Mapping Who

Mapping the Risk and Distribution of
Epidemics in the WHO African Region

A Technical Report
May 2016
WHO/AFRO Library Cataloguing – in – Publication Data
Mapping the Risk and Distribution of Epidemics in the WHO African
Region: a technical report
1. Disease Outbreaks – statistics and numerical data

2. Epidemics – statistics and numerical data
3. Communicable Diseases – statistics and numerical data
4. Risk Assessment – supply and distribution – statistics and numerical data
5. Data collection – utilization
6. Africa
I. Work Health Organization. Regional Office for Africa II. Title
ISBN: 978-9290233084-4 (NLM Classification : WA 105)

© WHO Regional Office for Africa, 2016
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Contact Information
Dr Ibrahima-Socé Fall, Director,
Health Security and Emergencies Cluster
WHO Regional Office for Africa, HSE Cluster,
Attention: IDS BP 6, Cité du Djoué, Brazzaville, Congo
Tel: (242) 241 39387/39412, (47) 241 38000
Fax: (47) 241 38005/6
Email: socef@who.int
WHO AFRO Technical Team

Dr Ibrahima-Socé FALL,
Dr Nestor NDAYIMIRIJE
Dr Zabulon YOTI
Mr Etienne MINKOULOU
Mrs Senait Tekeste FEKADU
Dr Vincent Dossou SODJINOU
Dr Soatiana RAJATONIRINA
Dr Ali Ahmed YAHAYA
Dr Magaran BAGAYOKO
WHO Technical Consultants

