Transboundary and Emerging Diseases

RAPID COMMUNICATION

Identification and Epidemiology of a Rare HoBi-Like

Pestivirus Strain in Bangladesh
N. Haider1, M. S. Rahman1, S. U. Khan1,2, A. Mikolon3, E. S. Gurley1, M. G. Osmani4, I. S. Shanta1,
S. K. Paul1, L. Macfarlane-Berry1, A. Islam5, J. Desmond5, J. H. Epstein5, P. Daszak5, T. Azim1,
S. P. Luby1,6, N. Zeidner1,7 and M. Z. Rahman1
1
2
3
4
5
6
7

International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh

College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
United States Department of Agriculture (USDA), 11850 S. La Cienega, Hawthorne, CA, USA
Department of Livestock Services, Ministries of Fisheries and Livestock, Dhaka, Bangladesh
EcoHealth Alliance, New York, NY, USA
Stanford University, Stanford, CA, USA
U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA

Keywords:
HoBi-like pestivirus; BVDV-3; cattle;
Bangladesh
Correspondence:
M. Z. Rahman. Virology Laboratory, Centre
for Communicable Diseases, icddr,b, 68,
Shaheed Tajuddin Ahmed Sarani, Mohakhali,
Dhaka 1212, Bangladesh.
Tel.: +880-209827001-10;
Fax: +880-2-8812529;
E-mail: mzrahman@icddrb.org
Received for publication November 3, 2013
doi:10.1111/tbed.12218

Summary
The genus pestivirus of the family flaviviridae consists of four recognized species:
bovine viral diarrhoea virus 1 (BVDV-1), bovine viral diarrhoea virus 2 (BVDV2), classical swine fever virus and border disease virus. A new putative pestivirus
species tentatively named as either HoBi-like pestivirus or BVDV-3 has recently
been identified in Brazil, Italy and Thailand. Despite reports of serological evidence of BVDV in Bangladesh, the types of the virus circulating in cattle have not
been identified. We conducted surveillance in cattle from May 2009 to August
2010 in three government veterinary hospitals to characterize BVDV in cattle of
Bangladesh. We tested serum for BVDV using an antigen-capture ELISA. Of 638
cattle samples, 3% (16/638) tested positive for BVDV antigen. The ELISA-positive
samples were selected for further molecular detection and characterization of
BVDV. Molecular analysis of the partial 50 untranslated region (UTR) nucleotide
sequences of BVDV-positive samples identified the rare HoBi-like pestivirus or
BVDV-3 virus circulating in cattle of Bangladesh. The identification of this rare
HoBi-like pestivirus or BVDV-3 strain in Bangladesh warrants further surveillance to evaluate its impact on livestock production.

Introduction
The genus pestivirus of the family flaviviridae consists of
four recognized species: bovine viral diarrhoea virus 1
(BVDV-1), bovine viral diarrhoea virus 2 (BVDV-2), classical swine fever virus and border disease virus. A new
putative pestivirus species, tentatively named HoBi-like
pestivirus or BVDV-3, has recently been identified in
Brazil, Europe and Thailand (Stahl et al., 2007; Liu et al.,
2009a; Decaro et al., 2011; Bauermann et al., 2013).
Pestivirus infections in cattle, particularly BVDV-1 and
BVDV-2, are of major concern worldwide as they can lead
to significant economic losses for livestock production

mainly due to abortion, foetal mummification, still birth,

congenital defects and premature death in persistently
infected animals (Mishra et al., 2011; Bauermann et al.,
2013). Bangladesh has one of the highest densities of livestock in the world with 145 domestic ruminants per
square kilometre and an estimated 24 million cattle (Bangladesh Agricultural Research Council, 2010). These animals contribute to nutritional needs and food security of
about 155 million people (The World Bank, 2012) and
play an important role in the national economy of Bangladesh with a direct contribution of approximately 3% to
the agricultural gross domestic product and providing
15% of total employment (Government of the Peoples

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N. Haider et al.

Republic of Bangladesh: Ministry of Fisheries and Livestocks, 2007).

