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Data for Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya
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Nokes, D. James and Otieno, James R. (2017) Data for Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya. [Dataset]
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Official URL: https://doi.org/10.7910/DVN/MNSYNF
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: | Dataset | ||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology | ||||||
| Divisions: | Faculty of Medicine > Warwick Medical School | ||||||
| Type of Data: | Experimental data | ||||||
| Library of Congress Subject Headings (LCSH): | Respiratory syncytial virus -- Research -- Kenya, Coasts -- Kenya | ||||||
| Publisher: | Harvard Dataverse | ||||||
| Official Date: | 14 May 2017 | ||||||
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| Status: | Not Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Media of Output: | .txt .fasta | ||||||
| Access rights to Published version: | Open Access | ||||||
| Copyright Holders: | University of Warwick | ||||||
| Description: | Data record consists of 2 data files in plain text format. |
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