Altmetric

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

Title: Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing
Authors: Agoti, CN
Otieno, JR
Munywoki, PK
Mwihuri, AG
Cane, PA
Nokes, DJ
Kellam, P
Cotten, M
Item Type: Journal Article
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.
Issue Date: 1-Apr-2015
Date of Acceptance: 11-Jan-2015
URI: http://hdl.handle.net/10044/1/69573
DOI: https://dx.doi.org/10.1128/JVI.03391-14
ISSN: 1098-5514
Publisher: American Society for Microbiology
Start Page: 3444
End Page: 3454
Journal / Book Title: Journal of Virology
Volume: 89
Issue: 7
Copyright Statement: © 2015 Agoti et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license (https://creativecommons.org/licenses/by/3.0/).
Keywords: Science & Technology
Life Sciences & Biomedicine
Virology
GROUP-A
60-NUCLEOTIDE DUPLICATION
MOLECULAR EPIDEMIOLOGY
PHYLOGENETIC ANALYSIS
CIRCULATION PATTERNS
O-GLYCOSYLATION
SUBGROUP-A
G-PROTEIN
GLYCOPROTEIN
CHILDREN
Child, Preschool
Cluster Analysis
Evolution, Molecular
Genome, Viral
Genotype
High-Throughput Nucleotide Sequencing
Hospitals, Rural
Humans
Infant
Infant, Newborn
Kenya
Molecular Sequence Data
Phylogeography
Respiratory Syncytial Virus Infections
Respiratory Syncytial Virus, Human
Sequence Analysis, DNA
Sequence Homology
06 Biological Sciences
07 Agricultural and Veterinary Sciences
11 Medical and Health Sciences
Publication Status: Published
Online Publication Date: 2015-03-10
Appears in Collections:Department of Medicine



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Creative Commons