielen, M., Stegeman, A., 2005.
Highly pathogenic avian influenza H5N1, Thailand, 2004. Emerging Infectious Diseases 11, 1664-
1672.
Yupiana Y, de Vlas SJ, Adnan NM, J.H., Richardus JH, Risk factors of poultry outbreaks and human
cases of H5N1 avian influenza virus infection in west java province, indonesia. - Int J Infect
Dis.14 :e800-5.
Integration and Cooperation
8. Integration of research and scientific results in the JRP

All projects within this JRP are interconnected. This project describes the contact structure of the
Indonesian poultry husbandry. The results will be used to create a mathematical model (project 3)
that can describe the transmission of HPAIv in the Indonesian poultry husbandry. For that
purpose parameters derived from project 2 will be integrated with the data of the contact
structure. Projects 4 and 5 will use this model to estimate the effect of changes in the value chain
and changes in the structure of the poultry husbandry on the transmission of HPAIv.
9. Information on the managing capacities of the Project Leader(s)

(Max. 250 words) Word count:176
Prof. Stegeman is professor of Farm Animal Health at Utrecht University. He has been a project
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leader for many research projects at Utrecht University and before that at the Central Veterinary
Institute. Moreover, he is programme leader of the research programme Advances in Veterinary
Medicine of the Faculty of Veterinary Medicine. In addition he was head of the department of
Farm Animal Health from 2004 2011.
Dr. Yusuf Ridwan is associate professor of Veterinary Parasitology at Veterinary Medicine Faculty
of Bogor Agricultural University (IPB). He has been a project leader for research projects at IPB. In
the last three years he was as one of project leaders in Multi-Intervention Pilot Project on the
control and prevention of HPAI in Cipunegara sub-district In Kabupaten Subang. This project was
a collaboration between IPB and IDP-HPAI. In recent year he is a project leader on epidemiology
and control parasite infections on cattle in West Java province collaboration between IPB and West
Java Province Livestock service. In addition he is head of Helminthology laboratory, Faculty of
Veterinary IPB since 2009.
10. Time table of the project and Milestones
Time Table
Year 1
SPIN/DIKTI fellow follows Master course Veterinary Epidemiology and Economics in Utrecht (18
months) and start with
Write the plan for the graduate school of Life Sciences Utrecht (GSLU)
- Literature review of contacts between poultry farms
- Elicitation of expert knowledge on contacts between poultry farms
- Developing an questionnaire and a log book to register contacts
- Select one, or a few areas for the field study and prepare the field study
Year 2
Collect data of the contact structure in the field
Develop a database
Clean up data and record data in the database
Year 3
Analyze the data of the contact structure
Writing research papers
Year 4
Writing research papers
Finalize PhD thesis
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Deliverables
- MSc degree (18 months)
- Quality plan for GSLSU (3 months)
- Literature review of contacts between poultry farms (9 months)
- Questionnaires and logbooks (12 months)
- Database for storing data developed (15 months)
- Data collection completed (24 months)
- First two research papers completed (36 months)
- PhD thesis completed (48 months)
11. Research location(s)
Field work : region of West-Java (exact location yet to be decided)
Desk work
Yalelaan 7
3584 CL Utrecht

Bogor 16680
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__________________________________
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: 72.000 From: Utrecht University + IPB
Purpose (e.g. specific activity)
Supervision of Prof J.A. Stegeman and Dr. drh. Yusuf Ridwan, MSI (Dr., MSc, DVM)
Gross salarycosts
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Signature
Project Leader Netherlands / supervisor
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Unravelling transmission of Highly Pathogenic Avian Influenza virus using molecular

epidemiology
2. Research Group
b. Project Leader in the Netherlands

Dr. G. Koch (virologist)
Postbox 65
8200 AB Lelystad
guus.koch@wur.nl
+ 31 320 238800
Male

Dr. Sri Murtini
Bogor Agricultural University (Institut Pertanian Bogor , IPB)
Bogor 16680
Tel.: +62 251 8629466
Fax: +62 2518342118
E-mail: smurtinifs@yahoo.com
Female
Dr. Michael Haryadi Wibowo

Universitas Gadjah Mada,
Jl. Fauna 2, Karangmalang, 55281 Yogyakarta, Indonesia
Tel.: +62274560862
Fax: +62 274 560861
E-mail: MHWibowo@ugm.co.id ; bowomikro@yahoo.com
Male
X SPIN PhD fellow
Prof. Dr. David H. Muljono MD, SpPD, PhD.

Eijckman Institute
Jl. Diponegoro 69, Jakarta 10430, Indonesia
Tel: +62213148695
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Fax: +62213917131
E-mail: davidhm@eijkman.go.id
Male

Yalelaan 7
3584 CL Utrecht
+31 30 253 1091 (phone)
+31 30 252 1887 (fax)
j.a.stegeman@uu.nl
Male
Dr. I. Claassen
Postbox 65
8200 AB Lelystad
tel: +31 320 238800
Fax: +31 320238668
ivo.claassen@wur.nl
male
Research Proposal
Highly Pathogenic Avian Influenza virus (HPAIv) H5N1 was first detected in 2003 and since that
year became endemic in Indonesian poultry. The disease causes considerable economic losses to
the poultry industry in particular to the small holders. Besides the economic impact, the virus also
caused 183 human cases of infection of which 156 had a fatal course (WHO March 1, 2012).
Effective control of HPAIv H5N1 in the poultry population is pivotal to reduce the risks posed to
humans.
Control programs based on vaccination or stamping out are either not effective or not feasible in
transmission routes of HPAIv within and between the sectors of the poultry husbandry. Once this
is known, one can examine the effect of interventions in simulation studies. As a first step to gain
such understanding in this project the contact structure of the Indonesian poultry husbandry is
quantified. In project 1 the transmission network will be constructed based on epidemiological
data. In project 2 the transmission network will be based on H5N1 sequence data. In project 3 a
model will be designed to combine the epidemiological and sequence data to obtain a better
resolution of the transmission network.
In project 1 of the SPIN an area in West-Java/Banten programme will be chosen in which
epidemiological data related to contacts between the different components of the poultry chain.
In the project at hand, we will start a syndromic surveillance programme in the same area. In the
programme farmers are requested to submit samples in case clinical signs such increased
mortality, drop in (egg) production or reduced water and food consumption is observed. The
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samples will be tested for AI in a RT-PCR. To increase willingness to participate the resulting PCR
data will be stored anonymously in a database although geographical location of the farm
concerned has to be stored for later analysis. In case of a positive PCR the neighbouring and
contact farms will be visited to evaluate the production numbers in those farms and collect
samples if findings indicate possible AI infection. Poultry collector houses/live bird markets will
also be included in the surveillance, although they may be outside the chosen area. Positive
samples will be processed for whole influenza genome sequencing. The sequence data will be used
in phylogenetics to produce a genetic transmission network.
farms. Besides the economic damage the virus affects public health. Indonesia is the country that
has reported the highest number of fatal human cases of HPAIv H5N1 infections; also in the year
2012 cases have been reported. Nevertheless, the biggest threat is that the virus acquires the
capability to transmit from human to human. The virus could acquire this capability by genetic
drift in poultry or humans or by reassortment with other human influenza viruses (Bataille et al
2010, Jonges, et al 2011). Recent not yet published studies (Science and Nature) revealed that only
a few mutation in diferent gene segments are sufficient to enable the virus to transmit from
mammal to mammal .
Several attempts have been initiated to control the spread of HPAIv in the Indonesian poultry
population, but despite these efforts the poultry sector is still confronted with outbreaks. Although
effective vaccines are available vaccination has not resulted in elimination of HPAIv from
Indonesia. Moreover, eradication of the virus by culling infected flocks and flocks considered at
risk for infection, which appeared successful in e.g. Thailand, has not been implemented in
Indonesia. Such an approach is very costly, because money to compensate farmers for their losses
is essential for its success. In addition, cooperation between veterinary authorities and poultry
industry in the control HPAI is suboptimal.
Poultry production in Indonesia is mainly oriented at the own consumption. Poultry farms in
Indonesia are distinguished in 4 sectors, according to their level of biosecurity. Level 1 has a very
high level of biosecurity, whereas level 4 is back yard farming with very limited biosecurity. Poultry
is the most important source of animal protein in Indonesia and Indonesian agricultural policy
endorses the maintenance of small poultry holdings. Consequently, many people are dependent on
poultry for their income or food, which has been compromised by HPAIv H5N1.
Sequencing of viruses obtained during an epidemic can help to answer a number of question like
genetic origin of the outbreak virus, evolution rates, selection pressure, reassorment history,
geographical spread of viruses, reproduction number (R0) etc (reviewed in Lam et al, 2007).
We applied these methods to analyse the Dutch outbreak of HPAI H7N7 in 2003. We sequenced
only the HA, NA and PB2 genes of numerous HPAI H7N7 viruses isolated during this outbreak and
observed a high level of genetic diversity driven mainly by a high neutral substitution rate,
purifying selection and limited positive selection. We also constructed a transmission network
using phylogenetics (Bataille et 2011). From the network we were able to identify some likely
transmission events between farms located 0.813 Km apart and one possible event at a distance
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of 65.8 km.
Ypma et al (2011) constructed a likelihood-based framework combining the transmission
network and epidemiological data and estimated probabilities of infection by taking weighted
averages over the set of possible transmission trees. The transmission tree obtained in such a way
was of higher resolution than analyses based on genetic or epidemiological data alone. Combining
this improved transmission tree with wind data a conservative estimate was made that wind-
mediated mechanism of transmission may have contributed around 18% of the total amount of
spread of HPAI (Ypma et all submitted, 2012).
Incorporation of sequences of human H7N7 isolates showed that most viruses were located at the
tips of the network. That the majority of human cases were dead-end infections suggests that
infection of humans did not contribute to virus spread per se (Jonges et al 2011). These analyses
demonstrate the power of the use of sequence information for epidemiological questions.
Recently more sequences of Indonesian poultry and human isolates have become available.
However, these relate to HA and to or lesser extent NA genes. Whole genome sequencing is scarce.
Furthermore no attempt was made to relate human to poultry sequences in depth.
To improve the HPAI situation control measures that fit the Indonesian situation have to be
developed and implemented. For that purpose it is essential to understand the (importance of)
various transmission routes of HPAIv within and between the sectors of the poultry husbandry.
Although several studies on risk factors for HPAI in Indonesia have been published, their results do
yet not enable construction of a model describing the transmission of HPAIv in Indonesian
poultry. Such a model is essential to study the effect of incentives and adaptation of control
measures on the transmission of HPAIv. In project 1 a model is constructed describing the contacts
within Indonesian poultry husbandry.
However, in order to get realistic out put from the model it is important to include valid
transmission parameters. In this project we will use molecular epidemiological tools to unravel the
transmission of HPAIv in Indonesian poultry.
1) Create a collection of isolates of HPAIv coming from different components of the Indonesian
poultry industry.
2) Perform a full genome sequencing of all isolates
3) Perform genetic analysis of the isolates
a. To create phylogenetic trees
b. Study phylogeography and -dynamics
c. Study virus evolution in poultry looking for antigenic evolution; emergence of
human virulence factors, antiviral resistance factors
d. Transmission networks.
4) Combining genetic and epidemiological data to unravel the transmission dynamics of HPAIv
between various poultry sectors using the model developed in project 3.
c. Workplan
1. Analysis of historical samples

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HPAIv samples collected in the framework of the Indonesian Dutch partnership will be available
for the project. The sample bank includes samples collected at poultry collector houses from
incoming poultry. The databank of the samples comprises epidemiological data such as origin of
the poultry type, geographical location of the farm of origin and date of collection. The samples
are available for full genome sequencing. Sequences will be compared by up-to-date phylogenetic
analytic techniques to assess genetic variation. Next analyses will be performed to determine
whether genotypes cluster according geographically and or according to poultry type.
2. An area of West-Java will be designated (same area as in project 1). Poultry farms in the area will
be visited and classified according to their poultry type (broiler, layer, duck, back yard) and sector
(I, II, III, IV). The location of the farm will be pointed in a Geographical Information System and
herd characteristics such as type of poultry, number of birds, biosecurity level, etc. will be
recorded. Farmers will be asked to notify IPB (the PhD student) in case the birds show signs of
systemic or respiratory disease or increased mortality. Upon notification samples will be collected
from 10 birds in the acute phase of disease (those showing typical signs) and recently deceased
birds will be submitted for necropsy. Samples will be pooled and tested for the presence of AIv by
RT-PCR. Clinical samples positive for AIv will be stored at -80 0C. Farms within a 3 km radius of the
infected farm and farms with known dangerous contacts will be visited asking for the presence of
disease. In case disease is reported, samples will be collected in a similar way as described above.
Samples will be collected for a period of one to one and a half year depending on the number of
positive farms.
3. Whole genomes of isolates will be sequenced and the genetic diversity will be analysed to create
phylogenetic trees of the viruses (as in Bataille et al., 2011). Next, genetic data will be combined
with epidemiologic data to refine the tree of transmission events (as in Ypma et al., 2012).
Recently it has been demonstrated using reverse genetics that only a few mutations are needed for
the H5N1 virus to acquire the property to transmit from human to human. All mutation needed for
this property are reported to be present in known isolates but have not yet been detected in the
right combination. Elucidating mechanisms that drive H5N1 genetic variation in poultry is of great
importance for risk assessment of a possible emergence of the pandemic H5N1.
Up to now H5N1 sequences has not been used for epidemiological studies probably because
isolates have been collected stochastically without the solid epidemiological data. Therefore
sequences could not be used to support epidemiological investigations. Collection of both
sequence and the underlying epidemiological data will allow us to combine both data. Combined
data will result in a transmission network of a better resolution. A better transmission network
provides better insight in transmission routes and their relative contribution to the epidemic.
Quantitated knowledge of transmission routes are crucial to develop targeted control, improved
intervention programmes. trolling or eradicating the H5N1 epidemic in Indonesia.
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6. Scientific performance of members of the research group(s) (as defined under 2)


press.
Bataille A, van der Meer F, Stegeman A, Koch G (2011)
Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian
Influenza Epidemic. PLoS Pathog 7(6): e1002094. doi:10.1371/journal.ppat.1002094 (IF 9,079)
Ypma RJ, Bataille AM, Stegeman A, Koch G, Wallinga J, van Ballegooijen WM.
Unravelling transmission trees of infectious diseases by combining genetic and epidemiological
data. Proc Biol Sci. 2012 Feb 7;279(1728):444-50. Epub 2011 Jul 6. (IF 5,064)
Comparative analysis of avian influenza virus diversity in poultry and humans during a highly
pathogenic avian influenza A (H7N7) virus outbreak. J Virol. 2011 85(20):10598-604. (IF 5,189)
Gonzales JL, Elbers AR, Bouma A, Koch G, de Wit JJ, Stegeman JA
Transmission characteristics of low pathogenic avian influenza virus of H7N7 and H5N7
subtypes in layer chickens. Veterinary Microbiology 2012;155(2-4):207-13. (IF 3,256)
Stegeman A, Bouma A, de Jong MC
Use of epidemiologic models in the control of highly pathogenic avian influenza. Avian Disease
2010 Mar;54(1 Suppl):707-12. Review (IF 1.623)
de Jong MC, Stegeman A, van der Goot J, Koch G.
Intra- and interspecies transmission of H7N7 highly pathogenic avian influenza virus during
the avian influenza epidemic in The Netherlands in 2003. Review Science Technology OIE. 2009
(1):333-40. Review. (IF 1,609)
Bos ME, Nielen M, Koch G, Bouma A, De Jong MC, Stegeman A
Veterinary Medicine. 2009 Apr 1;88(4):278-85. (IF 2,07)
pathogenic avian influenza. Veterinary Research 42(1) .
Poetri O. N., Bouma, A., Murtini S., Claassen I., Koch, G., Soejoedono R.D., Stegeman, J. A.,
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van Boven, M. (2009).

