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Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya

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Otieno, James R., Agoti, Charles N., Gitahi, Caroline W., Bett, Ann, Ngama, Mwanajuma, Medley, Graham F, Cane, Patricia A. and Nokes, D. James (2016) Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya. Journal of Virology, 90 (10). pp. 4990-5002. doi:10.1128/JVI.03105-15

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Official URL: http://dx.doi.org/10.1128/JVI.03105-15

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Abstract

The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing efficiency of pre-existing immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 – 2012) in Kilifi (n=649), Kenya, and contemporaneous sequences (n=1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%) and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2, then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3.58 x 10-3 [95% HPD: 3.04 – 4.16] nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.

Item Type: Journal Article
Subjects: Q Science > QR Microbiology > QR355 Virology
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Respiratory syncytial virus--Research--Kenya, Coasts--Kenya
Journal or Publication Title: Journal of Virology
Publisher: American Society for Microbiology
ISSN: 0022-538X
Official Date: May 2016
Dates:
DateEvent
May 2016Published
2 March 2016Available
25 February 2016Accepted
10 December 2015Submitted
Volume: 90
Number: 10
Page Range: pp. 4990-5002
DOI: 10.1128/JVI.03105-15
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Kenya Medical Research Institute

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