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Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017
BACKGROUND: Influenza viruses evolve rapidly and undergo immune driven selection, especially in the hemagglutinin (HA) protein. We report amino acid changes affecting antigenic epitopes and receptor‐binding sites of A(H3N2) viruses circulating in Kilifi, Kenya, from 2009 to 2017. METHODS: Next‐gener...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182596/ https://www.ncbi.nlm.nih.gov/pubmed/31943817 http://dx.doi.org/10.1111/irv.12717 |
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author | Owuor, D. Collins Ngoi, Joyce M. Otieno, James R. Otieno, Grieven P. Nyasimi, Festus M. Nyiro, Joyce U. Agoti, Charles N. Chaves, Sandra S. Nokes, D. James |
author_facet | Owuor, D. Collins Ngoi, Joyce M. Otieno, James R. Otieno, Grieven P. Nyasimi, Festus M. Nyiro, Joyce U. Agoti, Charles N. Chaves, Sandra S. Nokes, D. James |
author_sort | Owuor, D. Collins |
collection | PubMed |
description | BACKGROUND: Influenza viruses evolve rapidly and undergo immune driven selection, especially in the hemagglutinin (HA) protein. We report amino acid changes affecting antigenic epitopes and receptor‐binding sites of A(H3N2) viruses circulating in Kilifi, Kenya, from 2009 to 2017. METHODS: Next‐generation sequencing (NGS) was used to generate A(H3N2) virus genomic data from influenza‐positive specimens collected from hospital admissions and health facility outpatients presenting with acute respiratory illness to health facilities within the Kilifi Health and Demographic Surveillance System. Full‐length HA sequences were utilized to characterize A(H3N2) virus genetic and antigenic changes. RESULTS: From 186 (90 inpatient and 96 outpatient) influenza A virus‐positive specimens processed, 101 A(H3N2) virus whole genomes were obtained. Among viruses identified in inpatient specimens from 2009 to 2015, divergence of circulating A(H3N2) viruses from the vaccine strains A/Perth/16/2009, A/Texas/50/2012, and A/Switzerland/9715293/2013 formed 6 genetic clades (A/Victoria/208/2009‐like, 3B, 3C, 3C.2a, 4, and 7). Among viruses identified in outpatient specimens from 2015 to 2017, divergence of circulating A(H3N2) viruses from vaccine strain A/Hong Kong/4801/2014 formed clade 3C.2a, subclades 3C.2a2 and 3C.2a3, and subgroup 3C.2a1b. Several amino acid substitutions were associated with the continued genetic evolution of A(H3N2) strains in circulation. CONCLUSIONS: Our results suggest continuing evolution of currently circulating A(H3N2) viruses in Kilifi, coastal Kenya and suggest the need for continuous genetic and antigenic viral surveillance of circulating seasonal influenza viruses with broad geographic representation to facilitate prompt and efficient selection of influenza strains for inclusion in future influenza vaccines. |
format | Online Article Text |
id | pubmed-7182596 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-71825962020-05-01 Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 Owuor, D. Collins Ngoi, Joyce M. Otieno, James R. Otieno, Grieven P. Nyasimi, Festus M. Nyiro, Joyce U. Agoti, Charles N. Chaves, Sandra S. Nokes, D. James Influenza Other Respir Viruses Original Articles BACKGROUND: Influenza viruses evolve rapidly and undergo immune driven selection, especially in the hemagglutinin (HA) protein. We report amino acid changes affecting antigenic epitopes and receptor‐binding sites of A(H3N2) viruses circulating in Kilifi, Kenya, from 2009 to 2017. METHODS: Next‐generation sequencing (NGS) was used to generate A(H3N2) virus genomic data from influenza‐positive specimens collected from hospital admissions and health facility outpatients presenting with acute respiratory illness to health facilities within the Kilifi Health and Demographic Surveillance System. Full‐length HA sequences were utilized to characterize A(H3N2) virus genetic and antigenic changes. RESULTS: From 186 (90 inpatient and 96 outpatient) influenza A virus‐positive specimens processed, 101 A(H3N2) virus whole genomes were obtained. Among viruses identified in inpatient specimens from 2009 to 2015, divergence of circulating A(H3N2) viruses from the vaccine strains A/Perth/16/2009, A/Texas/50/2012, and A/Switzerland/9715293/2013 formed 6 genetic clades (A/Victoria/208/2009‐like, 3B, 3C, 3C.2a, 4, and 7). Among viruses identified in outpatient specimens from 2015 to 2017, divergence of circulating A(H3N2) viruses from vaccine strain A/Hong Kong/4801/2014 formed clade 3C.2a, subclades 3C.2a2 and 3C.2a3, and subgroup 3C.2a1b. Several amino acid substitutions were associated with the continued genetic evolution of A(H3N2) strains in circulation. CONCLUSIONS: Our results suggest continuing evolution of currently circulating A(H3N2) viruses in Kilifi, coastal Kenya and suggest the need for continuous genetic and antigenic viral surveillance of circulating seasonal influenza viruses with broad geographic representation to facilitate prompt and efficient selection of influenza strains for inclusion in future influenza vaccines. John Wiley and Sons Inc. 2020-01-13 2020-05 /pmc/articles/PMC7182596/ /pubmed/31943817 http://dx.doi.org/10.1111/irv.12717 Text en © 2020 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Articles Owuor, D. Collins Ngoi, Joyce M. Otieno, James R. Otieno, Grieven P. Nyasimi, Festus M. Nyiro, Joyce U. Agoti, Charles N. Chaves, Sandra S. Nokes, D. James Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title | Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title_full | Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title_fullStr | Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title_full_unstemmed | Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title_short | Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017 |
title_sort | genetic characterization of influenza a(h3n2) viruses circulating in coastal kenya, 2009‐2017 |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182596/ https://www.ncbi.nlm.nih.gov/pubmed/31943817 http://dx.doi.org/10.1111/irv.12717 |
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