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Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018

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Owuor, D. Collins, de Laurent, Zaydah R., Kikwai, Gilbert K., Mayieka, Lillian M., Ochieng, Melvin, Müller, Nicola F., Otieno, Nancy A., Emukule, Gideon O., Hunsperger, Elizabeth A., Garten, Rebecca, Barnes, John R., Chaves, Sandra S., Nokes, D. James and Agoti, Charles N. (2021) Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018. Viruses, 13 (10). e1956. doi:10.3390/v13101956

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Official URL: https://doi.org/10.3390/v13101956

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Abstract

The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009–2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012–2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.

Item Type: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Science > Mathematics
SWORD Depositor: Library Publications Router
Library of Congress Subject Headings (LCSH): Influenza A Virus, H1N1 Subtype -- Kenya, Hemagglutinin, Influenza viruses -- Research
Journal or Publication Title: Viruses
Publisher: MDPI
ISSN: 1999-4915
Official Date: 29 September 2021
Dates:
DateEvent
29 September 2021Available
22 September 2021Accepted
Volume: 13
Number: 10
Article Number: e1956
DOI: 10.3390/v13101956
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
107769/Z/10/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
1029745Wellcome Trusthttp://dx.doi.org/10.13039/100010269
GH002133Centers for Disease Control and Preventionhttp://dx.doi.org/10.13039/100000030
PZEZP3_191891[SNSF] Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschunghttp://dx.doi.org/10.13039/501100001711

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