Genomic surveillance of Respiratory Syncytial Virus in Arizona (2021-2023)
Respiratory Syncytial Virus (RSV) is a highly contagious RNA virus that commonly infects both infants and the elderly. While most cases cause minor upper respiratory symptoms, RSV can also lead to severe lower respiratory infections, often requiring hospitalization and intensive care. Despite RSV being a common pathogen, our understanding of its transmission patterns within Arizona’s at-risk populations remains limited. To address this knowledge gap, we applied genomic epidemiology to RSV cases across Arizona, analyzing transmission dynamics, importation events, and viral evolutionary patterns. We performed next-generation whole genomic sequencing of 180 RSV samples — 28 RSV-A subtypes and 152 RSV-B subtypes – and conducted a phylogenetic analysis with all available published RSV sequences. Our findings revealed the mutation rates of ~6 * 10-4 substitutions/site/year for RSV-A and ~7 * 10-4 substitutions/site/year for RSV-B, comparable to SARS-CoV-2. We conclude that the RSV peaks in Arizona from 2021 to 2023 peaks were driven by both local spread of unique state specific genotypes and numerous introductions. With the recent release of new vaccines and monoclonal treatments, we hypothesize that RSV’s evolutionary patterns will shift to evade monoclonal antibodies and vaccine protection, making genomic surveillance crucial in today’s world to accurately detect viral introductions, guide strategic healthcare response planning and therapeutic approaches.