Abstract
BACKGROUND: The COVID-19 pandemic resulted in multiple waves of infections in New York City, driven by evolving SARS-CoV-2 variants and shifting vaccine eligibility. We describe the trends in SARS-CoV-2 epidemiology in adults and children over consecutive waves during the height of the COVID-19 pandemic in New York City. METHODS: A retrospective observational cohort study was performed in adults and children who were tested for SARS-CoV-2 by PCR in a multi-hospital network in New York City from 10/1/2020 to 9/19/2022. Positivity rates and vaccination rates were determined over multiple waves of infections. A subset of nasopharyngeal specimens underwent whole genome sequencing to determine the SARS-CoV-2 variant distribution in adults and children. RESULTS: There were 243,457 SARS-CoV-2 PCR tests performed in adults (89.2%) and 29,333 in children (10.8%) with overall positivity rates of 6.2% in adults and 5.9% in children during the study period. The highest overall positivity rate (12.1%) was seen during Wave 4 when the Omicron variant was predominant and positivity rates in children surpassed those in adults for the first time (children 15.6%, adults 11.7%, p < 0.001). During Wave 4, SARS-CoV-2 positivity was associated with pediatric age (aOR 1.13, 95% CI 1.02, 1.25), non-White race (aOR 1.36, 95% CI 1.26, 1.47), Hispanic ethnicity (aOR 1.53, 95% CI 1.38, 1.69), and unvaccinated status (aOR 1.48, 95% CI 1.38, 1.58). SARS-CoV-2 variant distribution did not differ over time between adults and children. CONCLUSIONS: Our large cohort of SARS-CoV-2 PCR testing over multiple COVID-19 waves in New York City demonstrated a shift in positivity rates when the Omicron variant was predominant, with disproportionate positivity in children, unvaccinated individuals, and specific racial and ethnic groups. As vaccination rates decline in response to changes in vaccine recommendations, this scenario may recur with the emergence of a new virulent SARS-CoV-2 variant or re-emergence of vaccine-preventable diseases. These findings highlight the need for targeted public health strategies that prioritize vulnerable populations during respiratory viral surges. CLINICAL TRIAL: Not applicable. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11990-4.