Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.

TitleNovel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.
Publication TypeJournal Article
Year of Publication2022
AuthorsChen, J, Qiu, X, Avadhanula, V, Shepard, SS, Kim, D-K, Hixson, J, Piedra, PA, Bahl, J
JournalInfluenza Other Respir Viruses
Volume16
Issue3
Pagination492-500
Date Published2022 May
ISSN1750-2659
KeywordsChild, Child, Preschool, Genotype, Humans, Infant, Phylogeny, Respiratory Syncytial Virus Infections, Respiratory Syncytial Virus, Human, Sequence Analysis
Abstract

BACKGROUND: Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition.METHODS: We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances.RESULTS: In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored.CONCLUSIONS: This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.

DOI10.1111/irv.12936
Alternate JournalInfluenza Other Respir Viruses
PubMed ID34894077
PubMed Central IDPMC8983899
Grant ListU19 AI144297 / AI / NIAID NIH HHS / United States