Respiratory syncytial virus B sequence analysis reveals a novel early genotype

Abstract

Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

Factors associated with severe respiratory syncytial virus disease in hospitalised children: a retrospective analysis

“…While RSV subgroup was unrelated to disease severity, a lower Ct value (and by inference higher viral load) was observed in children with severe disease. ON1 and BA11 have been reported as the predominant genotypes of RSV A and RSV B subgroups in many places including Australia 18 19. Furthermore, we observed that RSV–PIV3 codetection was associated with greater than twofold higher risk of severe disease compared with the absence of codetection, which was a novel finding.…”

Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010–2019

“…Multiple sequence alignment using MUSCLE and further editing were performed using MEGA X [ 18 ]. Reference sequences representing each subtype corresponding to 13 subtypes of RSV-A (n = 111) and 36 subtypes of RSV-B (n = 185) were retrieved from GenBank by referring to relevant publications [ 10 , 11 , 16 ] ( S1 and S2 Tables). Neighbor-joining (NJ) trees of RSV-A and RSV-B were constructed using the maximum composition likelihood model provided in MEGA X, followed by construction of maximum likelihood (ML) trees of RSV-A and RSV-B with the selected most suitable nucleotide substitution model, TN93 + G. Statistical significance of the tree topology was tested by bootstrapping in 1,000 replicates.…”

“…The categorization into specific genotypes is useful because the genetic variability of RSV is believed to be responsible for its ability to infect hosts repeatedly [ 9 ]. There are 13 genotypes (GA1-GA7, NA1-NA4, ON1, and SAA1) identified for RSV-A and at least 37 genotypes for RSV-B (GB1, GB2, GB3, GB4, GB5, GB6, GB12, GB13, SAB1, SAB2, SAB3, SAB4, URU1, URU2, CB1, THB, BA1, BA2, BA3, BA4, BA5, BA6, BA7, BA8, BA9, BA10, BA11, BA12, BA13, BA14, BA-C, BA-CCA, BA-CCB, JAB1, NZB1, and NZB2) so far worldwide [ 10 , 11 ].…”

Clinical and biological consequences of respiratory syncytial virus genetic diversity

“…The advent of deep sequencing approaches subsequently allowed for the broader characterization of RSV diversity. 40 Within these antigenic groups, there have been 37 identified genotypes documented for RSV-B 41 and 13 distinct genotypes documented for RSV-A. 42 , 43 The evolutionary rates for both subtypes differ from one another, with RSV-A proposed to have a lower rate at 1.48 × 10 – 3 nucleotide substitutions/site/year as opposed to RSV-B at 1.92 × 10 – 3 substitutions/site/year.…”