BVDV-1 was first identified in the 1940s and has a
worldwide distribution (Vilcek et al., 2001). Bovine viral
diarrhoea virus-2 was identified in the 1990s and was initially detected in North America but was recently identified
in Europe, Asia and South America (Mishra et al., 2011).
In 2004, an atypical bovine pestivirus was detected in
bovine samples collected from Brazil. This virus was named
as D32/00_HoBi (Stahl et al., 2007; Decaro et al., 2011;
Bauermann et al., 2013). Subsequently, a similar virus was
identified in Thailand and in Italy (Stahl et al., 2007;
Decaro et al., 2011). Phylogenetic analysis of this HoBi-like
virus revealed a strong affinity to BVDV-1 and BVDV-2.
This virus has been proposed as a new pestivirus species,
BVDV-3 (Liu et al., 2009a; Decaro et al., 2011; Bauermann
et al., 2013).
BVDV primarily infects ruminants, and genotypes of this
virus vary in antigenicity, cytopathology and virulence
(Baker, 1987; Ridpath et al., 2000). Bovine viral diarrhoea
virus infection is rarely fatal except in persistently infected
cattle where death before the age of two is common (Kahn,
2005). Clinically, BVDV infection is characterized by fever,
diarrhoea, respiratory distress, mucosal lesions and leucopenia (Baker, 1995; Mishra et al., 2011).
The first evidence of BVDV infection in the Indian
subcontinent was reported in 1982 in Orissa (Nayak
et al., 1982). Phylogenetic analysis conducted on serum
samples collected in 2000 and 2002 showed that all the
cattle BVDV isolates originating from India belonged to
BVDV-1. In 2011, BVDV-2 was also isolated from
Indian cattle (Behera et al., 2011). The first evidence of
BVD infection in cattle of Bangladesh was reported by
Samad (1999) by testing cattle sera collected from two
cattle farms and one veterinary hospital (Samad, 1999).
Of the 79 cattle sera tested, 22 (28%) were positive for
BVDV antibody by ELISA (Samad, 1999). However, the
type of BVDV circulating in Bangladesh was not confirmed, and HoBi-like pestivirus or BVDV-3 had not yet
been reported in Bangladesh and its neighbour countries.
The prominent antigenic differences between BVDV-1
and BVDV-2 isolates are important for diagnosis and
control, as prior exposure with BVDV-1, either through
infection or through vaccination, does not protect
against infection with BVDV-2 and vice versa (Mishra
et al., 2011). We do not know whether prior exposures
to or vaccination against BVDV-1 or BVDV -2 could
protect against HoBi-like pestivirus or BVDV-3. Antigenic differences have been found between HoBi-like
pestivirus or BVDV-3 as well as BVDV-1 and BVDV-2
(Stahl et al., 2007), which suggest that vaccines currently
available in the market may not protect animals against
HoBi-like pestivirus or BVDV-3.
194