Professor Abdisalan M Noor, FAAS, Visiting Professor, University of Oxford
Director, Nairobi Programme
KEMRI-Wellcome Trust Research Programme
Second Floor, 197 Lenana Place, Lenana Road, PO Box 43640, 00100
Nairobi Kenya
Email: anoor@kemri-wellcome.org
Assisted by
Mr Stephen Oloo, Mr Ezekiel Gogo, Mr Joseph Maina
Assistant Research Officers, Geographic Information Systems
KEMRI-Wellcome Trust Research Programme
Second Floor, 197 Lenana Place, Lenana Road, PO Box 43640, 00100
Nairobi Kenya
Email: soloo@kemri-wellcome.org
Cover photo: Modified climatic ecological zones of Africa (source: http://www.fao.org/docrep/004/y1997e)
Acknowledgements
The authors would like to thank Peter Macharia and Paul Ouma of the KEMRI/Wellcome Trust Research
Programme for their help in data assemblies and mapping. The authors are grateful to Raymond Bruce J Aylward
Sylvie Brand, Sandra Garnier, Olivier Ronveaux and Eric Gerard Georges Bertherat of WHO Geneva and Amadou
Sall Institut Pasteur, Senegal, for comments on earlier drafts of this report.
Contents
Executive Summary ................................................................................................................................. 1
1. Introduction ........................................................................................................................................ 3
2. Objectives............................................................................................................................................ 4
2.1 Specific objectives ......................................................................................................................... 4
3. Assembly of outbreak and epidemics data ........................................................................................... 4
3.1 Identification of sources and developing a unified database .......................................................... 4
3.2 Summary of epidemic data by country and PHEIC disease ............................................................. 6
4. Mapping ecological zones and district of occurrence of PHEIC and other diseases ............................. 10
4.1 Ebola ........................................................................................................................................... 12
4.2 Lassa fever virus .......................................................................................................................... 14
4.3 Crimean Congo Hemorrhagic Fever ............................................................................................. 16
4.4 Marburg ...................................................................................................................................... 18
4.5 Rift Valley Fever........................................................................................................................... 20
4.6 Dengue Fever .............................................................................................................................. 22
4.7 West Nile Virus ............................................................................................................................ 24
4.8 Chikungunya................................................................................................................................ 26
4.9 Yellow Fever ................................................................................................................................ 28
4.10 Zika Virus ................................................................................................................................... 30
4.11 Cholera ...................................................................................................................................... 32
4.12 Plague ....................................................................................................................................... 34
4.13 Meningitis ................................................................................................................................. 36
4.14 Anthrax ..................................................................................................................................... 38
4.15 Malaria ...................................................................................................................................... 40
5. Correlates of outbreaks and epidemics .............................................................................................. 42
5.1 Population ................................................................................................................................... 42
5.2 Urban Population ........................................................................................................................ 43
5.3 Gross Domestic Product (GDP) per capita .................................................................................... 44
5.4 Percentage GDP expenditure on health ....................................................................................... 45
5.5 Human Development Index ......................................................................................................... 46
5.6 Under 5 Mortality Rate ................................................................................................................ 47
5.7 Global Hunger Index .................................................................................................................... 48
5.8 Conflicts ...................................................................................................................................... 49
5.9 El Nino occurrence....................................................................................................................... 50
5.10 Forest cover............................................................................................................................... 51
6. References ........................................................................................................................................ 52
Annex A: Districts maps of outbreaks and epidemics from 1970-2016 ................................................... 56
Annex B: Outbreaks and epidemics reported at national level only and not by district ........................... 59
Annex C: Summary of correlates used in the analysis of association with outbreaks and epidemics ....... 62
*See Accompanying MS PowerPoint file for district maps of outbreaks and epidemics by time period.
Executive Summary
Disease epidemics result in substantial ill health and loss of lives and therefore pose a threat to global
health security, undermine socio-economic lives and destabilize societies. Disease surveillance is a
critical component in detecting and effectively responding to epidemics to minimize loss of live and their
disruptive consequences. Carefully assembled surveillance data at the highest possible spatial
resolutions also permit the understanding of the burden of epidemics, their co-occurrence and the key
biological, ecological, economic, health system and governance determinants. It is for this purpose that
the WHO-AFRO has commissioned this report. The overarching objective was to develop a
comprehensive spatially defined database of outbreaks and epidemics and delineate the ecological
zones of diseases that are classified as Public Health Emergency of International Concern (PHEIC)
according the International Health Regulations (IHR) 2005 and malaria.
The main tasks included the assembly of an inventory of all epidemics reported in Africa from 1970-2016
characterised by date of occurrence, length of epidemic and magnitude and district of occurrence;
definition of ecological zones of PHEIC diseases and malaria; the assembly of data on important socio-
economic, health systems and environmental correlate and an basic statistical analysis of their
relationship with occurrence and frequency of epidemics and outbreaks.
Through this study, several products have been developed including time series graphs of outbreak and
epidemic occurrence by country, maps of the ecologies of the PHEIC diseases and epidemics, the
distribution of these diseases by district. Overall, over 1730 outbreaks/epidemics have been reported in
the WHO African region in the period 1970 to 2016. Because the outbreak/epidemic thresholds of the
different diseases vary and the actual case data is incomplete, it is difficult to compare which diseases
are most prevalent or pervasive. However, in terms of frequency of events, cholera, the arboviruses,
measles and meningitis rank the highest. Of the nearly 5250 administrative 2 units analysed in this
study, almost each one has reported some form of a disease outbreak in the period 1970-2016, with
cholera being the most geographically widespread. The resulting databases are spatially defined and
should serve as the basis of subnational inventory of disease outbreaks and epidemics in the region.
Several challenges were encountered in the process of implementing this exercise:
 There is limited information on the definitions and thresholds of outbreaks used over time and
how this may have been affected by changing diagnostics and case definitions. This results in
uncertainties in the temporal comparison of data.
 There were inconsistencies between the major databases used in this report in terms of
occurrence and magnitude of outbreaks. Agreement across more than two databases supported
with literature review and consultation with the WHO AFRO and HQ teams helped with data
verification.
 Poor access to national surveillance bulletins, which are an important source of original
outbreak and epidemics data, was a challenge to the data verification process and the
development of online portals of national surveillance reports is critical.
 There is limited data before 1980, most likely as a consequence of poor reporting or archiving of
outbreak and epidemic data in libraries outside of Africa. In contrast, there is a greater
frequency of reported outbreaks in the last 15 years as diagnosis and surveillance improved. For
these reasons, extreme caution must be exercised when interpreting the trends in disease
outbreaks and epidemics in Africa.
1
 The description of the location of outbreak and epidemic events were variable. In some cases
the name of village, town or district were reported. In others, the spatial definition of data was
at regional or country levels. The aim of this project was to harmonize these data was to define
events by district and where this was not possible, the data were reflected in the time series
graphs but are not shown on the district maps.
 Most of the potential correlates of epidemics, particularly those on socio-economic and health
system development, are rarely available by district restricting the analysis to national level.
The databases and maps produced in this report should be considered as the foundation for tracking
epidemics sub-nationally within the WHO African region. However, they require continuous verification,
improvements in spatial resolution and regular updating. Finally, these data can also serve as the inputs
for disease specific risk and vulnerability analysis. For example, the simple analysis in this report of the
correlates shows that urbanization, gross domestic product (GDP) per capita, percentage GDP
expenditure on health, human development index, global hunger index, conflicts, El Nino occurrence
and forest cover seemed to correlate with patterns of epidemics. Combining such correlates with the
detailed district level outbreak and epidemic data developed under this report could be the basis of
further analysis of the assessment of risk of and vulnerability to the PHEICs.
2
1. Introduction
There is an increasing recognition of the threat epidemics pose to global security, beyond its impact on
human health [https://ghsagenda.org/; WHO 2015a; Sands et al. 2016]. Epidemics impact on human
security through the catastrophic loss of life, the fear it creates in communities and the potential
disruption of political and public order [Sands et al. 2016]. It also impacts on economic activity through
the loss of labour and productivity and restrictions on travel and movement of goods. Low income
countries, where the burden of infectious diseases are also generally high and the health systems are ill
equipped to even respond to the basic health needs of the population, face greater vulnerabilities to the
consequences of epidemics, setting back hard-earned health and socio-economic gains. Increased global
connectivity and human population movement and economic interdependence mean that the risk and
consequences of infectious diseases spreading across borders has grown dramatically and the threat to
global security of an outbreak in a ‘distant’ corner of the world can no longer be ignored.
The recent Ebola virus disease (EVD) outbreak in West Africa and its consequences is a poignant
reminder of the global threat of epidemics [Moon et al 2015; Sands et al. 2016]. The outbreak began in
Guinea in December 2013 and rapidly spread to Liberia in March 2014 and Sierra Leone May 2014 as a
result of imported infections from Guinea [Moon et al 2015; WHO 2015b]. In all three countries, a full
blown epidemic occurred and has only recently being brought under control. Small outbreaks also
occurred in Nigeria and Mali and imported cases have been reported in Senegal, USA, the United
Kingdom and other parts of the world. In the three main affected countries, over 28,000 people have
become infected and 11,000 lives have been lost since [Moon et al 2015]. The economic losses as a
result of the Ebola epidemic were estimated to be up to 2.2 billion US dollars in 2015 alone [World Bank
2016]. Although the epidemic has been largely controlled, cases have been reported in all countries in
2015.
The rapid spread of the EVD and its catastrophic consequences were attributed to several national and
international weaknesses [Moon et al 2015; Sands et al. 2016]. In February 2014, the Global Health
Security Agenda (GHSA) was launched with a vision of ‘..a world safe and secure from the global health
threats posed by infectious diseases…’ [https://ghsagenda.org/about.html]. By November 2015, 48
countries, including 10 from the WHO African region, had become members of the GHSA. Eleven action
package areas (4 on prevention, 5 on detection and 3 on response) have been identified as part of the
roadmap to implement the IHR (2005) [https://ghsagenda.org/packages.html].
Throughout the post-Ebola discussions, the existence of important surveillance gaps in several African
countries was seen as a major obstacle to the prevention, preparedness, detection and response of
future epidemics on the continent. The WHO African Regional Office (AFRO) has undertaken several
activities including the critical assessment of country reading for International Health Regulations (IHR)
2005 requirements, the scale up and improvements of integrated disease surveillance and response
(IDSR) systems and the strengthening of country laboratory capacity to detect diseases of international
public health importance [WHO 2015c; CDC-IDSR 2015].
As part of this response, the WHO-AFRO has identified the need to develop a comprehensive, high
resolution and spatially defined database of past outbreaks and epidemics to understand the disease
specific epidemiological risks, the sub-national distribution of outbreaks and to support epidemic risk
vulnerability analyses necessary for prioritizing country support. It for these reasons that this work was
commissioned.
3
2. Objectives
The occurrence of disease causing pathogens, host susceptibility, and environmental and contextual
factors necessary for transmission are the key determinants of infectious outbreaks and epidemics
[Janeway et al 2001]. Epidemics are likely to occur under conditions where there has been an increase in
amount or virulence of the agent, introduction of the agent into a non-immune population, change in
the host susceptibility, or pathogen susceptibility to drugs or enhanced transmission pathways
increasing infection rates [Kelsey et al 1986].
The main objective of this project, therefore, was to develop a comprehensive spatially defined
database of outbreaks and epidemics and delineate the ecological niche of diseases that are classified as
Public Health Emergency of International Concern (PHEIC) according the International Health
Regulations (IHR) 20051, and malaria, in the WHO African region. Under the IHR (2005), diseases
classified as PHEIC were small pox, poliomyelitis due to wild-type poliovirus, human influenza caused by
a new subtype and severe acute respiratory syndrome (SARS), pneumonic plague, yellow fever, viral
hemorrhagic fevers, and West Nile fever and Zika virus.
2.1 Specific objectives
1) Develop an inventory of all epidemics reported in Africa from 1970-2016 and characterise data by
date of occurrence, length of epidemic and magnitude.
2) Define the ecological zones of diseases that are classified as PHEIC and malaria.
3) Link the assembled data on outbreaks and epidemics to highest geographic resolution, preferably by
district or equivalent
4) Identify and assemble data on important socio-economic, health systems and environmental factors
and implement a statistical analysis of their relationship with occurrence and frequency of
epidemics
3. Assembly of outbreak and epidemics data
3.1 Identification of sources and developing a unified database
A single complete reference database of epidemics in Africa does not exist. Therefore, the first step in
developing such a database was to identify all potential sources of epidemic data, harmonize them and
undertake additional searches of published and unpublished literature to develop a detailed database of
epidemics. The key data sources used were Emergency Events Database (EM-DAT) of the Centre for
Research on the Epidemiology of Disasters (CRED), the WHO/AFRO outbreaks database for the period
2007-2014, and the WHO-Disease Outbreak News (DON). Additional sources included the US Center for
Disease Control and Prevention CDC) Morbidity and Mortality Weekly Reports (MMWR), the ProMED
1
Global Health Security: International Health Regulations (IHR)
http://www.cdc.gov/globalhealth/healthprotection/ghs/ihr/
4
(the Program for Monitoring Emerging Diseases) database, the Poliomyelitis Global Status database and
other WHO disease specific databases.
The EM-DAT epidemic data is compiled from sources such as UN agencies, non-governmental
organizations, insurance companies, research institutes and press agencies who report epidemic events.
The epidemic reports are then validated before they are entered into the EM-DAT database [Guha-Sapir
et al 2015]. This data is available in the OFDA/CRED International Disaster Database and can be accessed
through the EM-DAT website (www.emdat.be). Data was obtained through an official request and the
data elements included were the actual location of the epidemic, origin of the epidemic and start and
end dates of the epidemic. These database was received via email on 11th September, 2015. The EM-
DAT epidemics data contained 778 epidemic events from 1970 to 2014.
As part of the project, the WHO-AFRO Health Security and Emergencies Cluster team provided a
database of disease outbreaks covering the period 2007-2015 in Africa. The database contained
information on 22 epidemic and pandemic diseases. The WHO/AFRO 2007-2014 dataset contained 439
public health events across 22 different diseases, which was reduced to 18 after naming all influenza
virus strains generally as “Influenza”.
The WHO-DON databased is run from Geneva and is based on notifications of public health events
caused by various infectious pathogens and other hazardous substances submitted to the WHO by
member states as required under the IHR 2005 [WHO 2008]. Public health events that are unusual or
associated with increased risk to humans are published weekly in the DON website
(http://www.who.int/csr/don/en/). Data on these events due to infectious disease outbreaks was
compiled from the reports published on the website from 1996 to 2015. The DON data reported 218
public health events.
Data on several notifiable diseases, particularly on viral hemorrhagic fevers, such as Ebola, were also
obtained from various outbreaks portals hosted on the US Centre for Disease Control and Prevention
(CDC) website [www.cdc.gov]. Most of the databases included information on disease, time and location
of outbreak. In some cases, data was reported on the various strains of the disease causing, but for
purpose of mapping these strains were grouped together. For example, 30 Ebola outbreaks were
reported from the CDC-Ebola dataset.
The ProMED (the Program for Monitoring Emerging Diseases) database is an open source online
reporting system established in 1994 by the Federation of American Scientists and SATELLIFE, to provide
up-to-date information on outbreak of diseases and exposures to toxins that affect humans as well as
animals and crops grown for food. The information disseminated by ProMED is collected through media
reports, official reports, online summaries and by local observers, and later verified by a team of experts
before it is posted on the ProMED website (www.promedmail.org) where it can be accessed freely.
Epidemic data from each data source was counter-checked with data from other data sources. The
various databases were compared on the basis of disease, location, start and end times, and magnitude
in terms of infections and deaths. Where one epidemic was reported from different data sources, the
record from the data source that had reported the disease causing the epidemic, the exact location of
the epidemic, the exact start and end dates of the epidemic, the actual number of people affected by
the epidemic, the number of deaths caused by the epidemic and the origin of the pathogen causing the
epidemic was retained. There was no data source that contained all of these variables for all the
epidemics reported, therefore the higher the number of these variables in a particular record, the higher
5
the rank of that record. Where the retained records had missing data elements available in other data
sources, this information was transferred to final database. Where an epidemic was reported in only
one data source, online searches of published literature, new articles and any online references to
search epidemic was undertaken for verification. Unverified epidemic events were classified as being
from a single source.
A broad literature search was also undertaken to identify past and recent epidemics that were not
captured in any of the established databases. Specifically, a systematic literature review carried out to
identify malaria epidemics found 221 articles of which only 75 articles reported malaria epidemics.
Malaria epidemic events was extracted from these articles and duplicate events removed resulting in 62
malaria epidemic events reported in Africa since 1970.
3.2 Summary of epidemic data by country and PHEIC disease
Assembled epidemic data were summarized by country and year from the period 1970-2016. A 1970
starting point was selected simply for pragmatic reasons, however, there is limited data on epidemics
before this period. Where a disease outbreak or epidemic started in one year and continued in
consecutive years, this was considered to be one event unless there was evidence that they were totally
independent epidemiologically. For example, the Ebola epidemic that started in Guinea in 2013 and
continued through to 2015 was considered to be a single epidemic.
Figure 1 A graph of all the outbreak and epidemic events by disease in the countries of the WHO African region
6
Figure 2 A bubble plot of outbreaks and epidemics of 39 diseases from 1970 to 2016 in the WHO African region.
Figure 3 A bubble plot of PHEIC diseases (Ebola , Lassa, Crimean Congo , Marburg , Rift Valley Fever, Dengue, West
Nile virus, Chikungunya, Yellow Fever, Zika virus, Plague, Meningitis and Polio) from 1970 to 2016 in the WHO
African region.
7
Figure 4 A bubble plot of viral hemorrhagic diseases (Crimean Congo, Dengue, Ebola, Lassa, Marburg, Rift Valley
Fever, Yellow Fever and unknown or unspecified viral hemorrhagic fevers) from 1970 to 2016 in the WHO African
region.
Figure 5 A graph of the number of unknown or unspecified viral hemorrhagic diseases by country from 1970 to
2016 in the WHO African region.
8
Table 1 Summary of outbreaks or epidemics reported in the WHO African region period 1970-2016 by
known disease (n=38) and unknown conditions (n=2)
No. Disease Frequency
1 Acute Flaccid Paralysis 1
2 Acute Jaundice Syndrome 1
3 Acute Neurological Syndrome 3
4 Acute Respiratory Syndrome/Infection 7
5 Aflatoxicosis 1
6 Anthrax 46
7 Chicken Pox 1
8 Chikungunya 13
9 Cholera 476
10 Crimean Congo 20
11 Dengue Fever 23
12 Diarrhoeal Disease 42
13 Ebola* 31
14 Fever with jaundice (Febrile Icterus) 1
15 Hepatitis (undefined) 1
16 Hepatitis A 1
17 Hepatitis B 2
18 Hepatitis E 8
19 Influenza 17
20 Lassa Fever 28
21 Leishmaniasis 2
22 Leptospirosis 1
23 Malaria 60
24 Marburg Disease 12
25 Measles 75
26 Meningococcal Disease 99
27 MERS-CoV** 3
28 Monkey Pox 16
29 Nodding 1
30 O'NyongNyong fever 2
31 Plague 47
32 Polio 439
33 Rift Valley fever 17
34 Schistosomiasis 1
35 Typhoid Fever 27
36 West Nile Fever 4
37 Yellow Fever 131
38 Zika Virus 1
39 Unknown Epidemic 96
40 Unknown Hemorrhagic Fever 22
Total 1779
* In Senegal one case was imported from Guinea; in South Africa one case imported from Gabon; in Cote
d’Ivoire the case was a nosocomial infection (laboratory accident)]
**Algeria –an imported case from Mecca in Saudi Arabia
9
4. Mapping ecological zones and district of occurrence of PHEIC and other
diseases
For the purpose of this analysis, the ecological zone of a disease is defined as any area within a country,
where transmission of pathogens to humans can occur. A combination of country data on reported local
cases, serological or genetic evidence of presence of pathogens in human hosts and the presence of
transmitting vectors or zoonotic reservoirs have been used to define the ecological zones of the various
PHEIC diseases.
Although an entire country may be classified as belonging to the ecological zone of a specific disease, it
is not uncommon that only a small area within the country has the ecological factors required for
transmission, and the risk assigned to a country may be exaggerated. Therefore, it is important that
reported cases are also described at the highest possible geographic resolution to reflect this
heterogeneity. Here, the district geographic unit, or its equivalent, was used as the highest spatial
resolution and epidemic data reported from a village, town and district were all assigned to the district
(Annex A). In a few cases, data were reported at regional, provincial and state level and for such data, all
districts in these geographic units were assumed to be affected by the epidemic. There were many
reports of disease outbreaks that were provided with information on the country of occurrence.
Although such data were used in country level ecological niche mapping, it was not possible to link them
to any district and are summarized in Annex B.
Almost all countries have undergone administrative boundary changes over time and these have
affected the boundaries of districts. In some countries, the boundaries have change multiple times. As a
first step, a decision was made to map the epidemic data at the current district extent to allow for
future updating of the data. Consequently, a process of boundary digitization of district boundaries was
undertaken in several countries using existing maps that are available online or other published sources.
For Algeria, an updated district map was not available and the province boundaries was used. Across the
47 countries of the WHO African region, data were linked to a total of 5,249 district polygons or
equivalent (Table 1).
Overall the ecological zone maps can be used by global and regional partners for country risk
assessment and prioritization while the district maps serve a useful purpose for local planning, risk
factor analysis and sub-national surveillance prioritization.
10
Table 2 The number of district units or equivalent (n=5249) that were used to map the outbreak and
epidemic data. For Algeria, the province level boundaries were used.
Country Number of administrative polygons

