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Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017
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Owuor, D. Collins, Ngoi, Joyce M., Otieno, James R., Otieno, Grieven P., Nyasimi, Festus M., Nyiro, Joyce U., Agoti, Charles N., Chaves, Sandra S. and Nokes, D. James (2020) Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017. Influenza and Other Respiratory Viruses, 14 (3). pp. 320-330. doi:10.1111/irv.12717
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Official URL: https://doi.org/10.1111/irv.12717
Abstract
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.
| Item Type: | Journal Article | ||||||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology | ||||||||||||
| Divisions: | Faculty of Science > Life Sciences (2010- ) | ||||||||||||
| SWORD Depositor: | Library Publications Router | ||||||||||||
| Library of Congress Subject Headings (LCSH): | Influenza viruses -- Research, Influenza -- Epidemiology, Influenza -- Prevention -- Kenya, Hemagglutinin, Influenza A virus -- Genetics | ||||||||||||
| Journal or Publication Title: | Influenza and Other Respiratory Viruses | ||||||||||||
| Publisher: | Wiley | ||||||||||||
| ISSN: | 1750-2640 | ||||||||||||
| Official Date: | May 2020 | ||||||||||||
| Dates: |
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| Date of first compliant deposit: | 29 January 2020 | ||||||||||||
| Volume: | 14 | ||||||||||||
| Number: | 3 | ||||||||||||
| Page Range: | pp. 320-330 | ||||||||||||
| DOI: | 10.1111/irv.12717 | ||||||||||||
| Status: | Peer Reviewed | ||||||||||||
| Publication Status: | Published | ||||||||||||
| Access rights to Published version: | Open Access | ||||||||||||
| RIOXX Funder/Project Grant: |
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