{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:02:23Z","timestamp":1774396943680,"version":"3.50.1"},"reference-count":32,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T00:00:00Z","timestamp":1725494400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"U.S. Centers for Disease Control and Prevention","award":["CDC 1U01GH002143"],"award-info":[{"award-number":["CDC 1U01GH002143"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/v16091417","type":"journal-article","created":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T02:34:06Z","timestamp":1725503646000},"page":"1417","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["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\u20132020"],"prefix":"10.3390","volume":"16","author":[{"given":"Peninah","family":"Munyua","sequence":"first","affiliation":[{"name":"Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Osoro","sequence":"additional","affiliation":[{"name":"Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joyce","family":"Jones","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Njogu","sequence":"additional","affiliation":[{"name":"Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Genyan","family":"Yang","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth","family":"Hunsperger","sequence":"additional","affiliation":[{"name":"Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine M.","family":"Szablewski","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruth","family":"Njoroge","sequence":"additional","affiliation":[{"name":"Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9716-6052","authenticated-orcid":false,"given":"Doris","family":"Marwanga","sequence":"additional","affiliation":[{"name":"Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harry","family":"Oyas","sequence":"additional","affiliation":[{"name":"Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8678-7478","authenticated-orcid":false,"given":"Ben","family":"Andagalu","sequence":"additional","affiliation":[{"name":"Influenza Division, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Romona","family":"Ndanyi","sequence":"additional","affiliation":[{"name":"Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7083-4735","authenticated-orcid":false,"given":"Nancy","family":"Otieno","sequence":"additional","affiliation":[{"name":"Centre for Global Health Research, Kenya Medical Research Institute, Kisumu P.O. Box 1578-40100, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2587-5359","authenticated-orcid":false,"given":"Vincent","family":"Obanda","sequence":"additional","affiliation":[{"name":"Department of Veterinary Services, Kenya Wildlife Services, Nairobi P.O. Box 40241-00100, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7559-3109","authenticated-orcid":false,"given":"Carolyne","family":"Nasimiyu","sequence":"additional","affiliation":[{"name":"Paul G. Allen School for Global Health-Kenya, Washington State University, Nairobi P.O. Box 72938-00200, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Obadiah","family":"Njagi","sequence":"additional","affiliation":[{"name":"Directorate of Veterinary Services, Ministry of Agriculture and Livestock Development, P.O. Box 29114, Kangemi, Nairobi 00625, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliana","family":"DaSilva","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunho","family":"Jang","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Barnes","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gideon O.","family":"Emukule","sequence":"additional","affiliation":[{"name":"Influenza Division, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clayton O.","family":"Onyango","sequence":"additional","affiliation":[{"name":"Division of Global Health Protection, US Centers for Disease Control and Prevention, Village Market, Nairobi P.O. Box 606-00621, Kenya"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C. Todd","family":"Davis","sequence":"additional","affiliation":[{"name":"National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, 1600 Clifton Road, NE Atlanta, GA 30333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/mr.56.1.152-179.1992","article-title":"Evolution and ecology of influenza A viruses","volume":"56","author":"Webster","year":"1992","journal-title":"Microbiol. Rev."},{"key":"ref_2","unstructured":"Swayne, D.E. (2016). Multicontinental panzootic of H5 highly pathogenic avian influenza (1996\u20132015). Avian Influenza, Wiley Blackwell."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"269","DOI":"10.4142\/jvs.2017.18.S1.269","article-title":"Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4","volume":"18","author":"Lee","year":"2017","journal-title":"J. Vet. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1126\/science.1122438","article-title":"Global patterns of influenza a virus in wild birds","volume":"312","author":"Olsen","year":"2006","journal-title":"Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e00445-13","DOI":"10.1128\/mBio.00445-13","article-title":"H7N9 avian influenza A virus and the perpetual challenge of potential human pandemicity","volume":"4","author":"Morens","year":"2013","journal-title":"mBio"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Peacock, T.H.P., James, J., Sealy, J.E., and Iqbal, M. (2019). A Global Perspective on H9N2 Avian Influenza Virus. Viruses, 11.","DOI":"10.20944\/preprints201906.0085.v1"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Pusch, E.A., and Suarez, D.L. (2018). The Multifaceted Zoonotic Risk of H9N2 Avian Influenza. Vet. Sci., 5.","DOI":"10.3390\/vetsci5040082"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1093\/bmb\/ldz036","article-title":"Avian influenza viruses in humans: Lessons from past outbreaks","volume":"132","author":"Li","year":"2019","journal-title":"Br. Med. Bull."