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

Agoti, C. N., Otieno, J. R., Munywoki, P. K., Mwihuri, A. G., Cane, P. A., Nokes, D. J., Kellam, P. and Cotten, M. (2015) Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. Journal of Virology, 89(7), pp. 3444-3454. (doi: 10.1128/JVI.03391-14) (PMID:25609811) (PMCID:PMC4403408)

[img]
Preview
Text
196560.pdf - Published Version
Available under License Creative Commons Attribution.

4MB

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. Importance: The new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development. Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Cotten, Professor Matthew
Authors: Agoti, C. N., Otieno, J. R., Munywoki, P. K., Mwihuri, A. G., Cane, P. A., Nokes, D. J., Kellam, P., and Cotten, M.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Journal of Virology
Publisher:American Society for Microbiology
ISSN:0022-538X
ISSN (Online):1098-5514
Published Online:10 March 2015
Copyright Holders:Copyright © 2015 Agoti et al.
First Published:First published in Journal of Virology 89(7): 3444-3454
Publisher Policy:Reproduced under a Creative Commons License

University Staff: Request a correction | Enlighten Editors: Update this record