We designed a pathogen discovery study among ruminant livestock in Bangladesh, a country identified as a hotspot for disease emergence (Jones et al., 2008) due to high
human and animal population densities and close contact
between humans and animals (The World Bank, 2012). In
this study, we included BVDV testing due to its prior serological reports in Bangladesh (Samad, 1999) and high prevalence in neighbouring India (Mishra et al., 2011). Thus,
we took the opportunity to characterize BVDV in cattle of
Bangladesh.
Materials and Methods
Blood samples were collected from cattle admitted in three
government veterinary hospitals located in Netrokona, Dinajpur and Chittagong districts between May 2009 and
August 2010. Veterinary hospitals were selected based on
their proximity to Indian borders, where many ruminants
are traded, and regional data from the Department of Livestock Services showed >20 sick animals attended to daily.
Veterinarians enrolled cattle with one or more of the following clinical signs: diarrhoea, respiratory distress and/or
fever. Veterinarians interviewed the animals owners to
record age, breed, and date of onset of illness, clinical signs
and nutritional status of ruminants. Dates of onset of illness were later classified as winter (November to February),
summer (March to June) and rainy season (July to October) (Bangladesh University of Engineering & Technology,
2008). Two weeks after sampling, a trained field research
assistant visited the animal owners house to record disease
outcomes. The protocol was approved by the International
Centre for Diarrheal Diseases Research Bangladeshs (icddr,
bs) research review committee, ethical review committee
and animal experimentation ethics committee.
We screened sera from all enrolled cattle for BVDV with
an enzyme-linked immunosorbent assay (ELISA) kit for
detection of BVDV antigen (HerdCheck BVDV Ag/Serum
Plus, IDEXX Laboratories, The Netherlands) as per the
manufacturers instructions. The ELISA-positive samples
were then selected for further molecular detection and
characterization.
We extracted viral RNA from 100 ll of serum using the
QIAamp viral RNeasy Mini Kit (QIAGEN, Leusden, Netherlands) according to the manufacturers instructions. For
detection and characterization of BVDV genotypes, a highly
conserved and characteristic region of the BVDV genome, a
290-bp-long 50 - untranslated region (50 UTR) was amplified
using the primer set DL1/DL2 followed by direct amplicon
sequencing (Kim and Dubovi, 2003). The 50 UTR PCRpositive samples were further subjected to genotype-specific
PCR according to the published protocol (Liu et al.,
2009b). The resultant gene sequence was compared with
the sequences deposited in the GenBank database (http://

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HoBi-Like Pestivirus or BVDV-3 in Bangladesh

www.ncbi.nlm.nih.gov/GenBank) using the Basic Local

Alignment Search Tool (BLAST). The sequences were further subjected to alignment using ClustalW, and a phylogenetic tree was constructed using the MEGA 5.05 software
package. Evolutionary distances in the phylogenetic tree
were computed using Kimura-2 parameter model constructed by the maximum likelihood method (Kimura,
1980; Tamura et al., 2011). The mismatched flanking positions were eliminated to get uniform nucleotide sequences
in multiple sequence alignment for phylogenetic tree construction. There were a total of 221 positions in the final
data set.
Results and Discussion
Of the 638 cattle enrolled in this study, 84% (533/638) had
fever, 44% (283/638) had respiratory distress, and 38%
(241/638) had diarrhoea. Overall, 3% of cattle (16/638)
tested positive for BVDV antigen (Table 1). The only other
study that demonstrated BVDV in Bangladesh reported
28% of cattle had antibodies to BVDV (Samad, 1999).
Although these studies cannot be directly compared, our
findings indicate active infection, as the ELISA detects
structural protein secreted from infected cells during virus
replication and chronic exposure to BVDV in cattle of
Bangladesh.
The most common clinical sign in antigen-positive animals that demonstrated fever, diarrhoea or respiratory distress was erosion in the mouth. Other noted clinical signs
included nasal discharge and excessive salivation (Table 2).
It was possible to follow up with 93% (594/638) of cattle to
measure disease outcomes. Among the 16 cattle that tested
positive for BVDV, all were followed up, and three had died
within 14 days (Table 2).

Table 1. Characteristics of BVDV ELISA-positive cattle enrolled from

three veterinary hospitals in Bangladesh between May 2009 and August
2010

Characteristics
Species
Districts

Breed
Age
Seasons of
onset of
illness

Cattle
Netrokona
Chittagong
Dinajpur
Total
Local
Cross
> 2 years
2 years
Winter (NovemberFebruary)
Monsoon (JulyOctober)
Summer (MarchJune)

Total
animals N

Positive
(%) n

638
340
40
258
638
541
97
323
315
141
265
232

16 (3)
10 (3)
3 (8)
3 (1)
16 (3)
11 (2)
5 (5)
2 (1)
14 (4)
3(2)
5 (2)
8 (3)

Table 2. Clinical signs and outcomes of ELISA-positive BVDV animals

enrolled from three veterinary hospitals in Bangladesh between May
2009 and August 2010

Clinical signs

Outcome of
cattle 14 days
post-sampling

Variables

N = 16 Positive (%)

Fever
Respiratory distress
Diarrhoea
Erosion in mouth
Nasal discharge
Salivation
Median rectal
temperature (range)
Recovered
Died*
Still sick
Sold
Slaughtered
Total

12 (75)
4 (25)
7 (43)
4 (25)
2 (13)
1 (6)
103 (100106)
9 (56)
3 (19)
4 (25)
0 (0)
0 (0)
16

*Case fatality rate.