Algeria 48
Angola 161
Benin 34
Botswana 27
Burkina Faso 70
Burundi 46
Cameroon 180
Cape Verde Islands 23
Central Africa Republic 24
Chad 62
Comoros 3
Cote d'Ivoire 82
DRC 512
Equatorial Guinea 7
Eritrea 58
Ethiopia 731
Gabon 48
Gambia 7
Ghana 216
Guinea 38
Guinea-Bissau 89
Kenya 295
Lesotho 10
Liberia 90
Madagascar 112
Malawi 29
Mali 63
Mauritania 53
Mauritius 12
Mozambique 156
Namibia 34
Niger 42
Nigeria 775
Republic of Congo 39
Rwanda 30
Sao Tome and Principe 2
Senegal 76
Seychelles 1
Sierra Leone 14
South Africa 354
South Sudan 79
Swaziland 55
Tanzania 171
Togo 40
Uganda 112
Zambia 72
Zimbabwe 67
11
4.1 Ebola
Figure 6: Ebola virus ecological zones mapped using a combination of reported cases and potential risk based on
environment factors that may support the habitation by the African fruit bat.
Ebola hemorrhagic fever is a rare disease

with a high fatality rate caused by
infection with one of the five Ebola virus
species [CDC-Ebola 2016]. There is no
known natural reservoir host of the virus,
however, the general consensus is that
initial infection may be due to contact
with to the fruit bats and some primates
such as monkeys and chimpanzees
followed by human-to-human
transmission [Chowell et al 2014; CDC-
Ebola 2016]. Transmission between
humans is through direct contact with
blood and other body fluids of infected
persons.
Ebola was first discovered in 1976 not far

from the Ebola River in the Democratic
Republic of Congo. In the same year, an
outbreak was reported in Nzara district
of South Sudan [CDC-Ebola 2016]. Since
1976, 31 outbreaks of the Ebola virus
have occurred in the WHO African
region. The most recent outbreak began
in Guinea in December 2013 and has
since spread extensively in Liberia and
Sierra Leone with smaller outbreaks
triggered by imported cases reported in
Nigeria and Mali [Baize et al 2014;
Bausch and Schwarz 2014; CDC-Ebola
2016]. In 2014, Ebola was recently
declared a PHEIC by the World Health
Organization [Funk and Piot 2014].
To define the ecological zones for Ebola