An inactivated H5N2 vaccine reduces transmission of highly pathogenic H5N1 avian influenza
virus among native chickens. Vaccine 27(21): 2864-2869 (IF 3,572)
Spekreijse D., Bouma A., Koch, G., Stegeman, J. A. (2011).
Airborne transmission of a highly pathogenic avian influenza virus strain H5N1 between
groups of chickens quantified in an experimental setting. Veterinary Microbiology 152(1-2): 88-
95. (IF 3,256)
Spekreijse D., Bouma A., Stegeman J. A., Koch G., de Jong, M. C. (2011).
The effect of inoculation dose of a highly pathogenic avian influenza virus strain H5N1 on the
infectiousness of chickens. Veterinary Microbiology 147(1-2):59-66. (IF 3,256)
Elbers AR, Loeffen WL, Koch G. Berl
Classical swine fever and avian influenza epidemics: lessons learned. Munch Tierarztl
Wochenschr. 2012 Jan-Feb;125(1-2):21-6.
Elbers AR, Gorgievski-Duijvesteijn MJ, Zarafshani K, Koch G.

To report or not to report: a psychosocial investigation aimed at improving early detection of
avian influenza outbreaks. Rev Sci Tech. OIE 2010 Dec;29(3):435-49. (IF 1,609)
Dundon WG, Heidari A, Fusaro A, Monne I, Beato MS, Cattoli G, Koch G, Starick E, Brown IH, Aldous
EW, Briand FX, Le Gall-Recule G, Jestin V, Jrgensen PH, Berg M, Zohari S, Metreveli G, Munir M,
Sta hl K, Albina E, Hammoumi S, Gil P, de Almeida RS, Smietanka K, Doman ska-Blicharz K, Minta Z,
Van Borm S, van den Berg T, Martin AM, Barbieri I, Capua I;
Genetic data from avian influenza and avian paramyxoviruses generated by the European
network of excellence (EPIZONE) between 2006 and 2011--review and recommendations for
surveillance. EPIZONE Network of Excellence Molecular Epidemiology of AI; APMV working
group. Veterinary Microbiology 2012 Jan 27;154(3-4):209-21 (IF 3,256)
Loeffen WL, Stockhofe N, Weesendorp E, van Zoelen-Bos D, Heutink R, Quak S, Goovaerts D,
Heldens JG, Maas R, Moormann RJ, Koch G
Efficacy of a pandemic (H1N1) 2009 virus vaccine in pigs against the pandemic influenza virus
is superior to commercially available swine influenza vaccines. Veterinary Microbiology 2011,
152(3-4):304-14 (IF 3,256)
Loeffen WL, de Vries RP, Stockhofe N, van Zoelen-Bos D, Maas R, Koch G, Moormann RJ, Rottier PJ,
de Haan CA.
Vaccination with a soluble recombinant hemagglutinin trimer protects pigs against a challenge
with pandemic (H1N1) 2009 influenza virus. Vaccine. 2011 29:1545-50. (IF 3,572)
Gonzales JL, Elbers AR, Bouma A, Koch G, de Wit JJ, Stegeman JA.
Low-pathogenic notifiable avian influenza serosurveillance and the risk of infection in poultry -
a critical review of the European Union active surveillance programme (2005-2007). Influenza
Other Respiratory Viruses. 2010 Mar;4(2):91-9. (IF 3,812)
van der Goot JA, Engel B, van de Water SG, Buist W, de Jong MC, Koch G, van Boven M, Stegeman A.
Bayesian analysis. Vaccine. 2010 28(7):1771-7. (IF 3,572)
Van Reeth K, Brown IH, Du rrwald R, Foni E, Labarque G, Lenihan P, Maldonado J, Markowska-
Daniel I, Pensaert M, Pospisil Z, Koch G.
Seroprevalence of H1N1, H3N2 and H1N2 influenza viruses in pigs in seven European countries
in 2002-2003. Influenza Other Respiratory Viruses. 2008 May;2(3):99-105. (IF 3,812),
Bouma A, Claassen I, Natih K, Klinkenberg D, Donnelly CA, Koch G, van Boven M.
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Pathogens 2009 Jan;5(1):e1000281. (IF 9,079)

Bos ME, Nielen M, Koch G, Bouma A, De Jong MC, Stegeman A.
Veterinary Medicine 2009 ;88(4):278-85. (IF 2,07)
Bos ME, Nielen M, Koch G, Stegeman A, De Jong MC.
Effect of H7N1 vaccination on highly pathogenic avian influenza H7N7 virus transmission in
turkeys. Vaccine. 2008; 26(50):6322-8. (IF 3,572)
van der Goot JA, van Boven M, Koch G, de Jong MC.
Variable effect of vaccination against highly pathogenic avian influenza (H7N7) virus on disease
and transmission in pheasants and teals. Vaccine. 2007;25(49):8318-25. (IF 3,572)
Maas R, Tacken M, Ruuls L, Koch G, van Rooij E, Stockhofe-Zurwieden N.
Avian influenza (H5N1) susceptibility and receptors in dogs. Emerging Infectious Disease. 2007
(8):1219-21.
van der Goot JA, van Boven M, de Jong MC, Koch G.
Effect of vaccination on transmission of HPAI H5N1: the effect of a single vaccination dose on
transmission of highly pathogenic avian influenza H5N1 in Peking ducks. Avian Disease. 2007;
51(1 Suppl):323-4. (IF 1.623)
Elbers AR, Holtslag JB, Bouma A, Koch G.
Within-flock mortality during the high-pathogenicity avian influenza (H7N7) epidemic in The
Netherlands in 2003: implications for an early detection system. Avian Disease 2007;51(1
Suppl):304-8. (IF 1.623)
Bos ME, Van Boven M, Nielen M, Bouma A, Elbers AR, Nodelijk G, Koch G, Stegeman A, De Jong MC.
Estimating the day of highly pathogenic avian influenza (H7N7) virus introduction into a
poultry flock based on mortality data. Veterinary Research 2007 38(3):493-504. (IF 3,765)
Velkers FC, Bouma A, Matthijs MG, Koch G, Westendorp ST, Stegeman JA.
Outbreak of avian influenza H7N3 on a turkey farm in the Netherlands. Vet Rec. 2006;159(13):403-
5.
van der Goot JA, Koch G, de Jong MC, van Boven M.
Quantification of the effect of vaccination on transmission of avian influenza (H7N7) in chickens.
Proceedings National Academy of Science U S A. 2005;102(50):18141-6. (IF 9.771)
Elbers AR, Koch G, Bouma A.
Performance of clinical signs in poultry for the detection of outbreaks during the avian
influenza A (H7N7) epidemic in The Netherlands in 2003. Avian Patholology. 2005;34(3):181-7
de Wit JJ, Koch G, Fabri TH, Elbers AR.
A cross-sectional serological survey of the Dutch commercial poultry population for the
presence of low pathogenic avian influenza virus infections. Avian Pathology, 2004;33(6):565-
70. (IF 1.967)
Stegeman A, Bouma A, Elbers AR, de Jong MC, Nodelijk G, de Klerk F, Koch G, van Boven M
Avian influenza A virus (H7N7) epidemic in The Netherlands in 2003: course of the epidemic
and effectiveness of control measures. Journal of Infectious disease 2004;190(12):2088-95. (IF
6,288)
Elbers AR, Fabri TH, de Vries TS, de Wit JJ, Pijpers A, Koch G.
The highly pathogenic avian influenza A (H7N7) virus epidemic in The Netherlands in 2003--
lessons learned from the first five outbreaks. Avian Disease, 2004; 48(3):691-705. (IF 1.623)
Fouchier RA, Schneeberger PM, Rozendaal FW, Broekman JM, Kemink SA, Munster V, Kuiken T,
Rimmelzwaan GF, Schutten M, Van Doornum GJ, Koch G, Bosman A, Koopmans M, Osterhaus AD.
Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute
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respiratory distress syndrome. Proceedings National Academy of Science U S A.

2004;101(5):1356-61.
van der Goot JA, de Jong MC, Koch G, Van Boven M.
Comparison of the transmission characteristics of low and high pathogenicity avian influenza A
virus (H5N2). Epidemiology and Infections. 2003;131(2):1003-13. (IF 2.257)
Thedja MD, Muljono DH, Nurainy N, Sukowati CH, Verhoef J, Marzuki S.
Ethnogeographical structure of hepatitis B virus genotype distribution in Indonesia and
discovery of a new subgenotype, B9. Archives of Virology, 2011;156(5):855-68. (IF 2.209)
Ie SI, Thedja MD, Roni M, Muljono DH.
Prediction of conformational changes by single mutation in the hepatitis B virus surface
antigen (HBsAg) identified in HBsAg-negative blood donors. Virology Journal, 2010; 7:326. (IF
2.546)
Nurainy N, Muljono DH, Sudoyo H, Marzuki S.
Genetic study of hepatitis B virus in Indonesia reveals a new subgenotype of genotype B in east
Nusa Tenggara. Archives of Virology 2008;153(6):1057-65. (IF 2.209)
Wibawa ID, Muljono DH, Mulyanto, Suryadarma IG, Tsuda F, Takahashi M, Nishizawa T, Okamoto
Prevalence of antibodies to hepatitis E virus among apparently healthy humans and pigs in Bali,
Indonesia: Identification of a pig infected with a genotype 4 hepatitis E virus. Journal Medical
Virology 2004; 73(1):38-44. (IF 2.895)
Thedja MD, Roni M, Harahap AR, Siregar NC, Ie SI, Muljono DH.
Occult hepatitis B in blood donors in Indonesia: altered antigenicity of the hepatitis B virus
surface protein. Hepatology International,. 2010;4(3):608-14. (IF 2.963)
Muljono DH, Nishizawa T, Tsuda F, Takahashi M, Okamoto H.
Molecular epidemiology of TT virus (TTV) and characterization of two novel TTV genotypes in
Indonesia. Archives of Virology 2001;146(7):1249-66. (IF 2.209)
one, 6, e26935. (IF 4,411)
Medicine, 98, 2004-8. (IF 2,07)
(IF 6,859)
Mulder, Y., Koopmans, M.P.G., and Stegeman, A., 2010.
High probability of Avian Influenza virus (H7N7) transmission from poultry to humans active
in disease control on infected farms. Journal of Infectious Diseases 201, 1390-1396. (IF 6,288)
Tiensin, T., Ahmed, S.S., Rojahnastien, S., Songserm, T., Ratanakom, P., Chaichoun, K., Kalpravidh, K.,
Wongkasemijt, K., Patchimasiri, S., Chanachai, K., Thanapongtam, W., Chotinan, S., Stegeman, A., and
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Nielen, M., 2009.

