Detecting and supporting COVID-19 outbreak response in a small-scale nursing home through passive wastewater surveillance of SARS-CoV-2

Passive wastewater sampling has emerged as a cost-effective approach for pathogen monitoring, but its application in very small populations has not been well studied. This study reports the use of tampons as passive samplers in a small-scale nursing home of 24 residents to detect respiratory viruses, including SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus (RSV). Weekly wastewater surveillance by reverse transcription digital PCR (RT-dPCR) for a 1-year period resulted in a cluster of consecutive SARS-CoV-2 detections over 4 weeks. When wastewater SARS-CoV-2 concentrations reached higher levels in the third and fourth weeks, whole-genome sequencing achieved >98% genome coverage, identifying lineage LB.1.5, while lower-concentration samples produced only partial genomes. Clinical testing was initiated in the fourth week when clinical symptoms also emerged, and confirmed SARS-CoV-2 infection in 15 of 24 residents and staff. Sequencing of the clinical samples confirmed LB.1.5 in 11 cases, corroborating the wastewater findings. Influenza A subtypes H3N2 and H1N1 were additionally detected in wastewater by targeted enrichment sequencing, and RSV was detected once by RT-dPCR, neither of which was associated with confirmed clinical cases. These results demonstrate that wastewater surveillance can precede clinical symptoms for early detection, and passive sampling using tampons is a practical and sensitive strategy for outbreak surveillance in small-scale facilities. The study also highlights the need for clear response protocols that include rapid clinical testing and cohorting measures when wastewater viral concentrations exceed defined thresholds.IMPORTANCENursing homes are among the highest-risk settings for infectious disease outbreaks, yet early detection remains challenging due to the high prevalence of asymptomatic infections and limited resources for routine clinical surveillance. This study demonstrates that inexpensive tampon-based passive wastewater samplers can detect SARS-CoV-2 up to 3 weeks before clinical symptoms emerge in a nursing home with only 24 residents, which is the smallest population in which this method has been validated. Wastewater-derived genomes matched clinical sequencing quality, enabling identification of a novel SARS-CoV-2 lineage new to Hawai'i. These findings support passive wastewater surveillance as a practical early warning tool for small congregate care facilities, provided that clear institutional response protocols are in place.