Expanded Genomic Surveillance and Seasonal Comparisons of Human Respiratory Syncytial Virus Infections in Minnesota, USA, 2023–2025

BACKGROUND: Human respiratory syncytial virus (HRSV) imposes a substantial burden in the United States. The use of whole-genome sequencing (WGS) for public health surveillance of HRSV lags that for other viral pathogens. The objective of this study was to expand the scope and depth of WGS-based surveillance of HRSV in Minnesota, USA. METHODS: HRSV-positive specimens collected from outpatients and inpatients from July 2023 to April 2025 were submitted to the Minnesota Public Health Laboratory for WGS. Genomes were sequenced using a tiled amplicon approach, characterized by lineage, phylogenetically compared to those from prior surveillance, and searched for mutations reported to affect monoclonal antibody susceptibility or fusion (F) protein function. Data from surveillance of HRSV-associated hospitalizations were incorporated for epidemiological analysis. RESULTS: Continuing WGS through 2025 generated 2975 HRSV genomes. Compared to those from 2023 to 2024, genomes from the 2024-2025 season were collected from greater proportions of patients with HRSV-associated hospitalizations, of older age, and from a broader geographical distribution. Subgroups A and B both exhibited significant differences in total genetic diversity by season (p < 0.001). Twenty subclades and lineage A.D.5.4 were not observed during the 2024-2025 season. F protein mutations were identified at 15 amino acid positions of epidemiological concern, of which 11 emerged homoplastically. Genomes from 39 hospitalized patients carried at least one of these mutations. CONCLUSIONS: Continuing WGS-based HRSV surveillance across multiple respiratory seasons yielded valuable insights into the emergence and evolution of viral lineages and the prevalence of mutations of concern among outpatient and inpatient infections.