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 nextgeneration
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. RESULTS
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 8.62 × 10-4). We found multiple clades
co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5
for RSVA and BA for RSVB.
Our analyses showed that RSV circulates on a global scale with the same predominant
clades of viruses being found in countries around the world. However, the distribution of
clades can change rapidly as new strains emerge. We did not observe a strong spatial
structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting
that the evolution of RSV is not strongly regionalized.
All genome sequence
files are available from the GenBank database
(bioproject id PRJNA73049 and accession numbers
KF530258 - KF530269 and KF826816 - KF826860).
All other relevant data are within the paper and its
Supporting Information files.