virus transmission, data on reported local
cases [CDC-Ebola 2016; WHO 2016a]
were combined with information from an
ecological niche model [Pigott et al 2014]
to classify countries into those where local cases (indigenous and introduced) were reported and those that can
support transmission based on the ecological niche modelling. The ecological niche model used data on reported
cases and fruit bat occurrence paired with environmental covariates to predict a zoonotic transmission niche in 22
countries across Central and West Africa. The environmental covariates used were vegetation, elevation,
temperature, evapotranspiration [Pigott et al 2014].
12
Figure 7: District map of reported Ebola virus disease cases reported from 1976 to 2015.
13
4.2 Lassa fever virus
Figure 8: Lassa fever virus ecological zones mapped using a combination of reported cases and potential risk based
on environment factors that support the habitation by the mouse Mastomys natalensis
Lassa fever is a viral haemorrhagic

illness and occurs as outbreaks across
West Africa. It is a zoonosis, with the
primary reservoir species identified as
the Natal multimammate mouse,
Mastomys natalensis. The host is
distributed across sub-Saharan Africa
while the virus’ range appears to be
restricted to West Africa. The majority
of infections result from interactions
between the animal reservoir and
human populations, although
secondary transmission between
humans can occur, particularly in
hospital settings [CDC-Lassa Fever,
2015].
Since its initial discovery, cases of Lassa

fever have been reported in Sierra
Leone, Liberia, Guinea, Nigeria, Niger,
Mali, Ghana, Togo, Cameroun, Benin
and Burkina Faso while serological
evidence have been shown in Togo and
Benin and in the rodent in Cameroon
[Fichet-Calvert & Rogers 2009; Mylne
et al 2015; CDC-Lassa Fever 2015].
Recent outbreaks of Lassa fever have
been reported in Nigeria, Togo and
Benin [WHO 2016]. The locations of
confirmed human and animal infections
with Lassa virus (LASV) were used to
generate a probabilistic surface of
zoonotic transmission potential across
sub-Saharan Africa using species
distribution models [Mylne et al 2015].
Lassa fever ecological zones were

developed using the data on reported
cases and rodents and the predicted geographic extent of the Natal multimammate mouse.
14
Figure 9: District map of reported Lassa fever virus cases reported from 1989 to 2016. Some outbreaks have only
being reported at national and could not be linked to a district (see Annex B)
15
4.3 Crimean Congo Hemorrhagic Fever
Figure 10: Crimean Congo Hemorrhagic fever virus ecological zones mapped using a combination reported cases,
serological evidence and potential risk of transmission based on tick vector
Crimean-Congo haemorrhagic fever

(CCHF) is caused by a tick-borne virus,
Nairovirus, of the Bunyaviridae family
[CDC-CCHF 2014]. Some wild and
domestic animals are asymptomatic
carriers of the virus. The virus was first
isolated in the Crimea in 1944 and later
identified as a cause of illness in 1969 in
the Congo, hence its name. The CCHF
virus causes severe viral hemorrhagic
fever outbreaks, with a case fatality rate
of 10%–40% and is found in many parts
Africa, the Balkans, the Middle East and
Asian countries across the geographical
limit of the principal tick vector [WHO
2013; Ergonul 2006]. Climatic factors that
influence the presence of the tick, such
as temperature, precipitation and
moisture indices, have been found to be
important drivers of CCHF infection
[Wilson et al 1990; Vescio et al 2012;
Messina et al 2015].
A combination of case reports,

serological evidence of the virus in
humans and the presence of the
Hyalomma tick were used to develop
probabilistic maps of CCHF virus risk
[Messina et al 2015]. Country
classification based on this map were
updated using newly assembled.
Countries with confirmed reported cases
of CCHF or serological evidence in
humans were classified as having
complete presence of CCHF virus.
Countries where the tick vector was
present were classified as having
moderate CCHF presence and the rest as
indeterminable.
16
Figure 11: District map of reported Crimean Congo Hemorrhagic fever cases reported from 1996 to 2015. Some
outbreaks have only being reported at national and could not be linked to a district (see Annex B).
17
4.4 Marburg
Figure 12: Marburg virus ecological zones mapped using a combination reported cases and potential risk of
transmission based on the presence of the Roussettus aegyptiacus vector.
Marburg virus disease (MVD)

(formerly known as Marburg
haemorrhagic fever) was first
identified in 1967 during epidemics in
Marburg and Frankfurt in Germany
and Belgrade in the former
Yugoslavia from importation of
infected monkeys from Uganda
[WHO n.d.(a); CDC-MVD 2014]. MVD
is a zoonotic disease, with the African
fruit bat (Rousettus aegyptiacus)
identified as a reservoir host and
affects both human and non-human
primates. Infection is suspected to
result from contact between this
reservoir and human populations,
with occasional secondary human-to-
human transmission.
In Africa, five countries have

confirmed or suspected instances of
animal-to-human zoonotic
transmission of Marburg, namely
Kenya, Uganda, Zimbabwe, Angola
and the DRC [CDC-MVD 2014; Pigott
et al 2015].
Countries in the WHO African region

were classified into two Marburg
ecological zones, those with reported
MVD cases [CDC-MVD 2014], those
without reported cases but with
ecology that support the occurrence
of Rousettus aegyptiacus [Pigott et al
2015] and those with no evidence of
risk. However, there is limited data
on both the distribution of the
disease and the zoonotic reservoir and this map may reflect the true extent of the likelihood of Marburg
transmission.
18
Figure 13: District map of reported Marburg virus disease cases reported from 1975 to 2014. Some outbreaks have
only being reported at national and could not be linked to a district (see Annex B).
19
4.5 Rift Valley Fever
Figure 14: Rift Valley fever virus ecological zones mapped using a combination reported cases, serological evidence
and potential risk of transmission based on the presence of the Aedes mosquito.
Rift Valley Fever (RVF) is viral zoonosis

transmitted mainly by mosquitoes of the
genus Aedes that primarily affects animals
but also has the capacity to infect
humans. Infection can cause severe
disease in both animals and humans
[Nanyingi et al 2015; CDC-RVF 2013]. The
disease also results in significant
economic losses due to death and
abortion among RVF virus infected
livestock. Since the first isolation of the
virus in humans in the 1930s there have
been multiple epizootics and epidemics of
the RVF in sub-Saharan Africa [Muriithi et
al 2011; Nanyingi et al 2015].
Outbreaks have been reported in many

parts of sub-Saharan and North Africa. In
1997-98, a major outbreak occurred in
Kenya, Somalia and Tanzania and in
September 2000, RVF cases were
confirmed in Saudi Arabia and Yemen,
marking the first reported occurrence of
the disease outside the African continent
and raising concerns that it could extend
to other parts of Asia and Europe [WHO
2010]. RVF virus outbreak was reported in
1987 in the lower Senegal River and was
linked with flooding as a result of the
Senegal River Project [CDC-RVF 2013].
Countries were classified into three RVF

ecological zones: reported large
outbreaks; reported periodic cases and/or
serological evidence in humans; and only
the presence of the Aedes mosquito was
reported.
20
Figure 15: District map of reported Rift Valley fever virus disease cases reported from 1997 to 2012. Some
21
4.6 Dengue Fever
Figure 16: Dengue hemorrhagic fever virus ecological zones mapped using a combination reported cases,
serological evidence and potential risk of transmission based on presence of the Aedes mosquito.
Dengue is a systemic viral infection

transmitted between humans by
Aedes mosquitoes, especially Ae.
aegypti and Ae. albopictus
[Simmons et al 2012; Kraemer et al
2015]. For some patients, dengue
is a life-threatening illness [WHO
and TDR 2009]. In Africa, dengue,
like many other arboviruses, is
considered to be under-reported
[Brady et al 2012; Bhatt et al 2013]
making its distribution uncertain
despite the widespread presence
of the transmitting vectors. The US
CDC and HealthMap have
developed a global dengue activity
map based on data derived from
the CDC Health Information for
International Travel (or the
YellowBook) and other data
sources.
These data on reported cases and

