HRSV has a single-stranded nonsegmented negative-sense RNA genome ≈15,191–15,277 nt long (Figure 2, panel A) (7). The HRSV genome contains 10 genes, each encoding a separate mRNA with a single open reading frame (ORF) (Figure 2, panel A; Table), except for the M2 mRNA, which contains 2 overlapping ORFs. The 11 HRSV proteins are 2 nonstructural proteins (NS1 and NS2), nucleoprotein (N), phosphoprotein (P), matrix protein (M), small hydrophobic envelope protein (SH), attachment glycoprotein (G), fusion glycoprotein (F), the transcription processivity factor (M2–1), RNA regulatory factor (M2–2), and large RNA polymerase protein (L) (Table) (24,25). The F glycoprotein is the major viral neutralization and protective antigen, followed by the G glycoprotein (26).

HRSV subgroups A and B exhibit genomewide nucleotide and amino acid divergence (Figure 2, panel A) (25,27). The reference sequences for the 2 subgroups are derived from strains HRSV A2 (28–31; GenBank accession number M74568.1; RefSeq accession number NC_038235) and HRSV B1 (32; GenBank accession number AF013254.1; RefSeq accession number NC_001781.1; Figure 2, panel B). F glycoprotein sequences between the 2 subgroups are well conserved (89% aa identity), whereas the G glycoproteins are the most divergent (53% aa identity between the subgroups) among the HRSV proteins (Figure 2, panel A) and undergo continuous molecular evolution. The ectodomain of the G glycoproteins of both subgroups contains a conserved central domain, representing an important antigenic site, flanked by 2 hypervariable domains (33). Except for the central conserved region, the antigenic cross-reactivity between G glycoproteins of the 2 subgroups is low (26).

Because the G ORF exhibits the greatest degree of genetic variability between isolates, it is most commonly used for studies on the molecular evolution of HRSV. The genetic variability of HRSV strains over time has been commonly determined by sequencing the distal C-terminal third of the G ORF, which includes the second hypervariable domain. The variability in the G ORF is characterized by a high rate of nonsynonymous nucleotide changes, suggesting that evolution may be driven by immune pressure, even though this factor may be partially antibody independent (34). It is likely that variability in the G protein contributes to the capacity of HRSV to cause yearly outbreaks in the community (35–37). The nomenclature proposal outlined herein will be useful for the sequence analyses required to follow the molecular evolution of HRSV.

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. HRSV genotyping designations will need to capture present molecular evolutionary status and be adaptable to changes and will need to be reevaluated periodically by a global consortium.

For molecular epidemiology studies, a concise standard for short identifiers of specific HRSV sequences, suitable for the short definition lines that give context to a sample and its derived sequence, would be useful. Ideally, concise standardized identifiers should convey key information about each individual sequence in an alignment or phylogram, including source, date, and type, if known. Here, we aim to define this type of common naming convention for HRSV samples and isolates. We also propose using standard names and appropriate annotations for HRSV genes, provide examples to guide the annotation of sequence data during the sequence submission process, and suggest how to submit metadata associated with the source materials of HRSV sequences.

GenBank records available through the National Center for Biotechnology Information (NCBI) are identified by 2 elements: a unique alphanumeric accession number and a definition line. The definition line is the portion of the identifier commonly associated with GenBank records shown in BLAST results and other searches. Definition lines are generated by the submitter during the sequence submission process and include the species and isolate name (e.g., Human orthopneumovirus isolate HRSV/A/USA/001/2011, complete genome [proposed]). (40). We propose a standardized format to capture 5 sample-specific parameters of HRSV-positive clinical samples or isolates to be included in sequence definition lines compatible with database naming requirements (Figure 3), in this specific order: [virus name abbreviation]/[HRSV subgroup]/[geographic identifier]/[unique sequence identifier]/[year of sampling].

To support efficient data analysis, uniform designations must be used at the database submission stage. Commonly accepted names for HRSV genes and proteins are shown in the table. An HRSV gene comprises a gene start signal GGGGCAAAT(A/G), an ORF with adjacent noncoding regions, if present, and the gene end signal through the last adenosine residue [AGT(T/A)A(T/A/G)(A/T)(A/T)(A/T)A_n] (Figure 4; 41). Each HRSV gene contains a single ORF, except for the M2 gene, which has 2 overlapping ORFs, M2–1 and M2–2. Nucleotide annotations of genes and ORFs for the HRSV A2 (Figure 4) and HRSV B1 reference sequences are shown in the table.

What is the most pertinent host data will depend on the interests and objectives of individual study groups. For example, when studying HRSV in a pediatric setting, prematurity may be of interest, but when studying HRSV in an adult setting, researchers may be more interested in whether participants are immunocompromised. We suggest information that could be included in metadata fields for HRSV:

Molecular surveillance has revealed that multiple HRSV genotypes circulate simultaneously in communities. Circulating genotypes often vary between communities, and circulation patterns within a community can change from year to year. Extended monitoring of circulating viruses is necessary to better understand transmission and molecular evolution (42). As HRSV vaccine candidates and antivirals are being developed, molecular epidemiology studies may reveal potential effects of prevention strategies on viral evolution and possible antibody-escape variants. Timely sharing of HRSV data worldwide through the use of public databases is essential. We propose that sequence data be uploaded to publicly accessible databases, such as NCBI (31). Although NCBI is the most complete repository for HRSV sequence information, studies may require that sequences first be submitted to other databases, such as GISAID (https://www.gisaid.org).

Public access will provide useful availability for investigators to submit, query, and analyze HRSV sequence data, enabling the evolutionary analysis of sequence diversity within or between HRSV genotypes. The utility of public access has been clearly demonstrated with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the critical role that genetic sequence analysis has played. Notably, a nomenclature model for SARS-CoV-2 similar to what we have proposed for HRSV has been adopted, although some differences remain between databases (e.g., NCBI, SARS-CoV-2/human/USA/COVID20–1096/2020; GISAID, hCoV-19/Australia/VIC12/2020). When an HRSV vaccine becomes available, high-quality, geographically representative, country-specific data on circulating strains and rich datasets of well-curated, standardized, and parsable data will be required to monitor and trace possible evolutionary changes in response to vaccine-induced selective pressure (43,44). This proposal will profit from strong support by members of the International RSV Society, a special interest group of the International Society for Influenza and other Respiratory Virus Diseases (https://isirv.org), members of the WHO Global RSV Surveillance Project, and the HRSV research community.

Background genomic sequencing information on human respiratory syncytial virus.