Identification and characterization of influenza a viruses among domestic animals in selected sites in Kenya

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.