Toward unified molecular surveillance of RSV: A proposal for genotype definition

Abstract

Background: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. Methods: We evaluated clustering of RSV sequences published in GenBank untilFebruary 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. Results:We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome.Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. | 275GOYA et Al.

Respiratory syncytial virus B sequence analysis reveals a novel early genotype

“…Genotype description is usually based on analysis of a fragment of the G gene of this virus. However, there is no consensus regarding criteria that should be met in order to identify a new genotype, particularly the size of the G gene sequence that needs to be analyzed and the number of sequences that should be included in the analysis 8 , 20 , 28 , 29 . Of relevance, many studies have included a limited number of sequences and have analyzed only the hypervariable region of the G gene.…”

“…While RSV-A strains can be grouped into seven distinct genotypes, there have been at least 37 RSV-B genotypes described in the literature (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-Ly, BA-C, BA-CCA, BA-CCB, JAB1, NZB1, and NZB2) 4 , 9 – 27 . Of note, at present there is no consensus regarding criteria to discriminate between genotypes 4 , 8 , 17 , 20 , 28 , 29 . Identification and description of many genotypes has relied on sequencing of the second hypervariable region of the G gene; however, analyses limited to this region are not always able to distinguish between strains that might be considered as part of the same or different genotype 8 , 30 .…”

Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

“…In a parallel effort, several research groups are working together on a genotyping proposal to provide a consensus on uniform genotype designations ( 38 , 39 ). As virus evolution continues, we expect new genotypes to emerge and older genotypes to become extinct.…”

Comparative analysis of spatial-temporal patterns of human metapneumovirus and respiratory syncytial virus in Africa using genetic data, 2011–2014

“…Additionally, there are two distinct clades within A2b, A2b1 and A2b2 [ 18 ].Similarly, RSV is classified into two groups (A and B) that are both antigenically and genetically distinct [ 19 ]. The two groups are further divided into multiple genotypes based on nucleotide differences within the RSV G gene [ 20 ]. Clinically, there is no difference in disease severity between the subgroups for both HMPV and RSV [ 5 , 21 ].…”