Ecologic risk factor investigationof clusters of avian influenza (H5N1) virus infection in
Thailand. Journal of Infectious Diseases, 199, 1734-43. (IF 6,288)
The role of backyard poultry flocks in the epidemic of highly pathogenic avian influenza (H7N7)
Field trial for assessment o Avian Influenza vaccination effectiveness in Indonesia. Review
Scientific. Technology OIE, 27, 633-642. (IF 1,609)
Van der Goot, J., van Boven, M., Stegeman, A., van de Water, S.J., De Jong, M.C.M., and Koch, G., 2008.
Transmission of highly pathogenic avian influenza H5N1 virus in Pekin ducks is significantly
reduced by a genetically distant H5N2 vaccine. Virology, 382, 91-97. (IF 3,305)
1664-1672. (IF 6,859)
2,07)
Murtini S, Murwani R, F. Satrija, E Handaryani, 2010.
Anti Mareks Disease Virus Activity of Scurrula oortiana ( Tea Mistletoe) Stem Extract in
Embryonated Chicken Eggs. International Journal of Poultry Science 9 (9): 879-885.
He F, Soejoedono RD, Murtini S, Goutama M and Kwang J. 2010.
Complementary monoclonal antibody-based dot ELISA for universal detection of H5 avian
influenza virus. BMC Microbiology 2010, 10:330 (IF 2,96)
Murwani R, Murtini S. 2009.
Effect of chlortetracycline additive in broiler fed local diets on antibody titers to NDV vaccine.
International Journal of Poultry Science 8 (8): 755-759.
National (refereed) journals

Elbers AR, Kamps B, Koch G.
Diagnostic possibilities for pathological lesions in poultry to trace disease outbreaks of classical
fowl pest in the Netherlands in 2003]. Tijdschrift voor Diergeneeskunde. 2005 Jan 1;130(1):14.
Dutch
Wibowo MH, Tabbu CR, Asmara W, and SusetyoH. 2012.
Receptor Binding Site Study of Avian Influenza Virus H5N1 Subtype Isolated from Various
Poultry Species Since 2003 to 2008. Journal Veteriner, Faculty of Veterinary Medicine, Udayana,
Bali. Indonesia, Accepted.
Wibowo MH, Nugroho SN, and Asmara W. 2011.
Plasmid Profile of Antibiotic Resistant Escherichia coli Isolated from Commercial Poultry Farm.
Journal of Sain Veteriner. Faculty of Veterinary Medicine, Gadjah Mada University. 27 (2): 43-50.
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Comparation of Several Newcastle Disease Vaccination Programs on the Native Chicken. Journal
Sofyan A, Julendra H, Damayanti E, Sutrisno B, and Wibowo MH. 2010.
Performance and Histopathology of Broiler Chicken Infected by Salmonella pullorum and Fed
Feed Additive Containing Earth Worm Meal (Lumbricus rubellus). Media Peternakan, Bogor
Agricultural Institute, Bogor. Indonesia. 33 (1): 31-36.
The Effectiveness of Treatment Using Combination of Amoxicillin and Colistine Sulfate
Compound against Artificial Infection of Pathogenic Escherichia coli on Broiler chicken. Journal
Susetyo U, and Wibowo MH. 2008.
Comparison of Antibody Titer in Broiler Chicken Vaccinated at 7 and 14 Days Old with Avian
Influenza H5N2 Subtype Heterologous Vaccine, Journal of Sain Veteriner, Faculty of Veterinary
Wibowo MH, and Wahyuni AETH. 2008.
Pathogenicity Study of Escherichia coli Isolated from Poultry on Broiler Chicken at 15-days of
Age. Journal Veteriner, Faculty of Veterinary Medicine, Udayana University, Bali, Indonesia. 9
(2): 87-93.
Wibowo MH, Susetyo H, Untari T, Wahyuni AETH, Tabbu CR, and Asmara W. 2007.
Molecular Identification of Avian Influenza Virus Isolated from Cases Both Specific and
Unspecific Symptoms for Avian Influenza Disease. Journal Veteriner, Faculty of Veterinary
Medicine, Udayana University, Bali, Indonesia. 8 (3):103-110.
Wibowo MH, Susetyo H, Untari T, Putri K, Tabbu CR, and Asmara W. 2006.
Molecular Study on the Pathogenicity of Avian Influenza Virus. Indonesian Journal of
Biotechnology Vol. 11, No. 2, December 2006, Research Center for Biotechnology, Gadjah Mada
University, Jogjakarta. 11 (2):901-907.
Wibowo MH, Asmara W, and Tabbu CR. 2006.
Isolation and Serological Identification of Avian Influenza Virus from Poultry Sample Obtained
from Jogjakarta Special Territory and Central Java. Journal of Sain Veteriner, Faculty of
Veterinary Medicine, Gadjah Mada University. 24 (1): 77-83.
Asmara W, Wibowo MH, and Tabbu CR. 2005.
Hemagglutinin H5 Subtype Identification of Avian Influenza Virus, Isolated from Various
Species of Birds Using RT-PCR. Journal of Sain Veteriner, Faculty of Veterinary Medicine, Gadjah
Mada University. 23 (1): 42-46.
Murtini S, R. Murwani, F. Satrija, MBM. Malole. 2006.

Penetapan rute dan dosis inokulasi pada telur ayam berembrio sebagai media uji khasiat
ekstrak benalu teh (Scurrula oortiana). Jurnal Ilmu Ternak dan Veteriner 11 (2): 137-143. ISSN :
0853-7380
Murtini S, R. Murwani, F. Satrija, E. Handharyani. 2006.
Efek imunomodulasi ekstrak benalu teh (Scurrula oortiana) pada telur ayam berembrio. Jurnal
Ilmu Ternak dan Veteriner 11(3): 188-194. ISSN : 0853-7380
Wibawan TWI, Murtini S, Soejoedono RD, Mahardika IGNK. 2009.
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Pasif. Jurnal Veteriner 10(3): 118-124. ISSN : 1411-8327
Angi AH, Wibawan TWI, Murtini S. 2009.
Keampuan Netralisasi Antibodi Spesifik Avian Influenza H5 terhadap Beberapa Virus H5N1
Isolat Lapang. Forum Pascasarjana IPB 32(1): 55-66. ISSN : 0126-1886

Bouma, A., and Stegeman, J.A., 2005.
Vaccination of poultry against avian influenza: epidemiological rules of thumb and
experimental quantification of the effectiveness of vaccination. In: Avian Influenza, Prevention
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de Jong MC, Stegeman A, van der Goot J, Koch G.
Intra- and interspecies transmission of H7N7 highly pathogenic avian influenza virus during
the avian influenza epidemic in The Netherlands in 2003. Rev Sci Tech. 2009; 28(1):333-40.
Review. (IF 1,609)
Koch G, Steensels M, van den Berg T
Vaccination of birds other than chickens and turkeys against avian influenza. Rev Sci Tech.
2009;28(1):307-18. Review. (IF 1,609)
Capua I, Schmitz A, Jestin V, Koch G, Marangon S.
Vaccination as a tool to combat introductions of notifiable avian influenza viruses in Europe,
2000 to 2006. Rev Sci Tech. 2009;28(1):245-59. Review.
Bouma A, Muljono AT, Jatikusumah A, Nell AJ, Mudjiartiningsih S, Dharmayanti I, Siregar ES,
Claassen I, Koch G, Stegeman JA.
Field trial for assessment of avian influenza vaccination effectiveness in Indonesia. Rev Sci Tech.
2008;27(3):633-42. (IF 1,609)
Koch G.
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Weijtens M, Maurice H, Van Langen H, Koch G.
Needs assessment for the use of vaccination. Dev Biol (Basel). 2007;130:85.
Alexander DJ, Capua, I, Koch G.
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Iowa, 1st edition, 2008, 217-239.
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7(6): e1002094. doi:10.1371/journal.ppat.1002094
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genomes of influenza A. PLoS One. 201; 6(4):e19075.
Comparative analysis of avian influenza virus diversity in poultry and humans during a
highly pathogenic avian influenza A (H7N7) virus outbreak. J Virol. 2011 85(20):10598-
604
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Halvorson DA, Sreevatsan S. The feasibility of using high resolution genome sequencing
of influenza A viruses to detect mixed infections and quasispecies. PLoS One. 2009
22;4(9):e7105.
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transmission trees of infectious diseases by combining genetic and epidemiological data
Proc Biol Sci. 2012 Feb 7;279(1728):444-50. Epub 2011 Jul 6

All projects within this JRP are interconnected. Project 1 describes the contact structure of the
Indonesian poultry husbandry. The results will be used to create a mathematical model (project 3)
that can describe the transmission of HPAIv in the Indonesian poultry husbandry. For that
purpose parameters derived from this project 2 will be integrated with the data of the contact
structure. Projects 4 and 5 will use this model to estimate the effect of changes in the value chain
and changes in the structure of the poultry husbandry on the transmission of HPAIv.

Dr. G. Koch, male, is trained as virologist and immunologist and has over 10 years of experience as
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a senior scientist at CVI mainly working with chickens. He coordinated research project related to
avian immunology, infectious bronchitis, Mareks disease, chicken anaemia, Newcastle and Avian
influenza. He is actiting head of the national reference laboratory for Avian Influenza and
Newcastle Disease and as such responsible for confirmaton of these disease in the Netherlands. He
was in charge as project leader during the Dutch HPAI outbreak in 2003.
He participated in several European projects also as work package leader and was coordinator of
the European project FLURESIST. He also participated in the Dutch Indonesian partnership and
in particular in surveillance programmes conducted in poultry and poultry collector houses in
Indonesia.
Dr. S. Murtini, is trained as virologist and immunologist and has over 10 years of experience as a
lecture and researcher at Faculty Veterinary Medicine, Bogor Agricultural University mainly
working with chickens. She has been appointed as person in charge in laboratory diagnostic of
HPAI in FVM IPB since of the outbreak of the disease in 2004. She participated as laboratory
coordinator of several HPAI surveillance conducted by FVM IPB in collaboration with Ministry of
Agriculture, and Provincial Governments of West Java, Banten, DKI Jakarta, as well as West
Kalimantan. She also participated in the Indonesian- Dutch partnership for controlling HPAI
project. In 2009, she was project coordinator of Small Grant Project from Community Based Avian
Influenza Control (CBAIC)-USAID, to conduct dissemination of AI awareness through Indonesia's
Scout Movement activity in Bogor Area. With financial supports from Ministry of National
Education and Ministry of Research and Technology, she conducted a number of research projects
on possible role of stray cat on AI transmission, and the use of colostrum and IgY as
immunotherapy for HPAI.
Dr. Michael Haryadi Wibowo, male, is trained as microbiologist in the Laboratory of Microbiology,
Gadjah Mada University. His interest dedicated to work on avian viral and bacterial diseases and
have strong contact with poultry sector as poultry practitioner. Was among the first to isolate
avian influenza virus (AIV) H5N1 in Indonesia and since then has been involved in a number of AI
project funded of government of Indonesia. His AIV isolates have been shared to international
community, e.g.: FAO in collaboration with Australian Animal Health Laboratory, Geelong,
Australia. Currently, he involved in the international partnership research funded by ACIAR,
Australia.

2012
2013 2014 2015 2016 2017

4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
Selection Spin fellow
Kick off mmeeting
English training /IPB
UU Literature, design, SPIN
Collection samples
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PCR analyses
Full genome sequencing
Phylogenetic analyses
Analysing/writing thesis
Meetings in IND /NL
Defending thesis
University/ InstituteFaculty of Veterinary Medicine

Bogor 16680
Indonesia
Eijkman Institute
Jl. Diponegoro 69,
Jakarta 10430,
Indonesia

Houtribweg 39
8221 RA Lelystad
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__________________________________
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: From: (add specification)
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Signature
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Signature
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Epidemiological model for Highly Pathogenic Avian Influenza virus transmission in Indonesia
2. Research Group

Dr. Don Klinkenberg, PhD
University Utrecht
Yalelaan 7
3584 CL Utrecht
Tel.: +31 30 253 1248
Fax: + 31 30 - 2521887
E-mail: d.klinkenberg@uu.nl
Male

Dr. Ir. Etih Sudarnika, MSi (Dr, MSc, Ir)
Bogor 16680
Phone/Fax : +62-251-8628811
HP : +62-8128322058
email address : etih23@yahoo.com / etih@ipb.ac.id
Female
c. Proposed Researcher: PostDoc, candidate yet to be determined
Yalelaan 7
3584 CL Utrecht
+31 30 253 1091 (phone)
+31 30 252 1887 (fax)
j.a.stegeman@uu.nl
Male
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Research Proposal
3. Summary of the Project Proposal (Max. 400 words) Word count:
farms. Besides the economic damage, however, the virus is important from the perspective of
public health. Effective control of HPAIv H5N1 in the poultry population is pivotal to reduce the
risks posed to humans.
In this project we will develop an epidemiological model describing the transmission of HPAIv in
the Indonesian poultry husbandry. For that purpose the contact network from project 1 and the
transmission parameters collected in project 2 will be combined. The resulting model can be used
to investigate the effect of changes in contact structure on the transmission of HPAIv.
First, an epidemiological model will be developed that includes the contacts within a poultry
production chain and the interactions that exist with other poultry chains. The poultry production
chains of interest here are those of broilers, layers, ducks and backyard chickens. Besides contacts
within and between these chains, the spatial network of these farms will be included in the model.
Next, the contact rate as established in project 1 will be incorporated into the model as well as the
transmission parameters generated in project 2.
Once the model has been parameterized, it will be (partly) validated using available datasets. Next,
different scenarios will be tested in order to examine the effect of differences in contact rate at the
transmission of HPAIv in Indonesian poultry. In addition the transmission parameters in the
model can also be varied in order to estimate the effect of intervention measures like vaccination
or cleaning and disinfection.
The model will provide insight in the highly complex transmission dynamics within the
Indonesian poultry industry.
4. Detailed description of the Project (Max. 2000 words) Word count:
flocks (Anonymous, 2012a). Besides the economic damage, however, the virus is important from
the perspective of public health. Indonesia is the country that has reported the highest number of
fatal human cases of HPAIv H5N1 infections; also in the year 2012 new cases have been reported
(Anonymous, 2012b). Nevertheless, the biggest threat of the virus to public health is its capability
to re-assort with other Influenza viruses creating the potential for a virus able to cause a pandemic
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in humans (Peiris et al, 2007). Effective control of HPAIv H5N1 in the poultry population is pivotal
to reduce the risks posed to humans.
Several attempts have been initiated to control the spread of HPAIv H5N1 in Indonesian poultry,
but despite these efforts the poultry sector is still confronted with outbreaks. Although effective
vaccines are available, vaccination has not resulted in elimination of HPAIv from Indonesian
poultry. Moreover, eradication of the virus by culling infected flocks and flocks considered at risk
for infection, which appeared successful in e.g. Thailand, has not been implemented in Indonesia.
Such an approach is very costly, because compensating farmers for their losses is essential for its
success (Lubroth, 2007). In addition, cooperation between veterinary authorities and poultry
industry in the control of HPAI is suboptimal in Indonesia, which obscures a comprehensive
picture of the HPAIv situation in Indonesia.
Having seen that control programs based on vaccination or stamping out are either not effective or
not feasible in the Indonesian situation the question can be raised whether effective control
programs can be developed that fit the Indonesian situation. In order to answer that question it is
crucial to understand the transmission network, e.g. the quantitative contribution of the relevant
transmission routes of HPAIv within and between the sectors of the poultry husbandry. By
mapping and quantifying epidemiological links between the different types of farms, it should be
possible to identify those routes that are most crucial for transmission of the virus. If these are
known, the effect of interventions affecting these routes can be calculated or tested in simulation
studies. Although several studies have been performed in the past years to identify risk factors
(Yupiana et al, 2010; Loth et al, 2011), these studies do not provide detailed quantitative
knowledge for understanding the HPAIv transmission between the different actors in the poultry
chain.
The data collected in projects 1 and 2 will be used to build the transmission model of HPAIv in the
Indonesian poultry husbandry. The data in project 1 should provide the most complete picture of
all actors in the network (e.g. farm types), and the estimated contact rates can be used for
quantification of the proportional contributions of all links between the actors. The data in project
2 can probably identify only part of the relevant links, but for these links actual transmission rates
can be identified rather than contact rates, giving a better quantification of the underlying risk of
these links. By combining the two projects it will be possible (1) to test whether the
proportionality in contact rates can indeed be translated to proportionality in transmission rates,
and (2) to estimate the proportionality constant and thus quantify the complete transmission
network. The resulting network transmission model can be used to investigate the effect of
changes in contact structure on the transmission of HPAIv, and to identify those contacts
contributing most to transmission.
1. Develop an epidemiological network transmission model for a quantitative description of HPAIv

