Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018
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 hospitali...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/10/1956 |
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| author | D. Collins Owuor Zaydah R. de Laurent Gilbert K. Kikwai Lillian M. Mayieka Melvin Ochieng Nicola F. Müller Nancy A. Otieno Gideon O. Emukule Elizabeth A. Hunsperger Rebecca Garten John R. Barnes Sandra S. Chaves D. James Nokes Charles N. Agoti |
| author_facet | D. Collins Owuor Zaydah R. de Laurent Gilbert K. Kikwai Lillian M. Mayieka Melvin Ochieng Nicola F. Müller Nancy A. Otieno Gideon O. Emukule Elizabeth A. Hunsperger Rebecca Garten John R. Barnes Sandra S. Chaves D. James Nokes Charles N. Agoti |
| author_sort | D. Collins Owuor |
| collection | DOAJ |
| description | 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 (<i>R</i><sub>e</sub>) 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. |
| first_indexed | 2024-03-10T06:08:53Z |
| format | Article |
| id | doaj.art-d446ea429ce2484a8f8c7c8fd9b6a8d0 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T06:08:53Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d446ea429ce2484a8f8c7c8fd9b6a8d02023-11-22T20:18:36ZengMDPI AGViruses1999-49152021-09-011310195610.3390/v13101956Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018D. Collins Owuor0Zaydah R. de Laurent1Gilbert K. Kikwai2Lillian M. Mayieka3Melvin Ochieng4Nicola F. Müller5Nancy A. Otieno6Gideon O. Emukule7Elizabeth A. Hunsperger8Rebecca Garten9John R. Barnes10Sandra S. Chaves11D. James Nokes12Charles N. Agoti13Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, KenyaWellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, KenyaKenya Medical Research Institute (KEMRI), Nairobi 54840-00200, KenyaKenya Medical Research Institute (KEMRI), Nairobi 54840-00200, KenyaKenya Medical Research Institute (KEMRI), Nairobi 54840-00200, KenyaFred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USAKenya Medical Research Institute (KEMRI), Nairobi 54840-00200, KenyaCenters for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, KenyaCenters for Disease Control and Prevention, Division of Global Health Protection, Nairobi 606-00621, KenyaInfluenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USAInfluenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USACenters for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, KenyaWellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, KenyaWellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, KenyaThe 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 (<i>R</i><sub>e</sub>) 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.https://www.mdpi.com/1999-4915/13/10/1956next-generation sequencinghemagglutininphylodynamicstransmission |
| spellingShingle | D. Collins Owuor Zaydah R. de Laurent Gilbert K. Kikwai Lillian M. Mayieka Melvin Ochieng Nicola F. Müller Nancy A. Otieno Gideon O. Emukule Elizabeth A. Hunsperger Rebecca Garten John R. Barnes Sandra S. Chaves D. James Nokes Charles N. Agoti Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 Viruses next-generation sequencing hemagglutinin phylodynamics transmission |
| title | Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 |
| title_full | Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 |
| title_fullStr | Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 |
| title_full_unstemmed | Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 |
| title_short | Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 |
| title_sort | characterizing the countrywide epidemic spread of influenza a h1n1 pdm09 virus in kenya between 2009 and 2018 |
| topic | next-generation sequencing hemagglutinin phylodynamics transmission |
| url | https://www.mdpi.com/1999-4915/13/10/1956 |
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