Genomic Epidemiology and Evolution of Rhinovirus in Western Washington State, 2021–2022

Abstract

Abstract Background Human rhinoviruses (RVs) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in individuals who are immunocompromised. To date, therapeutic strategies have been hindered by the high diversity of serotypes. Global surveillance efforts have traditionally focused on sequencing VP1 or VP2/VP4 genetic regions, leaving gaps in our understanding of RV genomic diversity. Methods We sequenced 1078 RV genomes from nasal swabs of symptomatic and asymptomatic individuals to explore viral evolution during 2 epidemiologically distinct periods in Washington State: when the COVID-19 pandemic affected the circulation of other seasonal respiratory viruses except for RV (February–July 2021) and when the seasonal viruses reemerged with the severe outbreak of respiratory syncytial virus and influenza (November–December 2022). We constructed maximum likelihood and BEAST phylodynamic trees to characterize intragenotype evolution. Results We detected 99 of 168 known genotypes and observed intergenotypic recombination and genotype cluster swapping from 2021 to 2022. We found a significant association between the presence of symptoms and viral load but not with RV species or genotype. Phylodynamic trees, polyprotein selection pressure, and Shannon entropy revealed cocirculation of divergent clades within genotypes with high amino acid constraints throughout the polyprotein. Conclusions Our study underscores the dynamic nature of RV genomic epidemiology within a localized geographic region, as >20% of existing genotypes within each RV species cocirculated each studied month. Our findings also emphasize the importance of investigating correlations between RV genotypes and serotypes to understand long-term immunity and cross-protection.