Characterization of Avian Influenza Viruses Detected in Kenyan Live Bird Markets and Wild Bird Habitats Reveal Genetically Diverse Subtypes and High Proportion of A(H9N2), 2018–2020
Peninah Munyua,
Eric Osoro,
Joyce Jones,
George Njogu,
Genyan Yang,
Elizabeth Hunsperger,
Christine M. Szablewski,
Ruth Njoroge,
Doris Marwanga,
Harry Oyas,
Ben Andagalu,
Romona Ndanyi,
Nancy Otieno,
Vincent Obanda,
Carolyne Nasimiyu,
Obadiah Njagi,
Juliana DaSilva,
Yunho Jang,
John Barnes,
Gideon O. Emukule,
Clayton O. Onyango,
C. Todd Davis
Affiliations
Peninah Munyua
Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya
Eric Osoro
Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya
Joyce Jones
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
George Njogu
Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya
Genyan Yang
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
Elizabeth Hunsperger
Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya
Christine M. Szablewski
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
Ruth Njoroge
Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya
Doris Marwanga
Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya
Harry Oyas
Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya
Ben Andagalu
Influenza Division, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya
Romona Ndanyi
Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya
Nancy Otieno
Centre for Global Health Research, Kenya Medical Research Institute, Kisumu P.O. Box 1578-40100, Kenya
Vincent Obanda
Department of Veterinary Services, Kenya Wildlife Services, Nairobi P.O. Box 40241-00100, Kenya
Carolyne Nasimiyu
Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya
Obadiah Njagi
Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya
Juliana DaSilva
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
Yunho Jang
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
John Barnes
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
Gideon O. Emukule
Influenza Division, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya
Clayton O. Onyango
Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya
C. Todd Davis
National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA
Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and poultry workers in live bird markets and among wild migratory birds in various lakes that are resting sites during migration to assess introduction and circulation of avian influenza viruses in these populations. We tested 7464 specimens (oropharyngeal (OP) and cloacal specimens) from poultry and 6531 fresh fecal specimens from wild birds for influenza A viruses by real-time RT-PCR. Influenza was detected in 3.9% (n = 292) of specimens collected from poultry and 0.2% (n = 10) of fecal specimens from wild birds. On hemagglutinin subtyping, most of the influenza A positives from poultry (274/292, 93.8%) were H9. Of 34 H9 specimens randomly selected for further subtyping, all were H9N2. On phylogenetic analysis, these viruses were genetically similar to other H9 viruses detected in East Africa. Only two of the ten influenza A-positive specimens from the wild bird fecal specimens were successfully subtyped; sequencing analysis of one specimen collected in 2018 was identified as a low-pathogenicity avian influenza H5N2 virus of the Eurasian lineage, and the second specimen, collected in 2020, was subtyped as H11. A total of 18 OP and nasal specimens from poultry workers with acute respiratory illness (12%) were collected; none were positive for influenza A virus. We observed significant circulation of H9N2 influenza viruses in poultry in live bird markets in Kenya. During the same period, low-pathogenic H5N2 virus was detected in a fecal specimen collected in a site hosting a variety of migratory and resident birds. Although HPAI H5N8 was not detected in this survey, these results highlight the potential for the introduction and establishment of highly pathogenic avian influenza viruses in poultry populations and the associated risk of spillover to human populations.