in the Indonesian poultry population.
2. Identify contacts with greatest contribution to HPAIv transmission and examine the effect of
changes in the contact structure on the transmission of HPAIv in Indonesian poultry
c. Workplan
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This project will run in the third and fourth year of the JRP. In the project the contact structure of
the Indonesian poultry husbandry will be condensed into an epidemiological model describing the
transmission of HPAIv in Indonesian poultry. Using the data collected in project 1, the model will
include the contacts within and between each of the poultry production chains (broilers, layers,
ducks and backyard chickens), including contacts with live bird markets and poultry collector
houses to mimic Indonesian poultry production. If relevant, spatial data will be included. The rate
of contacts as observed in project1 will be used to do a first quantification of the model. Using the
data of project 2, the contact rates should be translated to actual transmission rates. This will be
done by estimating the transmission rates for some specific contacts identified in project 2, and
calculating the proportionality constant in relation to the contact rates of project 1. This
proportionality constant is subsequently used to estimate the transmission rates for all contacts in
the network. Literature data and data from previous studies (Bouma et al, 2008) will be used for
validation.
Next, the mathematical description of the transmission network will be analysed to estimate the
herd-reproduction ratio Rh (number of flocks infected by one infectious flock) and to identify those
contacts to which Rh is most sensitive. Those contacts should ideally be targeted for optimally
effective control. Additionally, simulations will be done to verify the effectiveness of targeting
these contacts, and to estimate how long it will take for control to be effective. This should result in
a list a control options such as disinfection, vaccination, or cleaning, that can be used for economic
optimization in projects 4 and 5.
Besides working on his or her own modelling project, we envisage that the postdoc will spend
time in Indonesia to get good inside knowledge on the data collection in projects 1 and 2, and to
be able to advice on which data are exactly collected. This will prevent the model from becoming a
theoretical exercise with little relation to reality and it will maximize applicability of the collected
data for the models.
The model will provide a quantitative description of transmission contacts in the Indonesian
poultry industry, and a first estimate of the reproduction ratio between herds R h. The model will
give insight into the highly complex transmission dynamics, that cannot be obtained otherwise.
Dr D Klinkenberg
How selection forces dictate the variant surface antigens used by malaria parasites. Journal of
the Royal Society Interface 9, 246-260. (IF 4,259)
Galsworthy S.J., Ten Bosch Q.A., Hoye B.J., Heesterbeek J.A.P., Klaassen M., Klinkenberg D., 2011.
Effects of infection-induced migration delays on the epidemiology of avian influenza in wild
mallard populations. PLoS ONE 6: e26118. (IF 4,411)
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Klinkenberg, D., Nishiura, H., 2011.

The correlation between infectivity and incubation period of measles, estimated from
households with two cases. Journal of Theoretical Biology 284, 52-60. (IF 2,371)
Fraser, C., Cummings, D.A.T., Klinkenberg, D., Burke, D.S., Ferguson, N.M., 2011.
Influenza transmission in households during the 1918 pandemic. American Journal of
Epidemiology 174, 505-514. (IF 5,745)
Klinkenberg, D., Thomas, M.E., Calvo, A.F.F., Bouma, A., 2011.
Salmonella Enteritidis surveillance by egg immunology: impact of the sampling scheme on the
release of contaminated table eggs. Risk Analysis 31, 1260-1270. (IF 2,344)
Courcoul, A., Hogerwerf, L., Klinkenberg, D., Nielen, M., Vergu, E., Beaudeau, F., 2011.
Modelling effectiveness of herd level vaccination against Q fever in dairy cattle. Veterinary
Research 42, 68. (IF 3,765)
Thomas, M.E., Bouma, A., Klinkenberg, D., 2011. A comparison of transmission characteristics of
Salmonella enterica serovar Enteritidis between pair-housed and group-housed laying hens.
Veterinary Research 42, 40. (IF 3,765)
Hollingsworth, T.D., Klinkenberg, D., Heesterbeek, H., Anderson, R.M., 2011.
Mitigation strategies for pandemic influenza A: balancing conflicting policy objectives. PLoS
Velkers, F.C., Swinkels, W.J., Rebel, J.M., Bouma, A., Daemen, A.J., Klinkenberg, D., Boersma, W.J.,
Stegeman, J.A., De Jong, M.C.M., Heesterbeek, J.A.P., 2010.
Effect of Eimeria acervulina infection history on the immune response and transmission in
broilers. Veterinary Parasitology 173, 184-192. (IF 2,458)
Thomas, M.E., Klinkenberg, D., Ejeta, G., Van Knapen, F., Bergwerff, A.A., Stegeman, J.A., Bouma, A.,
2009.
Quantification of horizontal transmission of Salmonella enterica serovar enteritidis
bacteria in pair-housed groups of laying hens. Applied and Environmental Microbiology 75,
6361-6366. (IF 3,778)
Nishiura, H., Klinkenberg, D., Roberts, M., Heesterbeek, J.A.P., 2009.
Early epidemiological assessment of the virulence of emerging infectious diseases: A case study
of an influenza pandemic. PLoS ONE 4, e6852. (IF 4,411)
Van Gerwe, T., Miflin, J.K., Templeton, J.M., Bouma, A., Wagenaar, J.A., Jacobs-Reitsma, W.F.,
Stegeman, A., Klinkenberg, D., 2009.
Quantifying transmission of campylobacter jejuni in commercial broiler flocks. Applied and
Environmental Microbiology 75, 625-628. (IF 3,778)
Bouma, A., Claassen, I., Natih, K., Klinkenberg, D., Donnelly, C.A., Koch, G., Van Boven, M., 2009.
Pathogens 5, e1000281. (IF 9,079)
van Boven, M., Klinkenberg, D., Pen, I., Weissing, F.J., Heesterbeek, H., 2008.
Self-interest versus group-interest in antiviral control. PLoS ONE 3, e1558. (IF 4,411)
Effects of heterogeneity in infection-exposure history and immunity on the dynamics of a
protozoan parasite. Journal of the Royal Society Interface 4, 841-849. (IF 4,259)
van Boven, M., Koopmans, M., Du Ry van Beest Holle, M., Meijer, A., Klinkenberg, D., Donnelly, C.A.,
Heesterbeek, H.J., 2007.
Detecting emerging transmissibility of avian influenza virus in human households. PLoS
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A model for the dynamics of a protozoan parasite within and between successive host
populations. Parasitology 134, 949-958. (IF 2,53)
Klinkenberg, D., Fraser, C., Heesterbeek, H., 2006.
The effectiveness of contact tracing in emerging epidemics. PLoS ONE 1, e12. (IF 4,411)
A simple model for the within-host dynamics of a protozoan parasite. Proceedings of the Royal
Society B: Biological Sciences 272, 593-600. (IF 5,064)
Klinkenberg, D., Nielen, M., Mourits, M.C.M., De Jong, M.C.M., 2005.
The effectiveness of classical swine fever surveillance programmes in the Netherlands.
Preventive Veterinary Medicine 67, 19-37. (IF 2,07)
Klinkenberg, D., Everts-Van Der Wind, A., Graat, E.A.M., De Jong, M.C.M., 2003.
Quantification of the effect of control strategies on classical swine fever epidemics.
MathematicalBiosciences 186, 145-173. (IF 1,593)
Klinkenberg, D., De Bree, J., Laevens, H., De Jong, M.C.M., 2002.

Within- and between-pen transmission of Classical Swine Fever Virus: A new method to
estimate the basic reproduction ratio from transmission experiments. Epidemiology and
Infection 128, 293-299. (IF 2,257)
Mangen, M.J., Jalvingh, A.W., Nielen, M., Mourits, M.C.M., Klinkenberg, D., Dijkhuizen, A.A., 2001.
Spatial and stochastic simulation to compare two emergency-vaccination strategies with a
marker vaccine in the 1997/1998 Dutch Classical Swine Fever epidemic. Preventive Veterinary
Medicine 48, 177-200. (IF 2,07)
Dr E Sudarnika
Sudarnika E, Sudarwanto M, Saefuddin A, Cahyaningsih U, Hadi UK, Kusriastuti R, Eng JV, Zhang D
Hawley WA. 2011.
Malaria incidence rate of heat assisted regeneration long lasting insecticidal nets area and
control. Jurnal Veteriner 12 (1): 40 49.
Sugiharti D. Purnamawati, A dan Sudarnika, E. 2009.
Kondisi Biosekuriti pada Tempat Penjualan Unggas Hidup di Pasar Tradisional Kabupataean
Tasikmalaya dan Risikonya terhadap penyebaran Avian Influenza. Buletin Laboratorium
Veteriner Balai Besar Veteriner Wates Jogjakarta 9(3): 17-27.
Purnamawati, A dan Sudarnika, E. 2009.
Kajian Vaksinasi Avian Influenza pada Ayam Buras Milik Rakyat di Kabupaten Tasik Malaya,
Jawa Barat. Buletin Laboratorium Veteriner Balai Besar Veteriner Wates Jogjakarta 9(1): 28-34.
Sudarnika, E., Zahid, A., Basri, C. and Saefuddin A. 2008.
The Use Of Logistic Regression Model To Identify The Risk Factor Of H5n1 Avian Influenza
Virus Of Native Chicken In Sumatera And Kalimantan Island, Indonesia. Mathematics Journal
Universiti Teknologi Malaysia. Special Edition Part II: 519-524.
Saefuddin A., Sudarnika E. 2008.
The Role of Statistics in Biological and Medical Sciences in
Developing Countries. Mathematics Journal Universiti Teknologi Malaysia. Special Edition Part
II: 379-384.
Sudarwanto M, Sudarnika E. 2008.
Association between pH and Somatic Cell Count in Milk as Parameter of Subclinic Mastitis.
Journal of Animal Science and Technology 31(2):107-113.
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Sudarnika, E. 2002.
The Application of Random Effects Regression Model for Meta-analysis on Estimating the
Efficacy of Newcastle Disease Vaccine in Native Chicken. Forum Statistika dan Komputasi
Special edition:172-178.
Sudarnika, E. 2001.
Description of Small Holder Native Chicken farm in Four District in West Java. Media
Peternakan Special edition. Bogor.
Koesharto, F.X., Soviana,S. Dan Sudarnika, E. 2000.
Population Fluctuation of Splangia endius Parasitoide (Hymoptera: Pteromalidae) from fly
(Diptera: Muscidae) on Chicken Farm in Bogor Distric. Media Veteriner 7:1-4.
Prof JA Stegeman
press.
one, 6, e26935. (IF 4,411)
Jonges, M., Bataille, A., Enserink, R.M., Meijer, A., Fouchier, R., Stegeman A., Koch, G., Koopmans
M., 2011.
Comparative analysis of avian influenza virus diversity during a highly pathogenic avian
influenza virus (H7N7) outbreak. J. Virology, 85, 10598-10604. (IF 5,189)
Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian
influenza epidemic. PLOS pathogens 7, e1002094. (IF 9,079)
Airborne transmission of a highly pathogenic avian influenza virus strain H5N1 between
groups of chickens quantified in an experimental setting. Veterinary Microbiology, 152, 88-95.
(IF 3,256)
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Poetri, O., Bouma, A., Claassen, I., Koch, G., Soejoedono, R., Stegeman, J.A., and Van Boven, M., 2011.
A single vaccination of commercial broilers does not reduce transmission of H5N1 highly
Medicine, 98, 2004-8. (IF 2,07)
(IF 6,859)
Mulder, Y., Koopmans, M.P.G., and Stegeman, A., 2010.
High probability of Avian Influenza virus (H7N7) transmission from poultry to humans active
in disease control on infected farms. Journal of Infectious Diseases 201, 1390-1396. (IF 6,288)
Gonzales, J.L., Elbers, A.R.W., Bouma, A., Koch, G., De Wit, J.J., and Stegeman, J.A., 2010.
Low-pathogenic notifiable Avian Influenza serosurveillance and the risk of infection in poultry
and other respiratory viruses 4, 91-99. (IF 3,812)
Van der Goot, J.A., Engel, B., Van de Water, S.G., Buist, W., De Jong, MC., Koch, G., Van Boven , M.,
and Stegeman A., 2010.
Bayesian analysis. Vaccine, 281, 1771-7. (IF 3,572)
Tiensin, T., Ahmed, S.S., Rojahnastien, S., Songserm, T., Ratanakom, P., Chaichoun, K., Kalpravidh,
K., Wongkasemijt, K., Patchimasiri, S., Chanachai, K., Thanapongtam, W., Chotinan, S., Stegeman, A.,
and Nielen, M., 2009.
Ecologic risk factor investigationof clusters of avian influenza (H5N1) virus infection in
Thailand.Journal of Infectious Diseases, 199, 1734-43. (IF 6,288)
Boven, M., 2009.
An inactivated H5N2 vaccine reduces transmission of highly pathogenic avian
The role of backyard poultry flocks in the epidemic of highly pathogenic avian influenza (H7N7
Field trial for assessment o Avian Influenza vaccination effectiveness in Indonesia. Rev. Scientif.
Tech. OIE, 27, 633-642. (IF 1,609)
Van der Goot, J., van Boven, M., Stegeman, A., van de Water, S.J., De Jong, M.C.M.,and Koch, G.,
2008.
Transmission of highly pathogenic avian influenza H5N1 virus in Pekin ducks is
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Bos, M.E., van Boven, M., Nielen, M., Bouma, A., Elbers, A.R.W., Nodelijk, G., Koch, G., Stegeman, J.A.,
and De Jong, M.C.M., 2007.
Estimating the day of highly pathogenic avian influenza (H7N7) virus
introduction into a poultry flock based on mortality data. Veterinary Research, 38, 493-504. (IF
3,765)
1664-1672. (IF 6,859)
2,07)
Stegeman, J.A., Bouma, A., Elbers, A.R.W., De Jong, M.C.M., Nodelijk, G., De Klerk, F., Koch, G., and
Van Boven, M., 2004.
The avian influenza A virus (H7N7) epidemic in The Netherlands. Course of the epidemic and
effectiveness of control measures. Journal of Infectious Diseases, 190: 2088-
2095. (IF 6,288)

Stegeman, J.A.
Epidemiology of livestock diseases. In: Yields of farmed species: constraints and
opportunities in the 21st century. (eds. Wiseman, J., and Sylvester Bradley, R). Nottingham
University Press, Nottingham, UK, 2005, 403-416.
Bouma, A., and Stegeman, J.A., 2005.
Vaccination of poultry against avian influenza: epidemiological rules of thumb and
experimental
quantification of the effectiveness of vaccination. In: Avian Influenza, Prevention and Control
(eds. R.S. Schrijver and G. Koch), Springer, Dordrecht, The Netherlands, 85-92.
Anonymous, 2012a. Avian influenza situation in indonesia update .