serological evidence were used to
classify countries into those with
complete, moderate or
intermediate presence of the
dengue virus. These classification
was further improved with an
updated dataset.
22
Figure 17: District map of reported Dengue hemorrhagic fever virus disease cases reported from 1973 to 2015.
Some outbreaks have only being reported at national and could not be linked to a district (see Annex B).
23
4.7 West Nile Virus
Figure 18: West Nile virus ecological zones mapped using a combination reported cases and serological evidence in
human or non-human hosts.
West Nile virus (WNV) is transmitted
through female mosquitoes and was
first isolated in 1937 from the blood of a
febrile female patient who was
examined in the context of a study of
sleeping sickness in the West Nile
district of Uganda [Smithburn et al
1940]. The largest outbreaks of WNV
have been in Greece, Israel, Romania,
Russia, and the USA. The outbreak of
WNV in America was from 1999-2010
and since then has spread more widely
across the world. This disease is seen as
more of a threat to birds and horses,
than the virus is to humans. Only 20% of
the people infected with WNV show
symptoms and less than 1% die from the
virus. About 1 in 5 people who are
infected will develop a fever with other
symptoms. Less than 1% of infected
people develop a serious, sometimes
fatal, neurologic illness [CDC-WNV
2015]. This virus is currently,
geographically, the most widely
distributed arbovirus in the world,
occurring on all continents except
Antarctica [Ciota & Kramer, 2013].
The West Nile Virus (WNV) risk map was

generated from the data presented by
Cabre et al 2006 and the updated
datasets collected for this report. The
map show areas of high risk defined as
countries that have reported frequent
WNV outbreaks. Countries that have
reported few sporadic WNV cases were
considered to be of medium risk, while
low risk class comprised countries that
have never reported any case of WNV but have serological evidence from either human or non-human host of the
virus circulation. The grey regions are regions that have never reported or there is no data to indicate the presence
of WNV transmission.
24
Figure 19: District map of reported West Nile fever virus disease cases reported from 2001 to 2014. Some
25
4.8 Chikungunya
Figure 20: Chikungunya ecological zones mapped using a combination reported cases, serological evidence and
the presence of the Aedes mosquito.
Chikungunya virus is transmitted to
people by the Aedes mosquito. The
most common symptoms of
chikungunya virus infection are
fever and joint pain. Other
symptoms may include headache,
muscle pain, joint swelling, or rash.
Outbreaks have occurred in
countries in Africa, Asia, Europe,
and the Indian and Pacific Oceans.
In late 2013, chikungunya virus was
found for the first time in the
Americas on islands in the
Caribbean [CDC-CHIKV 2015].
Chikungunya is a mosquito-borne
viral disease first described during
an outbreak in southern Tanzania in
1952 [WHO 2015d]. The 2005 -
2007 outbreak was the most severe
and one of the biggest eruptions
caused by this virus [Jadav et al
2014].
Chikungunya fever has an

epidemiological pattern with both
sporadic and epidemics cases in
West Africa, from Senegal to
Cameroun, and in many other
African countries including
Democratic Republic of Congo,
Nigeria, Angola, Uganda, Guinea,
Malawi, Central African Republic,
Burundi, and South Africa [Pialoux
et al 2007; Jain et al 2008].
Ecological zones were based on

reported cases and the presence of
the Aedes mosquito.
26
Figure 21: District map of reported Chikungunya viral disease cases reported from 2005 to 2015. Some outbreaks
have only being reported at national and could not be linked to a district (see Annex B).
27
4.9 Yellow Fever
Figure 22: Yellow fever virus ecological zones mapped using a combination reported cases and potential risk of
transmission based on serological evidence and the presence of the Aedes aegypti vector. Areas shaded grey are
considered to be free of yellow fever transmission.
Yellow fever is an acute viral
hemorrhagic disease transmitted
by infected Aedes mosquitoes.
The "yellow" in the name refers
to the jaundice that affects some
patients. The virus is endemic in
tropical areas of Africa and Latin
America [WHO 2014a].
The yellow fever ecological zones

were defined according to the
risk of infection. There are two
transmission classes presented
in this map. The first class is the
moderate to high risk which
includes the endemic and
transitional zones [Jentes et al
2011]. These are areas which
have a long history of reported
enzootic yellow fever, both the
vector and non-human host
exist, and/or there were high
numbers of reported human
yellow fever cases before high
coverage of the vaccine or there
is serological evidence of high
levels of yellow fever virus.
Transitional zones are regions
bordering the endemic area and
include areas that experience the
virus transmission during
epidemic expansions.
The second class is the low risk

zone. This class covers the areas
where yellow fever vectors and
non-human host exist but no
human or non-human yellow
fever infection have been
reported. The serological
evidence in this zone might also indicate low levels of yellow fever transmission in the past.
Figure 23: District map of reported Yellow fever virus disease cases reported from 1978 to 2016. Some outbreaks
have only being reported at national and could not be linked to a district (see Annex B).
28
29
4.10 Zika Virus
Figure 24: Zika virus ecological zones mapped using a combination of reported cases and potential risk of
transmission based on serological evidence and the presence of the Aedes aegypti vector.
Zika viral disease is transmitted through the

bite of an infected mosquito, primarily Aedes
aegypti. The virus was first identified in 1947
in rhesus monkeys in the Zika forest of
Uganda [Dick et al. 1952], and human disease
was first identified in 1952 in Uganda and the
United Republic of Tanzania. Zika virus
disease outbreaks were reported for the first
time from the Pacific in 2007 and 2013 in Yap
and French Polynesia, respectively. The
geographical spread of Zika virus has since
been steadily increasing.
Zika virus disease has similar clinical

presentation as chikungunya and dengue,
although it generally causes a milder illness.
Symptoms of Zika virus disease include fever,
skin rashes, conjunctivitis, muscle and joint
pain, malaise, and headache, which normally
last for 2 to 7 days. Neurological
complications have been reported in
Polynesia and in Brazil in 2014 and 2015
respectively. More recently increased number
of microcephaly cases has been reported in
Brazil since October 2015[WHO 2016b].
For many years, despite lack of systematic

surveillance mechanism for Zika virus disease,
sporadic human cases were detected in
Africa. Since 2007 the spread of the virus has
been confirmed in 8 Pacific islands, 25
countries and territories of the Americas, and
a few Asian countries. In the African region,
Cape Verde has reported outbreak with over
7000 cases from October 2015 to January
2016. However, the number of cases has been
on the decline since December 2015
according to available data.
The Zika virus transmission zone map was developed from data on reported cases, serological evidence of
exposure in humans , confirmed transmission of dengue and/or chikungunya and confirmed presence of the
Ae.aegypti and/or Ae albopictus. Evidence of infection in humans through local transmission was weighted highest
followed by the serological data and reported transmission of dengue and chikungunya. Data on only the presence
of the vector was given the lowest weight. The confirmed transmission of the two arboviruses was used as a proxy
of sufficient vector density and/or efficiency. For more information please refer to the recent Zika virus risk
assessment in the WHO African region [WHO-AFRO 2016].
30
Figure 25: District map of reported Zika virus disease cases reported from 2015 to 2016
31
4.11 Cholera
Figure 26: Cholera ecological zones mapped using reported case data. Cholera outbreaks can occur in any country
of the WHO African region but more prevalent in areas with poor sanitation and low access to clean water.
Cholera is an acute, diarrheal illness caused

by infection of the intestine with the
toxigenic bacterium Vibrio cholerae
serogroup O1 or O139. Infection can be
asymptomatic, mild, or severe.
approximately 1 in 20 infected persons has
severe disease characterized by profuse
watery diarrhea, vomiting, and leg cramps.
In these persons, rapid loss of body fluids
leads to dehydration, electrolyte
disturbances, and hypovolemic shock.
Without treatment, death can occur within
hours [Sack et al 2004].
Cholera, has largely been eliminated from

the industrialized countries by water and
sewage treatment, but still remains a
significant cause of illness and death in
many low income countries. Sub-Saharan
Africa bears the brunt of the global cholera
burden. The region is broadly affected by
many cholera cases and outbreaks that can
spread across countries [Gaffga et al 2007].
This reflects the lack of access to basic
sanitation, clean water and health care
[WHO 2012].
Cholera outbreaks have been reported

across Africa and the ecological zones have
broadly been defined on the basis case
reporting. Countries have been classified
into those that have reported local
outbreaks and those that report imported
cases only.
32
Figure 27: District map of reported cholera cases reported from 1970 to 2016. Some outbreaks have only being
reported at national and could not be linked to a district (see Annex B).
33
4.12 Plague
Figure 28: Plague ecological zones mapped using a combination of reported cases in humans and potential risk of
transmission based on reported cases of plague in animals and countries with suitable ecology for transmission.
Plague is a bacterial disease, caused by