Mutually exclusive.

Of the 16 BVDV ELISA-positive sera, 14 samples underwent further characterization through 50 UTR PCR followed
by direct sequencing; two animals were not able to be tested
as no sera was left after ELISA screening. We were able to
retrieve five 50 UTR sequences from the 14 samples using
universal 50 UTR PCR. Bovine viral diarrhoea virus antigen-positive samples were not typeable when tested for different genotypes of BVDV- 1, 2 and 3, using primers based
on characteristic 50 UTR sequences for detection and identification of the three known genotypes of BVDV. In the
remaining samples, either high background or no specific
PCR product or sequence was found.
Chromatographic analyses of the five PCR-positive
sequence data revealed that only three were of the desired
nucleotide length for further phylogenetic analyses, and
two were excluded due to shorter length sequence. The
BLAST analysis of these partial 50 UTR nucleotide
sequences
(accession
no:
KF204448,
KF204449,
KF204450) revealed that BVDV virus strains collected
from Bangladesh clustered with recently reported HoBilike pestivirus or BVDV-3 strains in the phylogenetic tree
(Fig. 1). However, they shared only 923% nucleotide
similarity with concomitantly identified HoBi-like pestivirus or BVDV-3 strains in Thailand (DQ897641), South
America (FJ232692), Australia (JN967707), Italy
(JN703311), Mexico (JN967747), China (JX469119) and
Brazil (JN967729). The BVDV strains found in this study
shared more than 90% homology with each other, and
one of the three strains identified in this study (BDVD
3/BD/ZS-5) demonstrated a relatively tight affiliation
with the previously reported BVDV-3 strain found in
Thailand (DQ897641). This strongly suggests an occurrence of a rare HoBi-like pestivirus or BVDV-3 strain in

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Fig. 1. Phylogenetic analysis of the isolates BDVD-3/BD/ZS-1, BDVD 3/BD/ZS-3, and BDVD 3/BD/ZS-5 compared with reference strains using 50 UTR
sequences. The GenBank accession numbers for reference strains are AY278459, FJ387319, AF526381 and JN248741 for BVDV-1, GQ985457,
AF502399 and HQ444199 for BVDV-2, and FJ040215, JX469119, FJ232692, JN967729, JN703311, AB871953, JN967747 and JN967707 for BVDV3 and NC_003679, NC_003678, NC_002657 for three other strains.

Bangladesh. Moreover, we identified a number of insertions that varied from one to five nucleotides long
(Fig. 2) in the 50 UTR of these rare HoBi-like pestivirus
or BVDV-3 strains. The multiple sequence alignment of
the 50 UTR sequences of the previously reported HoBi-like
pestivirus or BVDV-3 strains had a unique three to five
nucleotide insertion when compared to BVDV-1 and
BVDV-2 strains (Fig. 2, nucleotide position 114117). In
contrast, the identified rare HoBi-like pestivirus or
BVDV-3 Bangladesh strains had a new five-nt long
sequence variable inserted at the same nucleotide position
when compared to a reference strain (nucleotide position
227231, bovine viral diarrhoea virus 3 strain JS12/01,
complete genome, accession no. JX469119). In addition,
there was a nucleotide insertion in the HoBi-like pestivirus or BVDV-3 Bangladesh strains when compared to
other HoBi-like pestivirus or BVDV-3 strains (Fig. 2,
nucleotide position 34).This nucleotide insertion was also
reported for BVDV-2 and BVDV-1 strains (Fig. 2).
Indeed, the multiple sequence analysis in the present
study revealed genetic diversity among emerging HoBilike pestivirus or BVDV-3 strains in Bangladesh.
Although an earlier study in Bangladesh indicated serological evidence of BVDV in cattle of Bangladesh, conclusive evidence of BVDV with antigen detection was not
accomplished before this study (Samad, 1999). This study
provides evidence that a rare HoBi-like pestivirus or
BVDV-3 is circulating in cattle in Bangladesh. The origin
of emergence of HoBi-like pestivirus or BVDV-3 is
unknown. It was hypothesized that this virus originated in
South America and was introduced in Europe (Italy) and
196

