Functional Characterization of RSV Clades Associated with Prophylactic Breakthrough Infections in Pediatric Transmission Clusters

Abstract

The recent development of new respiratory syncytial virus (RSV) prophylactics for the prevention of severe lower respiratory tract infections in infants and older adults promises in lowering disease burden in these vulnerable populations. However, it remains unclear if periodic breakthrough infections in these populations may drive the emergence of resistant isolates or clades and what factors might contribute to these breakthroughs. In this retrospective cohort study, we performed whole-genome sequencing of RSV isolates from infants and adults during the past two RSV seasons (2023-2025) to assess viral and clinical correlates of nirsevimab breakthrough. RSV infections from nirsevimab breakthrough cases were associated with less severe clinical outcomes in the first, but not second, season after administration. While breakthrough isolates did not share any Fusion glycoprotein mutations in predicted antigenic sites, they largely belonged to only a few circulating clades that were responsible for driving temporally distinct pediatric transmission clusters. To determine if these transmission clusters and breakthrough infections were in part driven by differences in the Fusion proteins of these clades, we compared the relative fusogenicity and neutralization susceptibility of Fusion proteins from contemporary circulating clades. Notably, RSV-A clade A.D.3 exhibited modestly reduced susceptibility to nirsevimab neutralization, though it wasnt associated with any transmission clusters or breakthrough infections. Collectively, these data suggest that clade associations with prophylactic breakthrough are driven by pediatric transmission clusters rather than clade-associated resistance, though continued surveillance will be vital as prophylactic coverage continues to rise.