Anonymous, 2012b. Health in the world/ update on avian influenza. 2012, .
Bouma, A., Muljono, A.T., Jatikusumah, A., Nell, A.J., Mudjiartiningsih, S., Dharmayanti, I., Siregar,
E.S., Claassen, I., Koch, G., Stegeman, J.A., 2008.
Field trial for assessment of avian influenza vaccination effectiveness in indonesia. OIE Revue
Scientifique et Technique 27, 633-642.
Leo, L., Marius, G., Wu Jianmei, Christina, C., Muhammad, H., Xiao Xiangming, 2011.
Identifying risk factors of highly pathogenic avian influenza (H5N1 subtype) in indonesia. Prev.
Vet. Med. 102, 50-58.
Lubroth J, 2007.
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Control strategies for highly pathogenic avian influenza: A global perspective.

Dev Biol (Basel) 130, 13-21.
Peiris, J.S.M., de Jong, M.D., Guan, Y., 2007.
Avian influenza virus (H5N1): A threat to human health. Clin. Microbiol. Rev. 20, 243-+.
Yupiana, Y., de Vlas, S.J., Adnan, N.M., Richardus, J.H., 2010.
Risk factors of poultry outbreaks and human cases of H5N1 avian influenza virus infection in
westjava province, indonesia. International Journal of Infectious Diseases 14, E800-E805.

This research project is the link between the data collected in projects 1 and 2, and the economic
analyses carried out in projects 4 and 5. The project translates all available information obtained
from literature and projects 1 and 2 into a single quantitative description of HPAIv transmission in
Indonesian poultry. The resulting model is used to come up with a list of epidemiologically
effective control options, which will be analysed in projects 4 and 5 for economic consequences
and practical consequences for implementation by the different stakeholders.

Dr D Klinkenberg is Assistant Professor at the Faculty of Veterinary Medicine, at Utrecht

University. He has ample experience in collaborating with veterinarians and biologists in analyzing
experimental and field data, resulting in many peer-reviewed publications. He teaches statistics,
epidemiology and mathematical modelling, and has successfully supervised a number of MSc and
PhD students.
Dr. Ir. Etih Sudarnika is Assistant Professor at the Faculty of Veterinary Medicine, at Bogor
Agricultural University. He has a statistics and veterinary science degree, and has been involved in
many successful research projects on the Indonesian Poultry Industry, relating to influenza,
biosecurity, and contact rate quantification, some of which as team leader.
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Year 3 : Epidemiological model is constructed, assistance with data collection is given, and the
parameterization method (based on the type of data being collected) is developed.
Year 4 : Model is parameterized, mathematically analysed, and different control scenarios are
being tested and identified.

University Utrecht
Yalelaan 7
3584 CL Utrecht

Bogor 16680
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__________________________________
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: From: (add specification)
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Signature
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Economic benefits of a reduction of viral poultry diseases
2. Research Group
c. Project Leader in the Netherlands

Dr. Henk Hogeveen
Department of Farm Animal Health
Faculty of Veterinary Medicine, Utrecht University
PO Box 80151
` 3508 TD Utrecht
The Netherlands
e-mail h.hogeveen@uu.nl
tel.: + 31 30 2539104
mobile: +31 317 485335
Male

Dr. Ir. Arief Daryanto, M.Ec.
Graduate Program of Management and Business
Jalan Raya Pajajaran Bogor 16151
Indonesia
Tel.: +622518313813
Mobile: +628129997947
Fax: +622518318515
E-mail: adaryant@indo.net.id; adaryant@mb.ipb.ac.id
Male
X DIKTI PhD fellow
If known:
Name / Title(s): Albertus T. Muljono, M.Sc.
Jalan Raya Pajajaran Bogor 16151
Indonesia
Male
Name / Title(s):
University/ Institute:
Address:
Tel.:
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Fax:
E-mail:
Male Female
Research Proposal
3. Summary of the Project Proposal (Max. 400 words) Word count:

Programs to reduce the level of infection of HPAI in Indonesia are not always successful Lack of
(proven) economic efficiency of preventive measures explain part of this lack of success. Another
part might be explained by the fact that farmers, especially smaller family farms, might be driven
by other motivators than only economics. In order to correctly estimate the economic effects of
interventions, more viral poultry diseases than only HPAI should be taken into account, for New
Castle Disease and infectious bursal disease. An important gap in the research approach towards
improved health and safety in Indonesia is the explicit incorporation of economics and farmer
behaviour. By studying the economics of combined prevention of viral poultry diseases in Western
Java as well as the motivators for uptake of preventive measures for the different actors in the Java
poultry value chain, policy making towards an improved and safer Java poultry chain can be
supported. The proposed research consists of 5 parts. Subproject 4.1 aims at the development of a
quantitative value chain simulation model, using existing knowledge about the poultry value chain
in Western java. In subproject 4.2 Monte Carlo simulation models will be developed to estimate the
costs of viral poultry diseases for different stakeholders in the Western Java poultry chain. These
models are based on existing knowledge of the pathogenesis of viral poultry diseases and existing
expertise on the economic effects of these diseases. The developed models will be applied to
estimate the costs and benefits of interventions. In order to be able to predict the behaviour of
stakeholders, in subproject 4.3, the motivation of stakeholders in Western Java to implement
interventions will be studied, based on the Theory of Planned Behaviour and a questionnaire. All
information will be synthesized in an agent-based model (subproject 4.4) to simulate the effect of
stimulation of interventions over the full poultry chain in Western Java.
4. Detailed description of the Project (Max. 2000 words) Word count:
Animal disease pose significant threats to livestock sectors throughout the world, both from the
standpoint of the economic impacts of the disease itself and the measures taken to mitigate the
risk of disease introduction (Rich and Perry, 2010). A good understanding of these impacts is
necessary for effective policy response. When describing economic effects of chicken diseases, in
many cases only attention is given to the notifiable disease avian influenza (AI). Especially since
the occurrence of highly pathogenic AI (HPAI), this disease has gained much interest. Especially
because of the risk that the capability of this virus to re-assort with other Influenza viruses, which
might lead to a pandemic in humans (Peiris et al, 2007). In order to decrease the risk of infections
by humans, farmers in the poultry chain have to take preventive measures to reduce the levels of
infection. Programs to reduce the level of infection of HPAI are not always successful (Anonymous,
2010). Lack of (proven) economic efficiency of preventive measures explains part of the lack of
success of preventive measures (Anonymous, 2010). Another part might be explained by the fact
that farmers, especially smaller family farms, might be driven by other motivators than only
economics (e.g., Lam et al, 2010) and that uptake of new insights is more than explaining these
insights to farmers (Garforth and Usher, 1997).
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Besides HPAI, there are more viral poultry diseases, being endemic in Indonesia, such as New
Castle Disease (NCD) and infectious bursal disease (Gumboro). Although the economic effect of
these diseases is substantial, no efforts have been undertaken to reduce the levels of these
infectious diseases in the Indonesian poultry chain. A search of Web of Science did only deliver
publications on prevention of HPAI. No papers were published on prevention of other viral
diseases in Indonesia. However, a combined approach towards these diseases is expected to
generate an improved value of the poultry chain as well as a reduction in infection level, also for
HPAI.
An important gap in the research approach towards improved health and safety in Indonesia is the
explicit incorporation of economics and farmer behaviour. By studying the economics of combined
prevention of viral poultry diseases in Western Java as well as the motivators for uptake of
preventive measures for the different actors in the Java poultry value chain, policy making towards
an improved and safer Java poultry chain can be supported.
The overall objective of this project is to strengthen the chicken value chain in Java by economic
optimization of chicken health for different types of farmers.
Specific sub-objectives are:

1) Quantifying the chicken value chain in Western Java
2) Creation of stochastic simulation models to estimate the effect of improved chicken health
management for the main actors in the Western Java poultry value chain .
3) Generate knowledge on motivation of uptake of chicken health improving measures by the
various actors in the Western Java poultry value chain
4) Estimate the economic effect on the complete Western Java poultry value chain of
stimulation of improved chicken health management
c. Workplan
The basis for our work will be the development of a quantitative value chain simulation model
(subproject 4.1). In this model, relationships, characteristics and dynamics that take place among
actors in the Indonesian poultry chain will be systematically summarized (Kaplinsky and Morris,
2001). More qualitative value chains of (parts) of the Indonesian poultry sector have been created
in the past (e.g., Sudarman et al, 2008; McLeod et al., Siagian et al., 2008). Based on these and other
scientific papers and reports, a quantitative poultry value chain simulation model will be
developed for Western Java. Input for this value chain will be based on (scientific) literature,
available reports and databases and interviews with key persons in the Java poultry chain. The
quantitative value chain will be developed as a simulation model as is done recently for the Dutch
poultry chain in relation to the use of antibiotics (Muljono et al., 2012). This simulation model
enables the calculation of the effects of changes of, for instance, production efficiency because of a
reduced disease burden.
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In subproject 4.2, for the different farm types (actors) that can be distinguished in the value chain
(integrated farm companies, breeding farms, small commercial farms and backyard chicken
farms), stochastic Monte Carlo simulation models will be developed with specific emphasis on
estimating the economic effects of occurrence of viral diseases (HPAI, Gumboro and NCD). Using
these models, the expected costs of these diseases can be estimated. Input for the models will be
based on the developed value chain, scientific literature on the pathogenesis of the diseases under
study, local reports on occurrence of these diseases (if available) and interviews with veterinary
experts on these diseases (expertise). The developed stochastic simulation models will be used to
estimate the expected (economic) effect of implementation of preventive measures. Special
emphasis will be given to the combined effect of preventive measures for different poultry
diseases. The preventive measures that will be studied, will be selected in close collaboration with
veterinary field officers, so that the studied measures are measures that are expected to be
effective.
As a next step the intentions and motivations of stakeholders to implement preventive measures
will be studied (subproject 4.3). A questionnaire, based on the Theory of Planned Behaviour
(Azjen, 1991) will be constructed. The questionnaire will be tested on and discussed with a
limited number of the study population to test it. After adjustment, the questionnaire will be
carried out for 100 stakeholders, divided over the four different groups of stakeholders
(companies, breeder farms, commercial farms, backyard farms) and other important actors such
as traders. Besides the basic questions with regard to the farm and socio-demographic
information, questions will be aimed to generate knowledge on the behaviour of the farmer with
regard to viral poultry diseases, the intention to change behaviour, the attitude towards the
behaviour, the subjective norms with regard to the behaviour and the perceived behavioural
control. Questionnaires will be held by means of individual semi-structured interviews. Data will
be statistically analysed (correlation analysis) to quantify the importance of factors with regard to
the motivation of farmers to change their behaviour and their attitude towards the disease and
behaviour to improve the disease status (e.g., Ellis-Iversen et al., 2010).
Finally, in subproject 4.4, for the most important groups of farmers and traders (actors) identified
in the poultry value chain, agent-based models will be created, where a farmer is an agent acting in
interaction with other actors in the system. By applying agent-based modelling, the actions and
interactions of farmers, given certain disease prevention policies, can be modelled and the effects
of the individual behaviour on the total farm system can be estimated. This type of multi-agent
models have been applied to model the spread of disease (e.g., Kim et al, 2010), but hardly to
model the behaviour of farmers (e.g., Valeeva and Verwaart, 2011). The parameters to be used in
the agent-based models will be derived from the economic analysis as well as the questionnaires
on motivation and behaviour of poultry farmers with regard to prevention of viral poultry diseases
and the information on contact structure and spread of HPAI as is studied in project 1 and 2.
Until now, economic work with regard to prevention of HPAI has hardly been carried out beyond
the value chain analysis. This work carries out cost-benefit analyses of preventive measures
against HPAI on Indonesian poultry farms and places this in perspective of other viral poultry
diseases (thus improving the efficiency of preventive measures). Moreover, this work looks at the
motivation and attitudes of different groups of poultry farmers with regard to prevention of viral
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poultry diseases. Within the field of animal health economics, the latter is novel as well. Only
sporadic publications on this item have been made.