Yersinia pestis, which primarily affects wild
rodents. It is spread from one rodent to
another by fleas. Humans bitten by an
infected flea usually develop a bubonic
form of plague, which is characterized by a
bubo, i.e. a swelling of the lymph node
draining the flea bite site. If the bacteria
reach the lungs, the patient develops
pneumonia (pneumonic plague), which is
then transmissible from person to person
through infected droplets spread by
coughing. Initial symptoms of bubonic
plague appear 7–10 days after infection. If
diagnosed early, bubonic plague can be
successfully treated with antibiotics.
Pneumonic plague, on the other hand, is
one of the most deadly infectious diseases;
patients can die 24 hours after infection.
The mortality rate depends on how soon
treatment is started, but is always very
high [WHO 2014b].
In Africa, plague cases generally occur in

seasonal pulses, and show a geographically
clearly discontinuous distribution in
circumscribed foci that are assumed to be
correlated with distributions of dominant
vectors and rodent reservoirs and their
ecology [Prentice & Rahalison 2007]. The
plague occurrence data set consists of 45
unique locations from central (Democratic
Republic of the Congo and Uganda),
eastern (Tanzania, Malawi, and
Mozambique), and southern Africa
(Botswana, Lesotho, Namibia, South Africa,
Zambia, and Zimbabwe [Neerinckx et al 2008] and WHO Weekly Epidemiological Records. The plague foci are
defined as areas where the bacteria is supposed to circulate in animal reservoirs and vectors and therefore are
areas with potential human plague occurrence. The Plague foci were extracted from the WHO/PED map of global
distribution of natural plague foci [WHO/PED Plague map – Personal Communication, Eric Gerard Georges
Bertherat] and was constructed from through literature review and WHO collaborating centres.
34
Figure 29: District map of reported plague cases in humans from 1970 to 2015. Some outbreaks have only being
reported at national and could not be linked to a district (see Annex B).
35
4.13 Meningitis
Figure 30: Meningitis ecological zone map showing countries in the meningitis belt, those with part of their areas
in the meningitis belt and countries outside the belt that have reported outbreaks or epidemics.
Neisseria meningitidis is found
worldwide, but the highest
incidence is in the “meningitis
belt” of sub-Saharan Africa
[WHO 2016c]. The meningitis
belt, 10° and 15° of latitude
North, was first defined by
Lapeyssonnie in 1963
[Lapeyssonnie 1963] and covers
26 countries from the west to
east of Africa.
Meningococcal disease is
hyperendemic in this region,
and periodic epidemics during
the dry season (December–
June) reach up to 1,000 cases
per 100,000 population.
Meningococcal outbreaks have
also been reported outside the
meningitis belt. Since 2004, the
enhanced surveillance network
has been operational [WHO
2016c]
Before the mass vaccination

campaigns that began in 2010,
the serogroup A accounted for
over 80% of cases in the
meningitis belt. Since 2010,
over 220 million persons
between 1-29 years of age have
received the meningococcal A
conjugate vaccine [WHO
2016c].
Three ecological zones have

been developed and these are
the meningitis belt, countries
with parts in the meningitis belt
and countries outside the belt
but have reported outbreaks.
36
Figure 31: District map of reported meningitis cases from 1970 to 2015. Some outbreaks have only being reported
at national and could not be linked to a district (see Annex B).
37
4.14 Anthrax
Figure 32: Anthrax ecological zones based on reported cases in humans and animals
Anthrax bacteria exist in the vegetative

form and as a spore, making the
bacteria more resistant to adverse
environmental conditions thus
ensuring its survival. Once the spore
enters a conducive environment
(inside a host), it germinates into a
vegetative form, multiplying and
rapidly colonizing the host. If untreated
this infection can be fatal. In a case the
host dies, the vegetative bacteria in
the presence of oxygen sporulates. The
spores are then shed from the dead
carcass ready for uptake by another
host.
Anthrax disease mostly affect

herbivores through transmission while
grazing on contaminated grounds.
Humans can get infected either
through direct or indirect contact with
infected animal, carcass or
contaminated animal products.
Infection in humans can occur in three
ways that is a) cutaneous infection,
which occurs when the bacteria enters
the body through a cut or abrasion on
the skin, b) pulmonary infection
occurring when one inhales the spores,
and c) gastrointestinal infection due
ingestion of contaminated substance.
All the three forms of infections are
fatal with gastrointestinal and
pulmonary infections having greater
fatality rates. Cutaneous anthrax is the
most common anthrax infection
covering 95% or more of human
reported cases [Turnbull 1998].
The World Health Organization Collaborating Center for Remote Sensing and Geographic Information Systems for
Public Health mapped the risk of anthrax infections by country using data on reported cases [WHO n.d.(b)]. These
was updated using recently assembled data.
38
Figure 33: District map of reported Anthrax cases from 1996 to 2016. Some outbreaks have only being reported at
national and could not be linked to a district (see Annex B).
39
4.15 Malaria
Figure 34: Map of malaria epidemicity developed from community P. falciparum parasite rate corrected to the age
range 2-10 years of age (PfPR2-10) in 2000 and 2010.
Malaria is transmitted to humans through
the bite of a female Anopheles mosquito
that is infected with the plasmodium
parasite. In Africa, the Plasmodium
falciparum is the main parasite although
other such as P. vivax, P. malariae and P.
ovale have been reported.
Malaria epidemics have been shown to

occur among nonimmune populations in
urban centres, highlands, arid and semi-
arid areas [Najera et al 1998; Abeku et al
2003] as a consequence of extreme
climatic anomalies, population
displacements, uncontrolled large scale
developments and/or failure of control
interventions [Najera et al 1998; RBM
2001]. The WHO defines a malaria
epidemic as a sudden increase in cases in
an epidemic beyond what is considered
normal [Najera et al 1998; Hook 2004].
There is an inverse relationship between

