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Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing

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Agoti, Charles N., Otieno, James R., Munywoki, Patrick K., Mwihuri, Alexander G., Cane, Patricia, Nokes, D. James, Kellam, Paul, Cotten, Matthew and Perlman, S. (2015) Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. Journal of Virology, Volume 89 (Number 7). pp. 3444-3454. doi:10.1128/JVI.03391-14

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Official URL: http://dx.doi.org/10.1128/JVI.03391-14

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Abstract

Human respiratory syncytial virus (RSV) is associated with severe childhood respiratory infections. A clear description of local RSV molecular epidemiology, evolution, and transmission requires detailed sequence data and can inform new strategies for virus control and vaccine development. We have generated 27 complete or nearly complete genomes of RSV from hospitalized children attending a rural coastal district hospital in Kilifi, Kenya, over a 10-year period using a novel full-genome deep-sequencing process. Phylogenetic analysis of the new genomes demonstrated the existence and cocirculation of multiple genotypes in both RSV A and B groups in Kilifi. Comparison of local versus global strains demonstrated that most RSV A variants observed locally in Kilifi were also seen in other parts of the world, while the Kilifi RSV B genomes encoded a high degree of variation that was not observed in other parts of the world. The nucleotide substitution rates for the individual open reading frames (ORFs) were highest in the regions encoding the attachment (G) glycoprotein and the NS2 protein. The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement. The novel sequencing method and the new RSV genomic sequences reported here expand our knowledge base for large-scale RSV epidemiological and transmission studies.

Item Type: Journal Article
Divisions: Faculty of Science > Life Sciences (2010- )
Journal or Publication Title: Journal of Virology
Publisher: American Society for Microbiology
ISSN: 0022-538X
Official Date: April 2015
Dates:
DateEvent
April 2015Published
11 January 2015Accepted
24 November 2014Submitted
Volume: Volume 89
Number: Number 7
Page Range: pp. 3444-3454
DOI: 10.1128/JVI.03391-14
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access

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