Genetic Characterization of Influenza A(H3N2) Viruses Circulating in Coastal Kenya, 2009-2017

Overview

Journal Influenza Other Respir Viruses

Publisher Wiley

Specialty Microbiology

Date 2020 Jan 17

PMID 31943817

Citations 8

Authors

D Collins Owuor

Joyce M Ngoi

James R Otieno

Grieven P Otieno

Festus M Nyasimi

Joyce U Nyiro

Charles N Agoti

Sandra S Chaves

D James Nokes

Affiliations

Soon will be listed here.

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.

Citing Articles

Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data.

Owuor D, Ngoi J, Nyasimi F, Murunga N, Nyiro J, Chaves S Sci Rep. 2024; 14(1):23426.

PMID: 39379445 PMC: 11461663. DOI: 10.1038/s41598-024-74218-6.

Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa.

Owuor D, de Laurent Z, Oketch J, Murunga N, Otieno J, Nabakooza G Sci Rep. 2024; 14(1):18987.

PMID: 39152215 PMC: 11329769. DOI: 10.1038/s41598-024-70023-3.

Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons.

Owuor D, de Laurent Z, Nyawanda B, Emukule G, Kondor R, Barnes J Sci Rep. 2023; 13(1):22342.

PMID: 38102198 PMC: 10724140. DOI: 10.1038/s41598-023-49157-3.

Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains.

Nabakooza G, Owuor D, de Laurent Z, Galiwango R, Owor N, Kayiwa J Sci Rep. 2023; 13(1):5516.

PMID: 37015946 PMC: 10072032. DOI: 10.1038/s41598-023-30667-z.

Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review.

Nabakooza G, Galiwango R, Frost S, Kateete D, Kitayimbwa J Microorganisms. 2022; 10(5).

PMID: 35630344 PMC: 9145646. DOI: 10.3390/microorganisms10050900.

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