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.

Figure 1

Phylogenetic tree of 1,334 unique RSV-B complete G gene ectodomain sequences constructed by Bayesian MCMC analysis. Genotype assignment was carried out with the use of 169 reference sequences including 37 previously described genotypes and prototype strains.

Figure 2

(A) Distinct genotypes identified through intergenotypic and intragenotypic p-distance analysis of 2,190 RSVB complete ectodomain sequences. The highest intragenotypic distance was observed for GB1 (0.0358). All clusters with intergenotypic distance higher than this threshold value were considered as distinct genotypes. (B) Several previously described genotypes or unique unidentified clusters were found to cluster together with BA-CC (BA-CCA and BA-CCB), CB1-THB (CB1 and THB), JAB1-NZB2 (JAB1 and NZB2), GB2 (GB2, GB5, and NZB1), GB3 (GB3, GB12-GB13, SAB3, URU1, BA1-BA6, U2-U4), and BA (BA7-BA14, U5-U10).

Figure 3

(A) Phylogenetic tree of 1,334 unique RSV-B complete G gene ectodomain sequences constructed by Bayesian MCMC analysis showing the 15 distinct genotypes defined through intragenotypic and intergenotypic p-distance analysis. (B) Temporal distribution of RSV-B genotypes since their first up to their last detection. Genotypes marked with stars indicate genotypes currently in circulation.

Figure 4

(A) Intergenotypic and intragenotypic p-distance analysis of complete NS1, NS2, N, P, M, SH, G, F, M2, and L genes of RSV-B sequences. (B) Unrooted phylogenetic tree of complete NS1, NS2, N, P, M, SH, G, F, M2, and L genes of RSV-B sequences constructed Maximum Likelihood analysis.

Figure 5

Distribution of molecular markers present in RSV-B genotypes. The location of all (upper panel) and unique (lower panel) molecular markers present in each genotype is shown. Dark bars indicate untranslated regions in which molecular markers were identified.

Figure 6

RSV-B genotype distribution since 1960 and each decade thereafter, according to continent of viral detection.