|dc.description.abstract||This thesis examines the epidemiology of avian influenza viruses (AIVs) in domestic
poultry in Pakistan. Major aim of the current research was: to identify risk factors
associated with the spread of these viruses; to quantify their prevalence in live bird
retail stalls (LBRSs) and backyard poultry in Lahore district and to genetically
characterize AIVs circulating in these stalls. Four independent studies were
conducted which included (i) a retrospective matched case-control study in
commercial poultry farms in Pakistan to identify the risk factors (ii) an estimation of
the seroprevalence of AI from a cross-sectional study of backyard poultry flocks in
Lahore district (iii) a cross-sectional study of LBRSs to estimate virus prevalence
and identify associated risk factors and (iv) the genetic characterization of isolates
collected from LBRSs.
The retrospective matched case-control study identified five risk factors for AI
infection. Multivariate conditional logistic regression model showed that distance of
less than 0.5 kilometer of a commercial farm from the nearest case farm (OR= 145.4;
95% CI: 13.6-1553.5), followed by “previous history of infection of flock with
infectious bursal disease (OR= 3.77; 95% CI: 1.18-11.97)”, selling of birds/eggs
directly to live bird retail stalls from the farm premises (OR= 9.5; 95% CI: 1.7-51.9)
have significant influence on spread of AI infection amongst the commercial farms.
Other significant potential risk factors are “age of flock at the time of testing (OR=
1.0; 95% CI: 1.00-1.02)” and “a truck entering the farm areas (OR= 30.74; 95% CI:
1.56-604.78)”. Complete fencing of the farm was observed to be a protective factor
(OR= 0.12; 95% CI: 0.02-0.63).
The cross-sectional survey of backyard poultry flocks for AI (H9, H7 and H5)
showed a seroprevalence of 67% (95% CI: 56.9-77.1) for H9 and 21% (95% CI:
13.8-28.1) for H5. Co-infection with both H9 and H5 was observed in 17 villages.
Seroprevalence for H9 was significantly associated with the breed of bird. No
samples were positive for H7.
The cross-sectional survey of LBRSs in 07 towns of Lahore district showed the
prevalence of H9N2 virus to be estimated at 10% (95% CI: 6.4-13.6). Subtypes
H5N1 and H7N3 were not detected in any sample. Three risk factors showed a
strong association with prevalence of H9N2 which are “adding new birds to the
cages that already contained birds (OR= 9.2; 95% CI: 2.4-35.1)”, “purchasing birds
for sale on the stall from mixed sources (other live poultry markets, auction markets,
farm/individual producers) (OR= 3.4; CI 95%: 1.3-8.8)”, and “keeping birds partially
inside and outside on the stalls during the day (OR= 1.7; CI 95%: 1.0-3.0)”.
Phylogenetic analysis of ten H9N2 viruses isolated from LBRSs of Lahore district
showed that four genes (HA, NA, M and NP) of all viruses belonged to G1-lineage
and clustered with A/Quail/Hong Kong/G1/97 reference virus while the other four
genes (PB2, PB1, NP and NS) from two of the viruses analysed clustered with a
group of viruses from Indian subcontinent, Persian Gulf and Middle East. One
recently reported H7N3 isolate from Pakistan also clustered with these genes. All
H9N2 viruses examined harboured the mutation known to alter the receptor binding
profile to one that preferentially binds to human receptors. The analysis shown in this
study confirmed that further gene assortment has occurred since its emergence in
poultry in Pakistan and Middle East, which could evolve into new genotype.
Understanding the epidemiology of avian influenza has always been considered
important in formulating and implementing control policies. Results from the current
studies illuminate various aspects of epidemiological features of avian influenza
viruses within poultry marketing systems in Asia. The current thesis has identified
different risk factors and has also reported the prevalence estimates in backyard birds
and LBRSs. The presence of reassortants of H9N2 with public health importance in
LBRSs has also been reported in the current thesis. These results could be considered
to plan future research and appropriate control and prevention strategiess for AIV by
the global community. Continued surveillance and monitoring is essential to identify
the viral gene pool circulating in live bird retail stalls and backyard poultry and to
better understand the public-health risk posed by these viruses.||en