The average impact factor of the journals of this list is 2.07. All but one of these papers are
Simulating E. coli O157 transmission to asess effectiveness of slaughterhouse inverventions.
Motivation of dairy farmers to improve mastitis management. Journal of Dairy Science, 90:
4466-4477.
127.
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Assessing the economic consequences of foot disorders in dairy cattle using a dynamic
stochastic simulation model. Journal of Dairy Science, 93: 2419-2432.
846.
Analysis of the economically optimal voluntary waiting period. Journal of Dairy Science 94:
3811-3824.
status in the Netherlands: an outline. Preventive Veterinary Medicine, accepted.
Almost all of Dr Daryantos publications are in national peer-reviewed journals, except for a few
publications which are in international peer-reviewed journals. No impact factors are known.
Refereed journals
Rochman, TR, Gumbira Said E, Daryanto A and Nuryantoro N (2011),

Analysis of National Agricultural Industry Competitiveness in Nanotechnology Development
Perspective Using SWOT-AHP Methods, International Journal of Business and Management,
6(8), 235-244.
Ananto N, Daryanto A, Marimin, and Eriyatno (2011).
Model Kebijakan Integrasi Perencanaan Pembangunan Sektor Pertanian: Studi Kasus
Swasembada Daging Sapi (Integrated Planning Policy Model for Agricultural Sector: Case Study
for Self Sufficiency in Beef). Jurnal Perencanaan Pembangunan Edisi 3 Tahun 2011, Bappenas,
Jakarta
Indahsari GK, Daryanto A, Gumbira-Said E, and Wibowo R (2011).
Indonesia's Bioethanol Industry Diamond Porter Model. Jurnal Analisis Kebijakan Pertanian.
Saptana, Daryanto A, Suwarsinah, HK, and Kuntjoro SU (2011). Analisis Efisiensi Produksi
Komoditas Cabai Merah Besar dan Cabai Merah Keriting di Provinsi Jawa Tengah: Pendekatan
Fungsi Produksi Frontier Stokastik, Jurnal Sosial Ekonomi Pertanian Indonesia 1 (1) : 24-31.
Liwang, T, Daryanto A, Gumbira-Said E, and Nuryartono N (2011).
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Analisis Perilaku Konsumen Benih Kelapa Sawit di Indonesia (Consumer Behaviour Analysis of
Palm Oil Seed in Indonesia). Jurnal Penelitian Ilmu-Ilmu Sosial 12 (1) :114-127
Daryanto A and Saptana (2011),
Dampak Kebijakan Pemerintah DKI di Bidang Perunggasan Terhadap Ketersediaan Ayam di DKI
Jakarta (The Impact of DKI Province Policy of Broiler Industry on the Avalaibility of Chicken).
Jurnal Analisis Kebijakan Pertanian 9 (3) : 219-236, Bogor.
Virgantari F, Daryanto A, Harianto, and Kuntjoro SU (2011).
Analisis Permintaan Ikan di Indonesia: Pendekatan Model Quadratic Almost Ideal Demand
System (QUAIDS) (Demand Analysis for Fish in Indonesia: QUAIDS Approach). Jurnal Sosial
Ekonomi Kelautan dan Perikanan 6 (2) : 191-203.

Strategi Manajemen Resiko Petani Cabai Merah Pada Lahan Sawah Dataran Rendah Jawa
Tengah (Risk Management Strategy of Low Land Red Chilli Farmers in the Central Java
Province). Jurnal Manajemen dan Agribisnis 7 (2): 115-131.
Saputra H, Daryanto A, and Hendrawan DS (2009).
Strategi Pengembangan Ternak Sapi Potong Berwawasan Agribisnis di Provinsi Aceh
(Development Strategy of Beef Cattle Based on Agribusiness Approach in the Aceh Province).
Jurnal Manajemen dan Agribisnis 6 (2): 152-162.
Priyarsono DS, Daryanto A, and Kalangi LS (2008).
Peranan Investasi Di Sektor Pertanian dan Agroindustri Dalam Penyerapan Tenaga Kerja dan
Distribusi Pendapatan: Pendekatan Sistem Neraca Sosial Ekonomi (The Role of Investment in
the Agricultural and Agribusiness Sectors on the Labour Absorption and Income Distribution).
SOCA Jurnal Sosek Pertanian dan Agribisnis 8 (1).
Daryanto A (2006).
Contract Farming: Linking Farmers to Markets. Business and Entrepreneurial Review 6 (1): 27-
30.
Priyarsono DS, Daryanto A and Herliana L (2004).
Dapatkah Pertanian menjadi Mesin Pertumbuhan Ekonomi Indonesia: Analisis Sistem Neraca
Sosial Ekonomi (Can Agriculture as an Engine of Growth in the Indonesian Economy: Social
Accounting Matrix Approach). Agro-Ekonomika (1): 37-47.
Daryanto, A (2000),
Indonesias Crisis and Agricultural Sector: the Relevance of Agricultural Demand-Led
Industrialization, Politics Administration and Change 33, 41-54
Simmons, P and Daryanto, A (1999),
Agribusiness in Indonesia After the 1997 Financial Crisis, UNEAC Asia Papers 2, 53-62
Simmons, P and Daryanto, A (1999), Indonesian Agribusiness in the Aftermath of the East
Asian Economic Crisis, Agrimedia 5 (3), 38-43
Books

Model-Model Kuantitatif Dalam Perencanaan Pembangunan Daerah: Konsep dan Aplikasi
(Quantitative Models for Regional Development Planning: Concepts and Applications), IPB Press,
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Bogor
Analisis Input-Output dan Social Accounting Matrix untuk Pembangunan Ekonomi Daerah
(Input-Output and Social Accounting Matrix Analysis for Regional Economic Development), IPB
Press, Bogor
Daryanto A (2009).
Dinamika Daya Saing Industri Peternakan (The Dynamics Competitiveness of Livestocks
Industry), IPB Press, Bogor
Daryanto A (2007).
Peningkatan Daya Saing Industri Peternakan (Improving Livestocks Industry Competitiveness),
PT. Permata Wacana Lestari (Penerbit Majalah TROBOS), Jakarta.
Patrick I, Simmons P, Daryanto A, Oktaviani R, Yusuf RP, Astiti NWS, Pitana IG, Mustadjab M,
Hanani N and Napitulu D (2004).
Contract Farming in Indonesia: Smallholders and Agribusiness Working Together, ACIAR
Technical Reports 54, Australia
Books chapters
Daryanto A dan Daryanto, HKS (2010),

Peranan Kewirausahaan dan Modal Sosial Dalam Peningkatan Daya Saing AgroFood Complex
(The Role of Entrepreneurship and Social Capital in Improving of the AgroFood Complex
Industries). In Baga LM, et al. (Eds.), Kewirausahaan dan Daya Saing Agribisnis), IPB Press,
Bogor
Daryanto, A dan Saptana (2009).
Global Value Chain Governace (GVCG) Pada Broiler di Indonesia: Memadukan Pertumbuhan,
Pemerataan, dan Keberlanjutan (Global Value Chain Governance for Broiler Industry in
Indonesia: Combining Growth, Equity and Sustainability). In Oktaviani R, et al. (Eds.),
Pembangunan Ekonomi Berkelanjutan Dalam Menghadapi Krisis Ekonomi Global, IPB Press,
Bogor
Daryanto A (2009),
Posisi Daya Saing Pertanian Indonesia dan Upaya Peningkatannya (Position of Agricultural
Competitiveness and Its Effort for Improvement). In Kusriyadi A, et al. (Eds.), Peningkatan Daya
Saing Agribisnis Berorientasi Kesejahteraan Petani, PSEKP Kementrian Pertanian, Bogor.
Ajzen, I. 1991.
The theory of planned behaviour. Organizational Behavior and Human Decision
Processes 50: 179-211.
Anonymous, 2010.
Assessment of farm level financial incentives and willingness to pay for HPAI
vaccination in Indonesia. Final Report, ICASEPS, Ministry of Agriculture, Indonesia.
Garforth, C. and R. Usher, 1997.
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Promotion and uptake pathways for research output: A review of analytical frameworks and
communication channels. Agricultural Systems 55: 301-322.
Kaplinsky, R. and Morris, M. 2001.
A Handbook for Value Chain Research. IDS working paper, IDS, Sussex, UK, 109 pp.
Kim, T., W. Hwang, A. Zhang, S. Sen and M. Ramanathan. 2010.
Multi-agent modeling of the South Korean avian influenza epidemic. BMC Infectious Diseases
10:236-249.
Lam, T.J.G.M., J. Jansen, B.H.P. van den Borne, R.J. Renes and H. Hogeveen, 2011.
udder health in dairy herds. New Zealand Veterinary Journal, 59: 8-15.
Mcleod, A., Kobayashi, M., Gilman, J., Siagian, A., and Young, M. 2009.
The use of poultry value chain mapping in developing HPAI control programmes. World's
PoultryScience Journal 65: 217-223.
Muljono, A.T., A.G.J. Velthuis, J. Rushton and H. Hogeveen. 2012.
A quantitative value chain analysis of the Dutch broiler industry with regard to the use of
antibiotics. In preparation
Peiris J. S.M., M.d. de Jong and Y. Guan 2007.
Avian influenza virus (H5N1): a threat to human health . Clinical Microbiology Reviews 20: 243-
267.
Rich, K.M. and B.D. Perry. 2011.

The economic and poverty impacts of animal diseases in
developing countries: New roles, new demands for economics and epidemiology. Preventive
Veterinary Medicine 101: 133-147.
Siagian, A., P. Sembiring, Z. Siregar, M. Tafsin, N. D. Hanafi, Rasmaliah, D. Suryanto and R.
Hasibuan, 2008.
Poultry market chain study in North Sumatra. FAO Report.
Sudarman, A., Sumiati, E. Handharyani, A. Setiyno, S. Mulatsih and R. Kusumaningrum 2008.
Poultry value chain study and Avian Influenza risk assessment in Jakarta surrounding area.
Final report. CENTRAS, Bogor Agricultural University and FAO.
Valeeva, N.I. and T. Verwaart (2011).
Udder health management improvement: Insights from agent-based modelling. Pages 149-156
in: Hogeveen H. and T.J.G.M. Lam (editors) Udder Health and Communication, Wageningen
Academic Publishers, Wageningen, the Netherlands

The first subproject of this project (subproject 4.1; development of a quantitative value chain
simulation model) will be used in projects 1, 2 and 5. For projects 1 and 2, this simulation model
(and the value chain analysis underneath it) will be the basis for determining the contact structure
and the spread of disease over the poultry chain in Western Java. In project 5, this model will be
used to estimate the added value of the poultry chain in Western Java. Moreover, in subproject 5.2,
this simulation model will be resemble the basic structure of the poultry production chain in
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Western Java.
Subprojects 4.2 and 4.3 will use information from projects 1, 2 and 3. Subproject 4.4 will use
results from project 5 (subproject 5.3) to see the effect of different structures on risk of AI.
Besides that, in subproject 4.4, knowledge gained in projects 1 and 3 about the existing contact
structure as well as the spread of HPAI throughout the poultry production chain in Indonesia will
be utilized.
During the JRP we will organize a joint workshop in Indonesia.

Dr Henk Hogeveen is a senior researcher and has since his MSc work been working in a
multidisciplinary research environment. He is used to build bridges between the veterinary
sciences and the social sciences. His research and teaching appointment as associated professor is
even at two Universities: Wageningen University (chair group Business Economics ) and the
Faculty of Veterinary Medicine of Utrecht University (department of Farm Animal Health). In order
to be successful in such a multidisciplinary field one must have the competence to work in teams
and to understand researchers from different disciplines.
Besides of his capabilities to build bridges between researchers and research fields, he has been
managing several large research projects, among which EU integrated projects as well as Dutch
Science Foundation funded projects.
Dr Arief Daryanto is currently Director of the Graduate Program of Management and Business and
a senior lecturer in the Faculty od Economic and Management at Bogor Agricultural University
(IPB). He received his PhD from the University of New England, Australia. Dr Daryanto has a long
and distinguished history of working on a range of successful ACIAR projects and EVD projects on
Round Table Indonesia (RTI) focusing on agricultural policy, poultry and livestocks, biosecurity,
value chains and contract farming with small farmers. He publishes widely on agricultural issues
in Indonesia and supervises numerous PhD and Masters students. He is also now serving as a task
force member at the Ministry of Agriculture to develop a new long term agricultural sector
development strategy.
The total project will take 5 years. The activities of this research are divided over the research time
as follows:
1. Year 1: Learning methods in the field of veterinary epidemiology and economics (MSc
courses) as well as preparation of the research
2. Year 2: Development of the quantitative value chain simulation model (subproject 4.1),
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development of a rough version of the Monte Carlo simulation models (subproject 4.2)
3. Year 3: Collection of input data for the Monte Carlo simulation models and establishment
of the intervention methods that will be studied (subproject 4.2) and collection of data on
the motivation of stakeholders to apply intervention (subproject 4.3). This year will be
spent in Indonesia.
4. Year 4:Finalizing the development of the Monte Carlo simulation models and estimation of
the costs and benefits of intervention methods (subproject 4.2) and statistical analysis of
collected questionnaire data on motivation of farmers to implement interventions
(subproject 4.3)
5. Year 5: Development of the agent-based model to simulate the behaviour of the poultry
system when several intervention methods are stimulated (subproject 4.4) and writing of
a final report.
Besides the submitted scientific papers (four papers are envisaged) on the performed research,
the following Milestones are defined:
1. Finalized quantitative value chain simulation model
2. Data collection on motivation of stakeholders to implement interventions is finished
3. Finalized analyses on the costs and benefits of interventions
4. Finalized statistical analyses on motivation data
5. Finalized agent-based model on the poultry chain in Western Java
6. Final report finished
Year 1 and 2 of the research will be spent at the Department of Farm Animal Health of the Faculty
of Veterinary Medicine of Utrecht University in the Netherlands. Year 3 of the project will be
carried out at the Division of Veterinary Public Health, Department of Animal Disease and
Veterinary Public Health of the Faculty of Veterinary Medicine of the Institut Pertanian Bogor in
Indonesia. The final two years of the project will be carried out in Utrecht again.
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_______________________________________________________
__________________________________
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: 84,000 From: Faculty of Veterinary Medicine of Wageningen University
For advisorship of this SPIN/DIKTI PhD fellow an associated professor (co-promotor; gross salary
costs 82 per hour) will spend 4 hours per week (40 weeks per year for 5 years) in daily
advisorship. A full professor (promotor; gross salary costs 92 per hour) will spend 1 hour per
week (40 weeks per year for 5 years) in advisorship.
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Signature
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Restructuring the poultry supply chain in Western Java
2. Research Group

Dr. H. Hogeveen, M.Sc.
Chair group Business Economics
Hollandseweg 1
6706 KN Wageningen
The Netherlands
Phone: + 31 (0)317 485335
E-mail: henk.hogeveen@wur.nl
Male

