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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

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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: Dataset
Subjects: Q Science > QR Microbiology > QR355 Virology
Divisions: Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Type of Data: Experimental data
Library of Congress Subject Headings (LCSH): Respiratory syncytial virus -- Research -- Kenya, Coasts -- Kenya
Publisher: University of Warwick, Warwick Medical School
Official Date: 14 May 2017
Dates:
DateEvent
14 May 2017Published
5 May 2017Submitted
Status: Not Peer Reviewed
Publication Status: Published
Media of Output (format): .txt .fasta
Access rights to Published version: Open Access (Creative Commons)
Copyright Holders: University of Warwick
Description:

Data record consists of 2 data files in plain text format.
The data is from an on-going study aimed at understanding the epidemiology and disease burden of RSV-associated pneumonia cases in Kilifi. This report details the evolutionary dynamics of RSV-A genotype in Kilifi. Respiratory swab samples (combined nasopharyngeal and oropharyngeal) were collected from January 2000 to December 2012 from: (i) LRTI cases for children <5 years admitted to Kilifi County Hospital (KCH) collected over the period from 2000 to 2012 (3, 24), (ii) KCH outpatient presentations for children <5 years with acute respiratory infection (ARI) from April to August 2002 (25, 26), and (iii) the Kilifi RSV birth cohort (KBC) ARI cases identified between January 2002 to August 2003. The samples were screened for RSV and G-gene sequenced (RSV positives) using the Sanger method. Also included is a global RSV-A contemporenous comparison sequence dataset used in the analyses.
The newly generated sequences analyzed here have been deposited in GenBank under accession numbers KT765213 to KT765836. The previously sequenced and reported RSV-A sequences from Kilifi added to this analysis had been archived in GenBank under accession numbers AY524573 to AY524663 and AY660667 to AY660684.

RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
UNSPECIFIEDKenya Medical Research Institutehttp://viaf.org/viaf/151310353
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Contributors:
ContributionNameContributor ID
Contact PersonNokes, D. James35965

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