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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
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 | ||||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology | ||||||||||
| Divisions: | Faculty of 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: |
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| Date of first compliant deposit: | 9 March 2016 | ||||||||||
| 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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