Denny Widaya Lukman, DVM, MSc, Dr.med.vet.
Division of Veterinary Public Health
Department of Animal Disease and Veterinary Public Health
Institut Pertanian Bogor
Jalan Agatis Kampus IPB Darmaga
Bogor 16680
West Java, Indonesia
Phone/Fax +62 251 8625588
Mobile +62 81513803047
E-mail dennylukman@hotmail.com
Male
d. Proposed Researcher:
X DIKTI PhD fellow
Dr. W.E. Kuiper
Chair group Business Economics
Hollandseweg 1
6706 KN Wageningen
The Netherlands
Tel.: + 31 (0)317 483865
E-mail: erno.kuiper@wur.nl
Male
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Research Proposal
As a consequence of its vulnerability to avian influenza (AI) the poultry sector in Indonesia should
be re-organised so as to optimise the disease prevention efficiency of the chain under the
condition of food security for the population. Since the external effects that are caused by the
current method of poultry production and marketing, are complex, government intervention is
needed. The project addresses the question which organisational forms of the Indonesian poultry
supply chain and government intervention provide the most efficient way of coordination under
the conditions of food safety and security. Principal-agent theory and cost-benefit analysis are
used for supply chain optimisation under different scenarios.
The poultry sector in Indonesia is of great economic importance, yet, the problems faced by the
sector are probably even greater of magnitude. On the one hand, poultry products (meat, eggs) are
a very popular and widely consumed food product by a large part of Indonesias Islamic
population. It is expected that the consumption of poultry will increase in the coming years due to
economic development and a higher level of welfare. This leads to a need for more production.
Poultry production provides also a living to many farmers, traders and company employees. An
important disease for the poultry production chain in Indonesia is avian influenza (AI). Because of
the risk of human disease the highly pathogenic variant of AI (HPAI) is even more important and a
reason that much research and control efforts are focussed on that poultry disease. In this
research program epidemiological research will provide decision makers with options to reduce
the spread of disease (projects 1, 2 and 3). Economic modelling will enable decision makers to see
the economic consequences of improved management (including biosecurity; project 4). When
decisions have to be taken by stakeholders, the results of those projects will be very useful.
However, these projects leave the structure of the poultry production in Indonesia intact, while
this structure of breeding, production, transportation, storage and marketing by the many small
and large actors in the poultry supply chain is, however, rather vulnerable to severe shortcomings
on food safety and animal health (Charnoz, O and P. Foster, 2011). In a recent poultry value chain
study and AI risk assessment in the Jakarta surrounding area Sudarman et al. (2008) therefore
recommend that () the Government of Indonesia should begin establishing, regulating and
negotiating with relevant stakeholders standard biosecurity regulations for all actors involved in
the poultry industry. As such, governmental intervention with regard to reduction of AI moves
beyond on-farm measures to provide incentives to change the current organisation of the poultry
production and marketing chain into a structure that guarantees a healthy and animal friendly
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production, control over diseases, improved food safety and a sufficiently increasing supply to
meet the ever larger demand through the growing number of wealthier consumers (FAO/WHO,
2012).
From an economic policy point of view, the hazards of animal diseases and unsafe food can be
considered as negative external effects of the method of poultry production and marketing.
Moreover, the number of stakeholders who suffer from and/or cause these external effects is
rather large, so that negotiations between those who are affected by, and hence, wish to reduce the
external effects, and those who cause the external effects, will be complex and vulnerable to free-
riders who benefit from but do not pay for the additional transactions needed to internalise the
external effects (Teulings et al., 2003). This implies, in accordance to the recommendations in
Sudarman et al. (2008), that the government should facilitate the processes to improve the
structure of poultry production in Indonesia.
However, before the government can stimulate a certain restructuring of the Indonesian poultry
sector, knowledge should be gained about its optimal structure. An optimal structure should fulfil
a number of conditions as to not only optimise the disease prevention efficiency of the chain.
These conditions are:
1. Providing food security. Prices should not rise but preferably decrease such that the food
security of the Indonesian people is not negatively affected.
2. Providing means of living for at least the same number of producers, traders and workers
as are currently working in the poultry production chain.
3. Production should remain in rural areas.
4. Improving the biosecurity of poultry production with regard to AI.
5. Improving the economic efficiency of production.
From a technical point of view, optimal supply chains can be formulated that maximize
performance under the restrictions of food safety and security, see, for example, Dabbene et al.
(2008), Almeder et al. (2009), Vo and Thiel (2011). Nevertheless, these models do not address the
question to what extent the market (price) mechanism must be replaced by organisational
coordination mechanisms (e.g. Mintzberg, 1979, 1989) in order to obtain optimal outcomes given
the constraints imposed. Enforcing transactions to satisfy these constraints is more difficult than
voluntary transactions in the market. Consequently, when collective insurance leads to inefficient
implementation, the government is more likely to opt for competition. One way out of this
dilemma is to introduce hybrid forms of coordination (Menard, 1996, 2004; Graversen et al., 2004)
by, for example, decentralised insurance groups (e.g. on a regional basis), so that compulsory
collective insurance can be combined with e.g. yardstick competition (competition based on
(price) comparisons between groups). In contrast, economies of scale can be achieved when fixed
costs must be paid, regardless of the scale of production. The average costs are then lower for
large-scale production. These economies of scale imply that only a limited number of suppliers can
be active in the market. This gives these suppliers a degree of market power, which means that
they can influence pricing or volumes. Access barriers can give existing suppliers even more
market power. Suppliers can abuse these dominant positions to fix prices at too high a level from a
social point of view (Teulings et al, 2003). In both cases, the government can take measures to
provide for more effective production. If producers cannot cover their fixed costs, the government
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can intervene by forcing consumers to contribute to these fixed costs and/or by limiting
competition, so that the fixed costs can be recovered (e.g. via patent law). If producers hold market
power, the government can address this power through price regulation, for example, or by
lowering access barriers (Teulings et al, 2003).
Consequently, in developing alternative structures optimally combining price and organisational
coordination mechanisms and incentives, research has to be done on how the government can
intervene so that the poultry sector will move towards a more effective, efficient and safe
production structure. Basically a government has three ways to intervene (Teulings et al., 2003):
1. Government regulation (legislation and regulations)

2. Outsourcing public tasks
3. Public organisation having private parties taking over the reins itself.
Which method of intervention is optimal depends on the type of intervention and on the features
of the concrete case under consideration. Questions have to be answered whether permanent
intervention powers are needed and which price-quality ratio can be obtained by which form of
intervention. Cost-benefits analyses (e.g. Campbell and Brown, 2003) will be employed to
determine to which extent the advantages of internationalizing the complex external effects or
and/or a more politically acceptable distribution of income are offset against the costs of
government intervention.
The overall objective of this project is to describe an improved structure of the Indonesian poultry
production chain and the methods describing how the government can intervene in such a way
that this improved structure will be reached while the public interests involved are safeguarded.
Specific subobjectives are:
1. Inventarisation of the public interests involved with the poultry sector in Indonesia.
2. Determination of the current and alternative structures of the Indonesian poultry
production chain.
3. Development of an organisational model to determine the optimal structure of the
Indonesian production chain under varying technical and economic circumstances.
4. Inventarisation of the government instruments to facilitate and direct stimulate a desired
change in the structure of the poultry sector.
c. Workplan
Subproject 5.1. Based on economic theory and an existing conceptual framework (i.e., the public
interest calculus framework; Teulings et al., 2003), the public interests in Indonesia with regard to
the poultry production chain will be inventoried. Based on economic theory, the framework first
addresses the definition of a public interest (the what is a public interest and what are the public
interests involved with the poultry supply chain in Indonesia? questions). Next, the framework
also considers the how to? question: if there is a public interest, which role should the
government play in protecting it? A social interest only becomes a public interest if the market is
unable to protect the social interest. Specifically, the government has three reasons to intervene: In
case of unequally distributed positive effects of a change, in case of complex external effects
(including free-riders) and in case that the distribution of income leads to a loss of livelihood (e.g.,
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because of large benefits for big companies and no benefits for small farmers). By means of a
participatory workshop in co-operation with FAO, including officials from various governmental
levels and stakeholders from the poultry production chain, the conditions for an improved poultry
production chain will be determined.
Subproject 5.2. Based on the quantitative value chain simulation model developed in subproject
4,1, the economic efficiency of production (added value) as well as the risks for spread of AI
(based on results from projects 1 and 3) of the current structure of the poultry production chain in
Western Java will be determined. With participation of stakeholders, several elements for
alternative structures (e.g., fixed farmer-trader relations, limited number of farmers per trader,
larger farm size, changed payment systems, etc.) will be defined. For all these different elements,
the effect on economic efficiency (using partial equilibrium models) spread of AI, food security
and other conditions that were found to be important during subproject 5.1 will be estimated.
Subproject 5.3. Using the estimations calculated in subproject 5.2, several hybrid forms of supply
chain organisation will be developed. Minimal conditions that need to be met according to the
information derived during subproject 5.1 (e.g., for number of jobs, price of meat or availability of
poultry given a growing population and an increasing purchasing power) will be modelled as
constraints. Using these constraint models and principal-agent theory (e.g., Schneeweiss, 2003),
first- and second-best solutions for the poultry sector in Western Java can be derived, based on
different costs of input factors (feed, barns, veterinary services) and scenarios (e.g. different
growth scenarios of the population) under maximisation of the added value and minimisation of
the risk of AI outbreaks. The difference in risk of AI outbreaks and added value of the optimal
structure will be compared with the added value and risk of AI outbreaks under the current
structure to estimate the value of the improved structure of the poultry production chain.
Subproject 5.4. When an improved (optimal) new structure of the poultry production chain in
Western Java has been developed (subproject 5.3), an analysis will be made whether this new
structure can be implemented in Western Java without governmental intervention. In order to do
so, again a participatory workshop will be organised. During this workshop, knowledge will be
elicited whether stakeholders will benefit from a change in structure. As a consequence of external
effects (free-riders) as well as stakeholders who might not benefit from a change in structure of
the poultry production chain, it is expected that governmental intervention is necessary. Such an
intervention poses new dilemmas. The four dilemmas on the basis of which public intervention
can be designed are (Teulings et al., 2003):
1. commitment versus flexibility;
2. specificity versus competition;
3. co-ordination versus segregation;
4. output versus input steering.
If the government wants to remain flexible in its steering, it will enter into principal/agent
relationships. In case of a specific relationship instead of competition, the activities to be co-
ordinated and those that can be segregated must be determined. The government must also
choose between output and input steering. The answers to questions with regard to these
dilemmas will assist in selecting the intervention instruments to be used: 1. regulation and
legislation; 2. outsourcing of public tasks; 3. public organisation. The choice of one of these forms
of intervention depends on the costs and benefits, which will be estimated, presented to and
discussed with the government and other stakeholders.
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Application and further development of a framework (criteria) to identify public interests and to
select the government instruments to protect the public interests while restructuring the poultry
production chain in Indonesia is new. Moreover, an optimisation model to define a first-best
structure has not only relevance to the Indonesian situation, but will also be of general scientific
interest because these types of studies are scarce.
Wageningen School of Social Sciences (WASS)
publications most pertinent to this application. Include journal impact factors. Mandatory if your
proposal is entered in the themes: Infectious diseases and Health or Food, Non-Food and Water
Research. Optional for Social and Economic Development)
The average impact factor of the journals of this list is 2.07. All but one of these papers are

Simulating E. coli O157 transmission to assess effectiveness of slaughterhouse inverventions.
Motivation of dairy farmers to improve mastitis management. Journal of Dairy Science, 90:
4466-4477.
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127.

Assessing the economic consequences of foot disorders in dairy cattle using a dynamic
stochastic simulation model. Journal of Dairy Science, 93: 2419-2432.
846.
Analysis of the economically optimal voluntary waiting period. Journal of Dairy Science 94:
3811-3824.
status in the Netherlands: an outline. Preventive Veterinary Medicine, in press.
D.W. Lukman has three papers in peer-reviewed scientific journals. The journals are non-ISI
journals and the impact factors are not known.
Suardana I W., Sumiarto B., and Lukman D.W. 2007.

Isolasi dan identifikasi Escherichia coli O157:H7 pada daging sapi di kabupaten Badung
Provinsi Bali. Jurnal Veteriner 8 (1): 16 23.
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Nugroho W.S, Sudarwanto M, Lukman DW, Naim R, Setyaningsih S, Hassan AA, Usleber E. 2008.
Deteksi Mycobacterium avium subspecies Paratuberculosis pada susu formula lanjutan di
Bogor. Jurnal Teknologi dan Industri Pangan 19:19-24.
Nugroho W.S, Sudarwanto M, Lukman DW, Naim R, Hassan AA, Usleber E. 2008.
Detection of Mycobacterium avium subspecies paratuberculosis in formula milk from Bogor
using PCR IS 900. Medical Journal of Indonesia 17:183-187.
Publications W. Erno Kuiper:

International (refereed) journals and edited books
Kuiper, W.E. and G.J. Thijssen (1996),

Determinants of private investment in Dutch agriculture, European Review of Agricultural
Economics 23, 455-472. (impact factor: 1.065)
Kuiper, W.E. and M.T.G. Meulenberg (1997),
Cointegration and prediction analysis of market supply in the Dutch pig-farming industry,
European Review of Agricultural Economics , 24, 285-312. (impact factor: 1.065)
Kuiper, W. E., C. Lutz and A. van Tilburg (1999),
Testing for the law of one price and identifying price-leading markets: an application to corn
markets in Benin, Journal of Regional Science, 39(4), 713-738. (impact factor: 1.029)
Kuiper, W. Erno and Matthew T.G. Meulenberg (1999),

