dc.description.abstract | Influenza A virus has been described in multiple mammalian including humans, and in most
domestic and wild avian species. Complex interspecies transmission of influenza A virus
subtypes have been reported between and within avian and mammalian hosts. While there is
evidence of influenza A virus circulation in avian hosts in Kenya, influenza A subtypes
circulating in non-human mammalian hosts has not been described.
The current study was carried out in Kibera in Nairobi County, Asembo in Siaya County and
Ndumbu-ini slaughterhouse in Kiambu County between August 2011 and December 2012
through a series of cross-sectional studies based at the household and slaughterhouse level.
Kibera and Asembo were selected because they provided an ideal ecosystem with human and
animal interaction and livestock diversity. In addition the sites provided logistical advantage of an
existing database of households that were available for random selection of households.
Ndumbu-ini slaughterhouse was selected based on the catchment area for small-holder pig farms.
The objectives of the study were to 1) determine and characterize influenza viruses circulating in
pigs, dogs, cats, chicken, turkeys, ducks and geese in the study sites and, 2) characterize the
genome of the influenza virus isolates obtained from the study sites. Nasal swabs were collected
from pigs, dogs and cats, oropharyngeal swabs from chicken, ducks, geese and turkeys and blood
samples from all the species. All specimens were tested for presence of virus and anti-influenza A
antibodies and virus isolation and subtyping carried out on all positive specimens.
A total of 8246 specimens comprising of 5110 (62.0%) swabs and 3134(38.0%) sera were tested.
Of these, 3837 (46.5%), 2702 (32.8%) and 1705 (20.7%) were from Asembo, Kibera and
Ndumbu-ini, respectively. A total of 143 sera (4.6%) were positive for anti-influenza A
antibodies. Influenza A sero-prevalence was highest in pigs 17.1% (n=136) followed by cats
1.5% (n=1), dogs 0.8% (n=3), ducks 0.6% (n=1) and chicken at 0.1% (n=2) while all sera from
geese and turkeys were negative. In addition, while 14/986 (1.4%) from Kibera were seropositive
none of the 1389 from Asembo were sero-positive. For the slaughterhouse specimens,
influenza A sero-prevalence was significantly (p<0.05) higher for the sampling periods in 2011
compared to the sampling periods in 2012. On serology subtyping by hemagglutination
inhibition, close to half (48.5%; n=67), of the influenza A sero-positive sera by ELISA were
positive for the A/California/04/2009(H1N1) pdm09.
A total of 19 of 5110 (0.4%) specimens were positive for influenza A M-gene by reverse
transcriptase real time polymerase chain reaction (rt RT-PCR). Influenza A virus prevalence was
0.8% in pigs and dogs, 0.3% in ducks and 0.2% in chicken while none of the specimens from
cats, turkeys and ducks were positive. Eight virus isolates were obtained from swabs collected in
pigs and subtyped as A(H1N1) pdm09. Full genome sequencing was conducted for four of the
isolates and sequences deposited in Gene bank (Accession numbers KJ680515 to KJ680545). On
phylogenetic analysis, the hemagglutinin segments of the swine isolates clustered together and
closely to human influenza isolates that circulated contemporaneous in Kenya.
This is the first report of circulation of influenza virus strain A (H1N1) pdm09 in pigs in Kenya
between 2011 and 2012. Molecular analysis of the swine influenza virus isolates suggested that
the pandemic virus strain was introduced into the pig population from humans an observation that
has been reported in multiple countries globally. Influenza A was also detected in respiratory swabs in a limited number of dogs, chicken and one duck in Kibera and Asembo. The identity of
other circulating influenza virus strains among pigs, dogs, chicken and ducks was not elucidated.
Continuous monitoring of influenza virus circulation in domestic animals and monitoring of
emergence of new strains of human, swine, and avian influenza viruses is key in providing data to
assist future emergence of novel virus strains with pandemic potential. | en_US |
dc.description.department | a
Department of Psychiatry, University of Nairobi, ; bDepartment of Mental Health, School of Medicine,
Moi University, Eldoret, Kenya | |