Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level

Abstract

A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.

Keywords: F; G; HRSV; RSV; classification; epidemiology; evolution; genome; genotype; glycoprotein; lineage; orthopneumovirus; phylogeny; respiratory infections; respiratory syncytial virus; surveillance.

Figure 1

The structure and genome of human respiratory syncytial virus (HRSV). A) Schematic of the HRSV virion structure detailing the location of structural proteins. B) Schematic of the HRSV genome organization with the approximated location of genes highlighted; the exact location slightly differs between subgroups and strains. The location of the second hypervariable region in the G gene, used originally for molecular epidemiology classification, is detailed. Red arrow in panel B indicates location of the G gene 72-nt duplication in HRSV-A and 60-nt duplication in HRSV-B. Figure created with BioRender (https://www.biorender.com). F, fusion glycoprotein; G, attachment glycoprotein; L, large polymerase protein; M, matrix protein; M2, M2 protein; N, nucleocapsid; NS, nonstructural protein; ORF, open reading frame; P, phosphoprotein; SH, small hydrophobic protein.

Figure 2

The global HRSV genomics surveillance landscape. HRSV genomes from GenBank and GISAID (https://www.gisaid.org) databases through March 11, 2023, that met inclusion criteria used for classification are shown by year of sample collection and subgroup (A) and by country of origin (B). HRSV, human respiratory syncytial virus.

Figure 3

Human respiratory syncytial virus A lineage classification. A) HRSV-A maximum-likelihood phylogenetic tree (1,480 sequences), colored by lineage classification. Black star indicates A.D lineage, defined by the 72-nt duplication in the G gene. Scale bar indicates substitutions per site. B) Simplified scheme of the lineage designation to highlight the presence of nested lineages. The amino acid changes in the F glycoprotein are listed next to lineage name and colored according to their location in the fusion protein.

Figure 4

Human respiratory syncytial virus B lineages classification. A) HRSV-B maximum-likelihood phylogenetic tree (1,385 sequences), colored according to lineage classification. Black star indicates B.D lineage, defined by the 60-nt duplication in the G gene. Scale bar indicates substitutions per site. B) Simplified scheme of the lineage designation to highlight the presence of nested lineages. The amino acid changes in the F glycoprotein are listed next to lineage name and colored according to their location in the fusion protein.

Figure 5

Temporal distribution of HRSV-A and HRSV-B lineages. A total of 2,744 HRSV-A genomes and 2,443 HRSV-B genomes available in public databases through March 2023 were included. HRSV, human respiratory syncytial virus.