Genomic Surveillance Uncovers a Shift in Respiratory Syncytial Virus Subtype Dominance and the Local Expansion of Subclade B.D.E.1.7

Abstract

Abstract Background Respiratory syncytial virus (RSV) is a leading cause of hospitalization among children under 5 and adults over 60 due to its ability to cause acute respiratory illness. Recent approvals of vaccines and monoclonal antibodies against RSV have raised concerns about the potential of prophylactic-evading viral mutations. Method We analyzed 126 RSV-positive nasopharyngeal swabs from Boston Medical Center during the 2024–2025 respiratory season via amplicon-based whole-genome sequencing. We identified nucleotide variants, assigned clades, and built maximum-likelihood phylogenetic trees to examine genetic changes and evolution. Results Out of the 126 genomes analyzed, 94 (74.6%) were RSV-A subtype, indicating a return to RSV-A dominance in the region. Within the RSV-B genomes, a large minority belong to the recently defined B.D.E.1.7 subclade (n = 12, 37.5% of RSV-B samples), which has only appeared sporadically in other US states. Mutations associated with monoclonal antibody or vaccine resistance were not observed. Conclusions These findings show that in the Boston metropolitan area, RSV subtype dominance continues to flip between seasons. Investigation of the clades within both subtypes did not reveal evidence of any virus seeding from the preceding season. Though no mutations associated with prophylactic resistance were identified, surveillance of RSV remains critical to study evolution and transmission dynamics, particularly at the local level.