South-East Asia (Thailand) through biological products

like foetal bovine serum (FBS), vaccines and semen, or
perhaps an independent evolution of pestiviruses (Bauermann et al., 2013). It is also possible that this strain was
circulating in cattle of Bangladesh but was not recognized
earlier. Alternatively, the virus may have been introduced
from countries where HoBi-like pestivirus or BVDV-3 is
circulating via infected animals, contaminated semen or
other biological products. We consider the latter explanation more plausible as Bangladesh customs regulations
allow the import of different biologically active products
including deep-frozen semen without any prior pathogen
screening, leading to the plausible introduction of such
new viruses in the country. The virus strains we are
reporting in this study (BD/ZS1; BD/ZS3; BD/ZS5) share
the most similarity with the virus isolated from Thailand
(Th/04_KhonKaen), a trading partner of Bangladesh
(Ministry of Commerce: Government of the Peoples
Republic of Bangladeshs, 2012). Live cattle trading
between Thailand and Bangladesh is not uncommon, and
Bangladesh imported live cattle from Thailand between
2007 and 2010 (FAO, 2013). Furthermore, numerous cattle are imported into Bangladesh from bordering Myanmar, which also shares a border with Thailand. It is
possible that this virus has been circulating a long time in
this part of the world without being detected.
This study has a limitation. Due to the lack of a biosecure cell culture facility, we undertook direct sequence
analysis of 50 UTR instead of virus culturing with only five
sequences retrieved from 14 ELISA-positive samples. The
50 UTR region is highly conserved among pestiviruses, and

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Fig. 2. Multiple sequence alignment of the HoBi-like pestivirus or BVDV-3 strains isolated from Bangladesh, 15 other BVDV reference strains of different genotypes and three other related strains. The rectangles indicate the significant nucleotide indels among the strains.

comparisons of the 50 UTR region are widely accepted for

phylogentic analysis (Harasawa and Giangaspero, 1998).
Better BVDV recovery is possible with recommended cell
culture facilities, and further analyses of viral sequences or
potentially whole genome sequence analysis can be carried
out with the cell culture supernatant for BVDV, but would
have not changed the final 50 UTR sequence results.
Conclusion
In this study, we confirmed the presence of BVDV in cattle
of Bangladesh. Molecular characterization of this virus
indicated a HoBi-like pestivirus or BVDV-3 in circulation
similar, but genetically distinct, to viruses identified in
other countries. In addition to Europe, South America and
South-East Asia, the circulation of BVDV in cattle of Bangladesh provides insight into the geographical distribution
of this virus. Further genetic characterization will more
fully elucidate whether these are indeed novel pestiviruses,
rare HoBi-like pestivirus or BVDV-3. Further surveillance
and monitoring is required to determine the impact of
BVDV circulating in Bangladesh.

Acknowledgement
This research was funded by Google and the Rockefeller
foundation through EcoHealth Alliance. icddr,b acknowledges with gratitude the commitment of Google and the
Rockefeller foundation to its research efforts . We acknowledge the Department of Livestock Services (DLS) of Bangladesh and the veterinarians Dr. Asma-Al-Hoseneara and
Dr. Rashidul Hoque and Dr. Shama Ranjan Barua from
DLS, Dr. Abdul Mannan and Dr. Shahneaz Ali Khan, from
Chittagong Veterinary and Animal Sciences University, and
Tahmina Sultana from icddr,b who were involved with this
project. We are grateful to Ms. Diana DiazGranados, icddr,
b, for her constructive support in editing this manuscript.
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