Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons
Abstract Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus gen...
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| Format: | Article |
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Nature Portfolio
2023-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-49157-3 |
| _version_ | 1797388392690876416 |
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| author | D. Collins Owuor Zaydah R. de Laurent Bryan O. Nyawanda Gideon O. Emukule Rebecca Kondor John R. Barnes D. James Nokes Charles N. Agoti Sandra S. Chaves |
| author_facet | D. Collins Owuor Zaydah R. de Laurent Bryan O. Nyawanda Gideon O. Emukule Rebecca Kondor John R. Barnes D. James Nokes Charles N. Agoti Sandra S. Chaves |
| author_sort | D. Collins Owuor |
| collection | DOAJ |
| description | Abstract Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines. |
| first_indexed | 2024-03-08T22:40:09Z |
| format | Article |
| id | doaj.art-29e15b8e4c074563952b391663f94dbc |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-08T22:40:09Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-29e15b8e4c074563952b391663f94dbc2023-12-17T12:13:18ZengNature PortfolioScientific Reports2045-23222023-12-011311910.1038/s41598-023-49157-3Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasonsD. Collins Owuor0Zaydah R. de Laurent1Bryan O. Nyawanda2Gideon O. Emukule3Rebecca Kondor4John R. Barnes5D. James Nokes6Charles N. Agoti7Sandra S. Chaves8Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research ProgrammeEpidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research ProgrammeKenya Medical Research InstituteInfluenza Division, Centers for Disease Control and PreventionInfluenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and PreventionInfluenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and PreventionEpidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research ProgrammeEpidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research ProgrammeInfluenza Division, Centers for Disease Control and PreventionAbstract Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.https://doi.org/10.1038/s41598-023-49157-3 |
| spellingShingle | D. Collins Owuor Zaydah R. de Laurent Bryan O. Nyawanda Gideon O. Emukule Rebecca Kondor John R. Barnes D. James Nokes Charles N. Agoti Sandra S. Chaves Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons Scientific Reports |
| title | Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons |
| title_full | Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons |
| title_fullStr | Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons |
| title_full_unstemmed | Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons |
| title_short | Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons |
| title_sort | genetic and potential antigenic evolution of influenza a h1n1 pdm09 viruses circulating in kenya during 2009 2018 influenza seasons |
| url | https://doi.org/10.1038/s41598-023-49157-3 |
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