Background Influenza A virus subtypes in non-human hosts have not been characterized in Kenya. We carried out influenza surveillance in selected domestic animals and compared the virus isolates with isolates obtained in humans during the same period. Methods We collected nasal swabs from pigs, dogs and cats; oropharyngeal and cloacal swabs from poultry; and blood samples from all animals between 2010 and 2012. A standardized questionnaire was administered to farmers and traders. Swabs were tested for influenza A by rtRT-PCR, virus isolation and subtyping was done on all positive swabs. All sera were screened for influenza A antibodies by ELISA, and positives were evaluated by hemagglutination inhibition (HI). Full genome sequencing was done on four selected pig virus isolates. Results Among 3,798 sera tested by ELISA, influenza A seroprevalence was highest in pigs (15.9%; 172/1084), 1.2% (3/258) in ducks, 1.4% (1/72) in cats 0.6% (3/467) in dogs, 0.1% (2/1894) in chicken and 0% in geese and turkeys. HI testing of ELISA-positive pig sera showed that 71.5% had positive titers to A/California/04/2009(H1N1). Among 6,289 swabs tested by rRT-PCR, influenza A prevalence was highest in ducks [1.2%; 5/423] and 0% in cats and turkeys. Eight virus isolates were obtained from pig nasal swabs collected in 2011 and were determined to be A(H1N1)pdm09 on subtyping. On phylogenetic analysis, four hemagglutinin segments from pig isolates clustered together and were closely associated with human influenza viruses that circulated in Kenya in 2011. Conclusion Influenza A(H1N1)pdm09 isolated in pigs was genetically similar to contemporary human pandemic influenza virus isolates. This suggest that the virus was likely transmitted from humans to pigs, became established and circulated in Kenyan pig populations during the study period. Minimal influenza A prevalence was observed in the other animals studied.
Bibliographical noteFunding Information:
This work was funded with funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services, contract no. HHSN266200700007C to CJC and Core Funding of the Global Disease Detection Division of CDC to PM. There was no additional external funding received for this study. This work was funded with funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services, Contract No. HHSN266200700007C and Core Funding of the Global Disease Detection Division of CDC. We thank the staff at the Kenya Medical Institute, Center for Global Health Research laboratories and One health program who tested and collected the specimens, respectively. We thank Scott Kraus Laboratory at the St. Jude Children’s Research Hospital, TN, USA that provided the reference antigens used in the HI assay. All the genome sequencing work was performed by Todd Davis and his team at the Virology, Surveillance and Diagnosis Branch, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention Atlanta Georgia, USA. We appreciate the collaboration and participation of the Kenya Ministry of Agriculture, Livestock and Fisheries and the animal owners who gave consent for their animals to be used in this study.