},{"key":"ref_9","unstructured":"WHO (2023). Cumulative Number of Confirmed Human Cases for Avian Influenza A(H5N1) Reported to WHO, 2003\u20132023."},{"key":"ref_10","unstructured":"WHO (2024). Monthly Risk Assessment Summary."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.3201\/eid2407.172120","article-title":"Highly Pathogenic Avian Influenza A(H5N8) Virus, Cameroon, 2017","volume":"24","author":"Wade","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"104074","DOI":"10.1016\/j.meegid.2019.104074","article-title":"Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets","volume":"78","author":"Kariithi","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kalonda, A., Saasa, N., Nkhoma, P., Kajihara, M., Sawa, H., Takada, A., and Simulundu, E. (2020). Avian Influenza Viruses Detected in Birds in Sub-Saharan Africa: A Systematic Review. Viruses, 12.","DOI":"10.3390\/v12090993"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"S512","DOI":"10.1093\/infdis\/jix018","article-title":"Risk of Human Infections With Highly Pathogenic H5N2 and Low Pathogenic H7N1 Avian Influenza Strains During Outbreaks in Ostriches in South Africa","volume":"216","author":"Venter","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_15","first-page":"1","article-title":"2016\u20132018 Spread of H5N8 highly pathogenic avian influenza (HPAI) in sub-Saharan Africa: Epidemiological and ecological observations","volume":"12","author":"Khomenko","year":"2018","journal-title":"FOCUS ON"},{"key":"ref_16","unstructured":"FAO (2017). H5N8 HPAI in Uganda Further Spread in Uganda and Neighbouring Countries (February 2017), FAO."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.meegid.2018.10.010","article-title":"Highly pathogenic avian influenza H5N8 Clade 2.3.4.4B virus in Uganda, 2017","volume":"66","author":"Ndumu","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1111\/j.1750-2659.2012.00365.x","article-title":"Detection of influenza A virus in live bird markets in Kenya, 2009\u20132011","volume":"7","author":"Munyua","year":"2013","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_19","unstructured":"John Wiley & Sons Inc. (2012). Sample Size. Sampling, John Wiley & Sons, Inc.. [3rd ed.]."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1089\/vbz.2011.0926","article-title":"Detection of avian influenza viruses in wild waterbirds in the Rift Valley of Kenya using fecal sampling","volume":"13","author":"Ofula","year":"2013","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/978-1-4939-0758-8_19","article-title":"Newcastle disease virus detection and differentiation from avian influenza","volume":"1161","author":"Miller","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"ref_22","unstructured":"Centers for Disease Control and Prevention (2013). CDC Laboratory Support for Influenza Surveillance (CLSIS), CDC."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Shepard, S.S., Meno, S., Bahl, J., Wilson, M.M., Barnes, J., and Neuhaus, E. (2016). Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics, 17.","DOI":"10.1186\/s12864-016-3030-6"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_25","first-page":"406","article-title":"The neighbor-joining method: A new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_27","unstructured":"WHO (2002). WHO Manual on Animal Influenza Diagnosis and Surveillance, 2012-06-17T00:55:01Z."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"SJCEIRS (St Jude Center of Excellence for Influenza Research and Surveillance) H9 Working Group (2013). Assessing the fitness of distinct clades of influenza A (H9N2) viruses. Emerg. Microbes Infect., 2, e75.","DOI":"10.1038\/emi.2013.75"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Ilyushina, N.A., Govorkova, E.A., Gray, T.E., Bovin, N.V., and Webster, R.G. (2008). Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. PLoS Pathog., 4.","DOI":"10.1371\/journal.ppat.1000043"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Arbani, O., Ducatez, M.F., Mahmoudi, S., Salamat, F., Khayi, S., Mouahid, M., Selim, K.M., Kichou, F., Ouchhour, I., and El Houadfi, M. (2023). Low Pathogenic Avian Influenza H9N2 Viruses in Morocco: Antigenic and Molecular Evolution from 2021 to 2023. Viruses, 15.","DOI":"10.3390\/v15122355"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Germeraad, E.A., Sanders, P., Hagenaars, T.J., Jong, M.C.M., Beerens, N., and Gonzales, J.L. (2019). Virus Shedding of Avian Influenza in Poultry: A Systematic Review and Meta-Analysis. Viruses, 11.","DOI":"10.3390\/v11090812"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.3201\/eid2308.170143","article-title":"Genesis of Influenza A(H5N8) Viruses","volume":"23","author":"Barman","year":"2017","journal-title":"Emerg. Infect. Dis."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/9\/1417\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:48:52Z","timestamp":1760111332000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/9\/1417"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,5]]},"references-count":32,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2024,9]]}},"alternative-id":["v16091417"],"URL":"https:\/\/doi.org\/10.3390\/v16091417","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,5]]}}}