levels of malaria endemicity and the
likelihood of epidemics as modulated by
the acquisition of immunity [Najera et al
1998]. Populations living in areas of stable
transmission to malaria develop immunity
early in life due to the high frequency of
exposure to infections [Snow & Marsh
2002]. Therefore, in areas of stable
transmission, the disease is concentrated
among children under the age of five years
and clinical episodes become rarer with
age.
In areas of unstable transmission, normally defined as areas of hypoendemicity (≤10% parasite rate among
children aged 2-10 years), populations are likely to be wholly susceptible or of partial immunity that is likely to be
lost due to reduced exposure during a prolonged drought or under sustained control. It is among populations in
unstable transmission, where majority of the infected people are likely to become clinically ill, that epidemics
occur [Najera et al. 1998]. Using a map of malaria transmission intensity developed from community P. falciparum
parasite rate corrected to the age range 2-10 years of age (PfPR2-10) for the years 2000 and 2010 [Noor et al 2014]
within the stable limits of transmission [Snow et al 2012] at 1 x 1 km spatial resolution, the following malaria
epidemic classification was developed (Figure 34):
Malaria free area – This include areas which have declared malaria free such as the whole of Algeria and Western
Sahara, parts of Zimbabwe and highland areas where low temperatures do not allow for the development of
parasite [Snow et al 2012]; Naturally epidemic prone – These are areas where P. falciparum malaria transmission
40
was ≤10% (hypoendemic) and therefore at risk of epidemics naturally; Epidemic prone due to loss of immunity
after control – These are areas where current (2010) P. falciparum transmission is ≤10% but where transmission in
2000 was >10%. Due to control, immunity in the population would have waned and if control is interrupted, an
epidemic is likely to occur; Desert areas – where epidemics are rare but could occur near water sources; and stable
transmission – where there is widespread parasite circulation and older children and adults are likely to have
functional immunity and epidemics are unlikely.
District level data on epidemics of malaria (Figure 35) were assembled from unpublished reports and systematic
review of the published literature.
Figure 35: Map of malaria epidemics reported from 1970-2015. In Algeria and Mauritania, outbreaks were
reported in specific villages and their location is shown on the map. The epidemic data were assembled through a
systematic review of the published literature.
41
5. Correlates of outbreaks and epidemics
Several contextual and environmental factors were assembled for the period 1995 to 2015 when data
on epidemics and the correlates were sufficient for analysis. Data on several correlates were assembled
(see Annex C for more details) and were classified into various categories based on their distribution and
natural breaks in the data. Box plots of the various categories of the correlates and the total
outbreak/epidemics events reported in the WHO African region since 1995 were developed to provide a
simple statistical description of their relationships. These descriptions are limited to 10 correlates.
Further analysis of these and other correlates and sophisticated modeling of the statistical relationships
are beyond the scope of this report. However, the analysis serves as a basis to begin developing a
conceptual framework for future epidemic risk and vulnerability assessments.
5.1 Population
Population data was obtained from the United Nations, Department of Economic and Social Affairs,
Population Division [http://esa.un.org/unpd/wpp/DVD/]. The annual total population is estimated yearly
and is consistent with previous census results and with estimates of subsequent trends in fertility,
mortality and international migration. The estimates are then rounded to the nearest 1,000. For this
study, World Population Prospects 2015, total population estimate for both sexes was downloaded
[United Nations 2015]. Population estimates for African states from 1970 - 2015 were then extracted
from the dataset.
Figure 36 A box plot of population size and the number of outbreaks and epidemic events reported in the period
1995-2016 in the WHO African region. The analysis shows increasing number of events in more densely populated
countries
42
5.2 Urban Population
The percentage of population in each country living in areas defined as urban by national statistical
offices was computed using the World Bank population estimates and urban ratios from the United
Nation World Urbanization Prospects [World Bank 2015a]. This data was downloaded from the World
Bank Open Data (http://data.worldbank.org/indicator/SP.URB.TOTL.IN.ZS). Percentage urban population
growth for African states were then extracted from the dataset from 1970 to 2015.
Figure 37 A box plot of percentage population in urban areas and the number of outbreaks and epidemic events
reported in the period 1995-2016 in the WHO African region. The analysis suggest lower number of events with
increasing urbanization.
43
5.3 Gross Domestic Product (GDP) per capita
The GDP data was downloaded from the World Bank Open Data website
(http://data.worldbank.org/indicator/NY.GDP.MKTP.KD.ZG). GDP per capita is gross domestic product
divided by midyear population. GDP is the sum of gross value added by all resident producers in the
economy plus any product taxes and minus any subsidies not included in the value of the products. It is
calculated without making deductions for depreciation of fabricated assets or for depletion and
degradation of natural resources. Data for this study was obtained from the World Bank Open Data
website (http://data.worldbank.org/indicator/NY.GDP.PCAP.CD) on 27, September, 2015. Where there
were gaps in data, the estimated of the closest preceding or following for a country was used.
Figure 38 A box plot of GDP per capita and the number of outbreaks and epidemic events reported in the period
1995-2016 in the WHO African region. A threshold of 600 USD was used based on distribution of the data and to
allow for sufficient power between categories. The analysis shows a slight decrease in number of events with
increasing GDP per capita.
44
5.4 Percentage GDP expenditure on health
These estimates were developed by the World Bank and used here as a broad indicator of health system
strength. The indicator is computed from the total health expenditure as percentage of GDP for a given
year. Total health expenditure is computed as the sum of public and private health expenditure and
covers the provision of health services (preventive and curative), family planning activities, nutrition
activities, and emergency aid designated for health but does not include provision of water and
sanitation [http://data.worldbank.org/indicator/SH.XPD.TOTL.ZS].
Figure 39 A box plot of percentage GDP expenditure on health and the number of outbreaks and epidemic events
reported in the period 1995-2016 in the WHO African region. As percentage GDP expenditure increases above 5
USD, there a slight decrease in outbreak or epidemic events but the difference is very small. This may be because
across the WHO African region, investment in health remains very low and not sufficiently discriminative of
epidemic risk.
45
5.5 Human Development Index
The Human Development Index (HDI) is a composite index measuring average achievement in three
basic dimensions of human development - long and healthy life, knowledge and a decent standard of
living. The HDI is the geometric mean of normalized indices for each of the three dimensions. This data
was available from 1980 to 2013 in the UNDP - Human Development Reports website -
http://hdr.undp.org/en/content/table-2-human-development-index-trends-1980-2013 but not for all
countries and years. For missing year data, the HDI from preceding or following nearest years in a
country was used. South Sudan was dropped from analysis as no HDI data was available throughout the
period 1995-2015.
The HDI is subdivided into four categories;- Very High HDI (0.80-0.99), High HDI (0.70-0.79), Medium HDI
(0.55-0.69) & Low HDI (0.00-0.54) - based on the Human Development report of 2014. In the WHO
African region, only Algeria, Mauritius and Seychelles were classified as having high HDI in the period
from 2009. Only 9 other countries were categories as medium HDI. For this reason, and to provide
sufficient power category, a threshold 0.4 HDI was used.
Figure 40 A box plot of HDI and the number of outbreaks and epidemic events reported in the period 1995-2016 in
the WHO African region. The analysis shows fewer events in higher HDI countries. However, majority of countries
in the WHO African region have low HDI.
46
5.6 Under 5 Mortality Rate
Under five child mortality dataset (U5MR) is seen as a strong measure of disease burden and health
system strength. U5MR is also a strong proxy for impact of potential large scale epidemics. Data was
obtained from the Child Mortality Estimate database, computed and maintained by the United Nation
Inter-agency Group for Child Mortality Estimation
(http://www.childmortality.org/index.php?r=site/index). The data included the minimum, median and
maximum estimates for the U5MR per 1000 live births for all countries in the world from 1950 to 2013.
The median estimates were categorized and categories for 2013 were maintained for subsequent years
with missing data.
Figure 41 A box plot of under-five mortality rate and the number of outbreaks and epidemic events reported in the
period 1995-2016 in the WHO African region. The analysis shows higher number of events in periods where under
five mortality was ≥100 deaths per 1000 child birth. This suggests, as expected, a strong contribution of outbreak
and epidemic events to child mortality.
47
5.7 Global Hunger Index
Global Hunger Index is computed annually by the International Food Policy Research Institute (IFPRI). It is used to
measure and track hunger globally, and by region and country. Undernourishment, child underweight and child
mortality are the indicators used to calculate the index. A country's GHI score is calculated by averaging the
percentage of the population that is undernourished, the percentage of children younger than five years old who
are underweight, and the percentage of children dying before the age of five. This calculation results in a 100 point
scale on which zero is the best score (no hunger) and 100 the worst. The data was reported between 1988-07 and
2009-13 [https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/27557]. The GHIS
classification is: Low < 5.0, Moderate 5.0 – 9.9, Serious 10.0 – 19.9, Alarming 20.0 – 29.9 & Extremely alarming
29.9< for each year [von Grebmer 2014]. For this report, low and moderate were combined and similarly alarming
and very alarming.
Figure 42 A box plot of Global Hunger Index (GHI) and the number of outbreaks and epidemic events reported in
the period 1995-2016 in the WHO African region. The analysis shows higher number of events with increasing level
of hunger, with the alarming or very alarming levels of GHI associated with greater frequency of outbreak and
epidemic events.
48
5.8 Conflicts
Data was obtained from http://www.pcr.uu.se/research/ucdp/datasets/ucdp_prio_armed_conflict_dataset/, the

