Respiratory syncytial virus (RSV) is a leading cause of hospitalisation in infants worldwide. New immunoprophylactic products, including long-acting monoclonal antibodies and maternal vaccines, have demonstrated high efficacy in prelicensure clinical trials. Understanding how these interventions perform outside controlled trials, and how viral evolution or host factors influence protection, is essential for sustaining confidence in RSV prevention programmes.

We will conduct a 5-year, test-negative case–control study among infants ≤12 months of age who present with acute respiratory illness (ARI) within a large healthcare delivery network serving a demographically diverse population. Cases will be infants testing positive for RSV by PCR, and controls will be RSV-negative infants meeting the same ARI criteria. Data will be obtained from electronic health records, structured caregiver surveys and state immunization registries to ensure accurate classification of exposures and covariates. Vaccine effectiveness will be estimated using multivariable logistic regression controlling for potential confounding. RSV-positive specimens will undergo full-genome sequencing to identify variant lineages and potential immune-escape mutations. A subset of participants will provide acute and convalescent blood samples for single-cell immune profiling to define innate and adaptive responses associated with breakthrough infection.

The study protocol has been approved by the Yale Human Investigation Committee (HIC #2000036550). Written informed consent will be obtained from all parents or legal guardians prior to participation. Study findings will be disseminated through peer-reviewed publications, scientific meetings and public repositories, with fully de-identified participant data to protect privacy and confidentiality. Viral genomic data will be shared in accordance with the National Institutes of Health Genomic Data Sharing Policy, and analytical code will be made publicly available to ensure reproducibility.

NCT06172660.