Whole-Genome Phylodynamic Analysis of Respiratory Syncytial Virus—Maryland, USA, 2018–2024

Respiratory syncytial virus (RSV) is a leading cause of respiratory infections in infants and older adults, with epidemiological patterns shaped by viral evolution and diversity. To investigate the molecular epidemiology of RSV before and after the COVID-19 pandemic, we conducted genomic surveillance and phylodynamic analyses of RSV-A and RSV-B circulating in Maryland from 2018 to 2024. Whole-genome sequencing of RSV-positive samples (n = 451) was performed, and genomes were analyzed with phylogenetic and Bayesian methods to estimate evolutionary rates, population dynamics, selection pressures, and genetic diversity. RSV-A predominated in most seasons, while RSV-B showed episodic surges in 2018 and 2023. All RSV-A genomes belonged to the ON1 genotype, and RSV-B belonged to BA9, with sequential clade dominances including A.D.1, A.D.5.2, A.D.1.6, and B.D.E.1 across different epidemic seasons in Maryland. Bayesian analyses estimated evolutionary rates of 7.07 × 10^-4 substitutions/site/year for RSV-A and 1.02 × 10^-3 substitutions/site/year for RSV-B and temporal fluctuations in effective population size linked to pandemic-related disruptions. RSV-A displayed greater overall entropy, yet RSV-B evolved slightly faster. Genetic variability was concentrated in the G glycoprotein, with positively selected sites at codon 273 (RSV-A) and codon 217 (RSV-B). These findings demonstrate temporal fluctuations in RSV-A and RSV-B predominance, clade replacement, and ongoing viral adaptation throughout the COVID-19 era, underscoring the importance of integrated genomic and phylodynamic studies.