website of the Peace Research Institute, Oslo and Uppsala Conflict Data Program (UCDP/PRIO) which documents
armed conflicts. UCDP/PRIO collects conflict data from news articles and report the status of armed conflict on a
yearly basis from 1946 to 2014. For this report, countries were classified into period of conflict or not and not
necessarily the intensity or nature of conflict.
Figure 43 A box plot of conflicts and the number of outbreaks and epidemic events reported in the period 1995-
2016 in the WHO African region. The analysis shows higher number of disease outbreak or epidemic events during
conflicts.
49
5.9 El Nino occurrence
According to National Oceanic and Atmospheric Administration (NOAA), an El Nino is a warm weather anomaly of
the sea surface temperature (SST) in the Equatorial Pacific that might result in adverse weather patterns around
the globe (http://www.pmel.noaa.gov/tao/elnino/el-nino-story.html). To identify an El Nino, NOAA computes five
consecutive three month running mean of SST anomalies in the Equatorial Pacific (specifically the Nino 3.4 region
which is between latitudes 50 N and 50 S, and longitudes 120 W and 170 W). This anomaly is known as Oceanic
Nino Index (ONI). If the ONI exceed a specified threshold (in this case +0.50C) then an El Nino episode is
experienced (https://www.ncdc.noaa.gov/teleconnections/enso/indicators/sst.php). El Nino years were obtained
from the most recent computed values of ONI, as of 26th September, 2015, from NOAA
(http://www.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ensoyears.shtml).
Figure 44 A box plot of El Nino occurrence and the number of outbreaks and epidemic events reported in the
period 1995-2016 in the WHO African region. There is no clear association between the occurrence of El Nino and
frequency of epidemics, although there is marginally more epidemics reported during El Nino events. Analysis of
specific vector borne diseases that have been reported to increase during El Nino, such as malaria, may reveal
more interesting patterns.
50
5.10 Forest cover
Several zoonotic disease that have eventually caused human epidemics have been shown to be associated with
forest areas. The percentage forest cover data was downloaded from the Food and Agriculture Organization of the
United Nations (FAO) website (http://www.fao.org/forest-resources-assessment/explore-data/en/). The data is
generated from country forest reports and remote sensing1. The forest cover data show the percentage of land in
a country that has natural or planted tress covering at least 5 meters in situ and exclude trees in agricultural
production systems such as fruit plantation as well as trees in urban gardens.
Figure 45 A box plot of percentage forest cover and the number of outbreaks and epidemic events reported in the
period 1995-2016 in the WHO African region. There is no clear association between the percentage forest cover
and frequency of epidemics. Analysis of specific zoonotic diseases that are spread by animal hosts found in forests
may reveal more interesting patterns.
51
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Annex A: Districts maps of outbreaks and epidemics from 1970-2016
56
57
58
Annex B: Outbreaks and epidemics reported at national level only and not by district
Chikunguny Crimea Dengu Meningiti Marb Monke West Typhoi
Countries Cholera Malaria Measles Plague Polio RVF Yellow Fever
a n Congo e Fever s urg y Pox Nile d Fever
Algeria 2012
1980-2006 and
Angola 2015 1995 1988
2008
1976-2000, 1995, 1997,
Benin 2001 2003, 2004, 1998, 2003
2008 and 2009 and 2004
1988,
1980-1989 and
Botswana 1993 and 1997
1997
1997
1983, 1984,
1985, 1996,
1997,
1980- 2004, 1999, 2002,
Burkina Faso 1991, 1998 and 2013 2012 and
2008 and 2009 2006, 2007,
2013
2009, 2010
and 2011
1980-1996 and
Burundi 1978 and 2015 2003 1998 1995
1999
1980, 1984,
1980-2005 and 1994, 2003,
Cameroon 1971, 1985 and 2015
2009 2006, 2012
and 2014
1974, 1976, 1996 and
Cape Verde 1976-1988
1998
Central 2003, 2010,
1980-2008,
Africa 1996 2016 2011 and
2009 and 2011
Republic 2013
1983-2000,
Chad 1971 and 1991 2008 2003, 2006, 2013
2012 and 2013
1980, 1989,
1990, 1994,
Comoros 2006 1975 2006, 2009, 1980 and 1983
2011 and
2012
1980-1988, 2012 and
Congo 2013 2015
1999 and 2000 2013
1982, 1997,
1970, 1971, 1991,
1980-2009 and 1999, 2012,
Cote d’Ivoire 1993, 1994, 1996, 2012
2011 2013 and
and 2015
2014
DRC
1980-2000,
2004 2001 2005
2006-2012
59
2011 1994, 1995,
Eritrea and 1997, 1999,
2014 2000 and 2005
Ethiopia 1970, 1971 and 1985 2015 1981 2015 2009 1980-2010 2013 2009
1980- 1996 and 1994 and
Gabon
2011 2006
1980-1992, 2003 and
Gambia 1997
1997 and 2000 2012
1980, 1981,
1982, 1983,
1970-1984, 1990-1996, 2011 and 1980-2003 and
Ghana 1993, 1994,
2012 and 2015 2014 2008
1997 and
2006
1980- 1999, 1987, 2004,
2014 and
Guinea 2007 2004, 2009 and 2013 and
2015
2011 2014
Guinea 1971-1988,
1999
Bissau 1990 and 1997
1992, 1993,
Kenya 2006 1997 and 1999 2003 1980-1999 1994 and
1995
1973, 1980, 1981,
2002, 2003,
1995, 1998, 2001, 1980-1989,
2005, 2006,
Liberia 2004, 2006, 2007, 1993-1999,
2010, 2012
2008, 2009, 2010 and 2009 and 2010
and 2014
2011
Madagascar 2012 2014
Malawi 1997 and 2000
Mali 2011 2009
1971, 1986, 1987, 1980-2001,
Mauritania 2003
1989, 1996 and 1997 2009 and 2010
Mauritius 2005
2014
Mozambiqu 1980-2000 and
1980 and 2015 and 2015
e 2011
2015
2013
1989, 1993-
Namibia and
1999
2014
1971, 1973, 1974,
Niger 1984, 1996, 1997 and 2015 1995 1980-2011
2015
1980, 1983,
1984, 1985,
1988, 1989,
Nigeria 1987 2015 1980-2005 1990, 1992,
1993, 1994,
1997, 2001
and 2011
60
1991-1993, 2000, 1980-1993,
Rwanda 2004, 2007, 2009 and 1995, 1998 and 2015
2012 1999
1971, 1972, 1979, 1981, 2003,
1981,1984 - 1988, 2004, 2006,
Senegal 2009 2010 1980-1998
1995, 1997, 2002 and 2012 and
2012 2013
Seychelles 2005 2015
1995, 2000,
2005, 2006,
Sierra Leone 1994 and 2007 1980- 2010
2009 and
2013
1972,
1978,
1985,
1981, 1982, 1984, 1993,
South Africa 1980-1999 2011
1985, 1986 and 2005 1997,
1998,
1999 and
2001
South Sudan 2015 2015 2013 2013 2011
Swaziland 1992 1980-1989
Tanzania 1991 1980-1998
1984, 1987,
Togo 1980-2009 2008 and
2012
1971-1980, 1992, 2000
Uganda 1994, 1997, 2010 and 2015 2015 and 1980-1998 2003
2015 2008
1980-1999 and
Zambia 2015 2007 2001 2015
2002
1992,
1992, 1993, 2000 and
Zimbabwe 1996 and 1980-1999
2010
2004
61
Annex C: Summary of correlates used in the analysis of association with outbreaks and epidemics
Data Data Source Link Date of data
download
Population United Nations, Department of Economic and Social Affairs, Population Division http://esa.un.org/unpd/wpp/DVD/ 9/24/2015
Urban Population Growth World Bank http://data.worldbank.org/indicator/ 9/24/2015
SP.URB.TOTL.IN.ZS
GDP Growth World Bank http://data.worldbank.org/indicator/ 7/24/2015
NY.GDP.MKTP.KD.ZG
GDP Health Expenditure World Bank World Bank, 8/7/2015
http://data.worldbank.org/indicator/
SH.XPD.PCAP
Vaccine Coverage WHO http://www.who.int/immunization/m 8/7/2015
onitoring_surveillance/
Under 5 Mortality Rate United Nations Inter-agency Group for Child Mortality Estimation http://www.childmortality.org/index. 8/9/2015
php?r=site/index
Corruption Perception Index Transparency International http://www.transparency.org/researc 7/27/2015
h/cpi
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Mapping Who

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Mapping the Risk and Distribution of

Epidemics in the WHO African Region

1. Disease Outbreaks – statistics and numerical data

I. Work Health Organization. Regional Office for Africa II. Title

ISBN: 978-9290233084-4 (NLM Classification : WA 105)

WHO AFRO Technical Team

WHO Technical Consultants

Cover photo: Modified climatic ecological zones of Africa (source: http://www.fao.org/docrep/004/y1997e)

Several challenges were encountered in the process of implementing this exercise:

2.1 Specific objectives

3. Assembly of outbreak and epidemics data

3.1 Identification of sources and developing a unified database

3.2 Summary of epidemic data by country and PHEIC disease

Country Number of administrative polygons

Ebola hemorrhagic fever is a rare disease

Ebola was first discovered in 1976 not far

To define the ecological zones for Ebola

Lassa fever is a viral haemorrhagic

Since its initial discovery, cases of Lassa

Lassa fever ecological zones were

Crimean-Congo haemorrhagic fever

A combination of case reports,

Marburg virus disease (MVD)

In Africa, five countries have

Countries in the WHO African region

Rift Valley Fever (RVF) is viral zoonosis

Outbreaks have been reported in many

Countries were classified into three RVF

Dengue is a systemic viral infection

These data on reported cases and

The West Nile Virus (WNV) risk map was

Chikungunya fever has an

Ecological zones were based on

The yellow fever ecological zones

The second class is the low risk

Zika viral disease is transmitted through the

Zika virus disease has similar clinical

For many years, despite lack of systematic

Cholera is an acute, diarrheal illness caused

Cholera, has largely been eliminated from

Cholera outbreaks have been reported

Plague is a bacterial disease, caused by

In Africa, plague cases generally occur in

Before the mass vaccination

Three ecological zones have

Anthrax bacteria exist in the vegetative

Anthrax disease mostly affect

Malaria epidemics have been shown to

There is an inverse relationship between

Data was obtained from http://www.pcr.uu.se/research/ucdp/datasets/ucdp_prio_armed_conflict_dataset/, the

Percentage forest cover FAO FAO. "Global Forest Resources 3/6/2016

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