Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes

PloS One
Michael BoseKelly Henrickson

Abstract

Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference. We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10(-4) substitutions/site/year (95% HPD 5.61 × 10(-4) to 7.6 × 10(-4)) and for RSVB the evolutionary rate was 7.69 × 10(-4) substitutions/site/year (95% HPD 6.81 × 10(-4) to ...Continue Reading

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Citations

Sep 27, 2015·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Koo NagasawaHirokazu Kimura
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Datasets Mentioned

BETA
U63644
PRJNA73049
M74568
AF013254
AY353550

Methods Mentioned

BETA
bronchoalveolar lavage
PCR
3Seq

Software Mentioned

SiScan
Datamonkey
BEAUti
clc
BootScan
MEGA
Minimus
BioEdit
Chimaera
TreeAnnotator

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