A structural vector error- correction model of price time series to detect bottleneck stages
within a marketing channel, chapter 7 in: G. Galizzi and L. Venturini (Eds.), Vertical
Relationships and Coordination in the Food System, Heidelberg: Physica Verlag.
Kuiper, W.E., J.M.E. Pennings and M.T.G. Meulenberg (2002),
Identification by full adjustment: evidence from the relationship between futures and spot
prices, European Review of Agricultural Economics , 29(1), 67-84. (impact factor: 1.065)
Vertical price leadership: a cointe-gration analysis, Agribusiness, 18(3), 317-331. (impact factor:
0.406)
Kuiper, W.E., C. Lutz and A. van Tilburg (2003),
Vertical price leadership on local maize markets in Benin, Journal of Development Economics, 71,
417-433. (impact factor: 1.747)
Price leadership within a marketing channel: a cointegration study, International Journal of
Research in Marketing, 21, 137-158. (impact factor: 1.365)
Kuwornu, J.K.M., W.E. Kuiper and J.M.E. Pennings (2004),
Time series analysis of a principal-agent model to assess risk shifting in agricultural marketing
channels: an application to the Dutch ware potato marketing channel, Chapter 17 in G.
Huylenbroeck, W. Verbeke and L. Lauwers (Eds.), Role of institutions in rural policies and
agricultural markets, Amsterdam: Elsevier.
Determining the causality between retail price and consumer demand in a linear function when
demand-shift variables are missing but wholesale prices are available, Agribusiness, 21(2), 167 -
176. (impact factor: 0.406)
Kuwornu, J.K.M., W.E. Kuiper, J.M.E. Pennings and M.T.G. Meulenberg (2005),
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Incentive provision and coordination costs in food marketing channels: a multi-stage channel-
agency theory perspective, Journal of Food Distribution Research, 36(1), 85 - 90.
Kuwornu, J.K.M., W.E. Kuiper, J.M.E. Pennings and M.T.G. Meulenberg (2005),
Time-varying hedge ratios: a principal-agent approach, Journal of Agricultural Economics,
56(3), 417 - 432. (impact factor: 0.969)
Lutz, C., W.E. Kuiper and A. van Tilburg (2007),
Maize Market Liberalisation in Benin: A Case of Hysteresis, Journal of African Economics, 16(1),
102 - 133.
Tilburg, A. van, W.E. Kuiper and R. Swinkels (2008),
Market performance of potato auctions in Bhutan, Journal of International Food and
Agribusiness Marketing, 20(2), 61 - 87. (impact factor: 0.167)
Bunte, F.H.J. and W.E. Kuiper (2008),
Promoting floriculture using VAT regulation, European Journal of Horticultural Science, 73(6),
248-253. (impact factor: 0.267)
Kooten, O. and E. Kuiper (2009),
Consumer acceptability in flower chains: how can we determine what the final customers really
want? Acta Horticulturae, 847, 17-26. (impact factor: 0.076)
Kuwornu, J.K.M., W.E. Kuiper and J.M.E. Pennings (2009),
Agency problem and hedging in agri-food chains: model and application, Journal of Marketing
Channels, 16(3), 265-289. (impact factor: 0.481)
Wagenberg, C.P.A. van, G.B.C. Backus, W.E. Kuiper, J.G.A.J. van der Vorst, H.A.P. Urlings (2010),
Incentive mechanisms for liver lesion control in finishing pigs in the Netherlands, Preventive
Veterinary Medicine, 93, 1924. (impact factor: 2.070)
Bunte, F.H.J., M.A. van Galen, W.E. Kuiper and G. Tacken (2010),
Limits to growth in organic sales, De Economist, 158, 387410. (impact factor: 0.622)
Kuiper, W.E. and A.J. Cozijnsen (2011),
The performance of German firms in the business-related service sectors revisited: Differential
evolution Markov chain estimation of the multinomial probit model, Computational Economics,
37, 331-362. (impact factor: 0.514)

Almeder, C., M. Preusser and R.F. Hartl (2009),
Simulation and optimization of supply chains: alternative or complementary approaches? pp.
29-53 in: H.-O. Gnther and H. Meyr (Eds.), Supply chain planning: quantitative decision
support and advanced planning solutions, Berlin: Springer.
Campbell, H.F. and R.P.C. Brown (2003),
Benefit-cost analysis, Cambridge: Cambridge University Press.Charnoz, O and P. Foster, 2011.
The global health impact of local power relations: Fragmented governance, big business and
organizational bias in Indonesian animal health policies. Working paper, Institute of Developing
Studies, University of Sussex, UK.
Dabbene, F., P. Gay and N. Sacco (2008),
Optimisation of fresh-food supply chains in uncertain environments, Part I: Background and
methodology, Biosystems engineering, 99: 348-359.FAO/WHO (1976), Assuring food safety and
quality: guidelines for strengthening national food control systems, Joint FAO/WHO publication
(http://www.who.int/foodsafety/
publications/fs_management/guidelines_foodcontrol/en/index.html).
Graversen, J.T., J.-M. Bramsen, M. Lund and J. Sondergaard (2004),
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Securing food quality in the Danish broiler supply chain - an economic and organizational
study, paper prepared for presentation at the 84th EAAE Seminar Food Safety in a Dynamic
World, Zeist, The Netherlands, February 8 - 11, 2004.Me nard , C. (1996), On Clusters, Hybrids
and other Strange Forms. The Case of the French Poultry Industry, Journal of Institutional and
Theoretical Economics, 152 (1): 154-183.Me nard, C. (2004), The Economics of Hybrid
Organizations, Journal of Institutional and Theoretical Economics, 160, 345376.
Mintzberg, H. (1979),
The structuring of organizations, Englewood Cliffs, NJ: Prentice Hall.
Mintzberg, H. (1989),
Mintzberg on management, New York: Free Press.
Schneeweiss, C. (2003),
Distributed decision making, Second Edition, Berlin: Springer.Sudarman, A., Sumiati, E.
Handharyani, A. Setiyono, S. Mulatsih, and R. Kusumaningrum (2008), Poultry value chain
study and avian influenza risk assessment in Jakarta surrounding area, Rome: FAO (report
from Center for Tropical Animal Studies of Bogor Agricultural University for FAO).
Teulings, C.N., A.L. Bovenberg and H.P. van Dalen (2003),
Key to the public interest calculus, The Hague: Knowledge Center for Economic Regulation
(publication id 04EP05).
Vo, T.L.H. and D. Thiel (2011),
Economic simulation of a poultry supply chain facing a sanitary crisis, British Food Journal,
113(8): 1011-1030.

The first subproject of project 4 (subproject 4.1), development of a quantitative value chain
simulation model, will be used in subproject 5.2. In this subproject the quantitative value chain
simulation model will be used to estimate the added value of the poultry chain in Western Java for
the sector analysis. Hence, this simulation model will resemble the basic structure of the poultry
production chain in Western Java and also forms the basis of the specification of the partial
equilibrium models for the empirical econometric analysis in subproject 5.2 and the integration of
these partial models into an overall econometric supply chain model for simulation and
optimisation purposes in subproject 5.3. The results from subproject 5.3 will be used in project 4
(subproject 4.4) to run the agent-based model with different structures. During the JRP we will
organise a joint workshop in Indonesia, which will be closely related to the participatory
workshops in subprojects 5.1 and 5.4. Finally, during the whole project we will use knowledge
from projects 1 and 3 about the existing contact structure as well as the spread of HPAI throughout
the poultry production chain in Indonesia.
During the JRP we will organize a joint workshop in Indonesia.
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_________________________________________________________________________________________

Dr Henk Hogeveen is a senior researcher and has since his MSc work been working in a
multidisciplinary research environment. His field of work is Animal Health Management where he
is used to build bridges between the veterinary sciences and the social sciences (mainly business
economics). His research and teaching appointment as associated professor is even at two
Universities: Wageningen University (chair group Business Economics ) and the Faculty of
Veterinary Medicine of Utrecht University (department of Farm Animal Health). In order to be
successful in such a multidisciplinary field one must have the competence to work in teams and to
understand researchers from different disciplines, something that Henk Hogeveen has shown to
be capable of. Besides of his capabilities to build bridges between researchers and research fields,
he has been managing several large research proposals, among which EU integrated projects as
well as Dutch Science Foundation funded projects.
Dr Denny Lukman is a lecturer in the field of veterinary public health. He has been long engaged
with the management of several projects in Indonesia mainly in veterinary public health and
zoonoses, the education the community on hygiene and biosecurity and the establishment of food
safety management. He has been collaborating before with Dutch researchers in several field
projects on HPAI control in Subang Subdistrict (West Java) supported by an Indonesia-Dutch
partnership. In the government, he is a member of expert committee on Animal Health and
Veterinary Public Health in the Ministry of Agriculture.
The total project will take 5 years. The activities of this research are divided over the resarch time
as follows:
6. Year 1: Learning methods in the field of economics (MSc courses in micro-, macro- and
mathematical economics, institutional economics, econometrics, statistics, operations
research and supply chain management) as well as preparation of the research.
7. Year 2: Organising a workshop in co-operation with FAO, including officials from various
governmental levels and stakeholders from the poultry production chain, to determine the
conditions for an improved poultry production chain. External effects are inventoried,
their complexity assessed (public interest?) and social constraints are formulated
(subproject 5.1).
8. Year 3: Assessing the current structure of the Indonesian poultry production chain using
value chain simulation model developed in project 4 and literature review on alternative
forms of co-ordination in supply chains discussed and analysed in terms of economic
efficiency and effectiveness (subproject 5.2). This year will be spent in Indonesia.
Page 111 of 117
_________________________________________________________________________________________
9. Year 4: Putting partial models and estimates of subproject 5.2 together into alternative
hybrid supply chain organisational forms and using simulation analysis and mathematical
programming to determine the optimal chain structure under different scenarios
(subproject 5.3).
10. Year 5: Organising a workshop to present and discuss the results of simulations in
subproject 5.3 with stakeholders to find out about conflicting interests with the optimal
supply chain structures vis-a -vis current practice and to assess the need and ways of
public intervention for re-structuring the poultry supply chain in Indonesia (subproject
5.4). Finishing the final report and Ph.D. thesis.
Besides the submitted scientific papers (four papers are envisaged) on the performed research,
the following Milestones are defined:
7. Finalised qualitative analysis and workshop on public interests involved with poultry
production in Indonesia.
8. Collection of secondary data for (partial equilibrium) econometric models of economic
behaviour of the supply chain actors.
9. Econometric supply chain model for simulation and optimisation purposes is finished.
10. Workshop and report on stakeholders interests vis-a -vis optimal organisation of poultry
production and need for and form of public intervention.
11. Final report and thesis finished.
Year 1 and 2 of the research will be spent at the Business Economics Group of the Department of
Social Sciences of Wageningen Unitersity. Year 3 of the project will be carried out in Indonesia at
the Division of Veterinary Public Health, Department of Animal Disease and Veterinary Public
Health of the Faculty of Veterinary Medicine of the Institut Pertanian Bogor as well as at the
Graduate School of Management and Business of Bogor Agricultural University. The final two years
of the project will be carried out in Wageningen again.
Page 112 of 117

_______________________________________________________
__________________________________
Page 113 of 117

_________________________________________________________________________________________
: 139,400 From: Wageningen University

For advisorship of this SPIN/DIKTI PhD fellow an associated professor (co-promotor; hourly tariff
for Ministry of EL&I 136) will spend 4 hours per week (40 weeks per year for 5 years) in daily
advisorship. A full professor (promotor; hourly tariff for Ministry of EL&I 153) will spend 1 hour
per week (40 weeks per year for 5 years) in advisorship.
Signature
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_________________________________________________________________________________________
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61 - SPIN - JRP Full Proposal Incl Projects 1-5

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61 - SPIN - JRP Full Proposal Incl Projects 1-5

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APPLICATION FORM FULL PROPOSALS JOINT RESEARCH PROJECTS SPIN 2012-2016

FILE NUMBER: 61-SPIN-JRP FULL

Joint Research Projects

1. Title of the Joint Research Programme

a. Main applicant in the Netherlands

c. Additional project partners in The Netherlands (minimum of one)

Dr. G. Koch (Virologist)

Dr. H. Hogeveen (Animal Health Economist)

d. Additional project partners in Indonesia (minimum of one)

Dr. Michael Haryadi Wibowo,

Prof. David H. Muljono

Jl. Agatis Kampus IPB Darmaga

Dr. Ir. Etih Sudarnika, MSi (Dr, MSc, Ir)

Dr. drh. Sri Murtini, MSi (Dr, MSc, DVM)

Prof.Dr. Ir. Arief Daryanto, M.Ec

a. Scientific Background (shared research question(s) or mutual research theme, problem

c. Workplan (approach, methods, deliverables, management)

Value chain analysis

Restructuring Indonesian Poultry production

government and other stakeholders.

d. Scientific Relevance (including relevance of anticipated results)

Project SPIN-61-JRP-2 Unraveling transmission of Highly Pathogenic Avian Influenza virus

Project 4 Economic benefits of a reduction of viral poultry diseases

Project SPIN-61-JRP-5 Restructuring the poultry supply chain in West Java

6. Relevant publications by members of the research group(s) (as defined under 2)

International (refereed) journals

Spekreijse D., Bouma A., Koch, G., Stegeman, J. A. (2011).

Maas R, Tacken M, Ruuls L, Koch G, van Rooij E, Stockhofe-Zurwieden N.

Thomas, M.E., Bouma, A., Klinkenberg, D., 2011.

Klinkenberg, D., Fraser, C., Heesterbeek, H., 2006.

International (refereed) journals

Huijps, K., H. Hogeveen, T.J.G.M. Lam and R.B.M. Huirne (2009).

Bruijnis, M.R.N., H. Hogeveen and E.N. Stassen (2010).

Murwani R, Murtini S. 2009.

Rochman, TR, Gumbira Said E, Daryanto A and Nuryantoro N (2011),

Books and Book chapters

Kapang Nematofagus Arthrobotrys oligospora, Kapang Endoparasit, dan Onacosporium

Wibowo MH, and Amanu S. 2010.

Wibowo MH, and Wahyuni AETH. 2008.

Sudarnika, E., Zahid, A., Basri, C. and Saefuddin A. 2008.

Saputra H, Daryanto A, and Hendrawan DS (2009).

Muljono, A.T., A.G.J. Velthuis, J. Rushton and H. Hogeveen. 2012.

Added Value and Cooperation

8. Added value of the integrated approach (including scientific disciplines involved)

9. Relevance of the programme for development issues in Indonesia

c. Dissemination and knowledge sharing;

11. International co-operation and network building (Max. 2000 words)

The Campaign Management Unit (CMU-UPPAI) at the ministry of Agriculture, Jakarta

c. Prior scientific collaboration between the research groups

12. Stakeholder participation (communication and dissemination)

13. Joint activities (Max. 1000 words) Word count: 167

Management and Administration

14. Information on the managing capacities of the Programme Coordinator

Duration and Planning

15. Time table of the programme and Milestones

16. Summary of Total JRP Costs and Personnel

: 212.602 From: Utrecht University

: 22.000 From: CVI Lelystad (add specification)

Purpose (e.g. specific activity or project number)

: 139,400 From: Wageningen University

REFERENCE NUMBER: 61-SPIN-JRP-1

Unraveling the contact structure within Indonesian Poultry Husbandry