Wastewater Monitoring of SARS-CoV-2 from Acute Care Hospitals Identifies Nosocomial Transmission and Outbreaks

Acosta, N.; Bautista, M.; Hollman, J.; McCalder, J.; Buchner Beaudet, A.; Man, L.; Waddell, B. J.; Chen, J.; Li, C.; Kuzma, D.; Bhatnagar, S.; Leal, J.; Meddings, J.; Hu, J.; Cabaj, J.; Ruecker, N. J.; Naugler, C.; Pillai, D. R.; Achari, G.; Ryan, M. C.; Conly, J. M.; Frankowski, K.; Hubert, C. R.; Parkins, M. D.

Background: SARS-CoV-2 has been detected in wastewater and its abundance correlated with community COVID-19 cases, hospitalizations and deaths. We sought to use wastewater-based detection of SARS-CoV-2 to assess the epidemiology of SARS-CoV-2 in hospitals. Methods: Between August and December 2020, twice-weekly wastewater samples from three tertiary-care hospitals (totalling >2100 dedicated inpatient beds) were collected. Wastewater samples were concentrated and cleaned using the 4S-silica column method and assessed for SARS-CoV-2 gene-targets (N1, N2 and E) and controls using RT-qPCR. Wastewater SARS-CoV-2 as measured by quantification cycle (Cq), genome copies and genomes normalized to the fecal biomarker PMMoV were compared to the total daily number of patients hospitalized with active COVID-19, confirmed cases of hospital-acquired infection, and the occurrence of unit-specific outbreaks. Results: Of 165 wastewater samples collected, 159 (96%) were assayable. The N1-gene from SARS-CoV-2 was detected in 64.1% of samples, N2 in 49.7% and E in 10%. N1 and N2 in wastewater increased over time both in terms of amount of detectable virus and the proportion of samples that were positive, consistent with increasing hospitalizations (Pearsons r=0.679, P<0.0001, Pearsons r=0.728, P<0.0001, respectively). Despite increasing hospitalizations through the study period, wastewater analysis was able to identify incident nosocomial-acquired cases of COVID-19 (Pearsons r =0.389, P<0.001) and unit-specific outbreaks by increases in detectable SARS-CoV-2 N1-RNA (median 112 copies/ml) versus outbreak-free periods (0 copies/ml; P<0.0001). Conclusions: Wastewater-based monitoring of SARS-CoV-2 represents a promising tool for SARS-CoV-2 passive surveillance and case identification, containment, and mitigation in acute- care medical facilities.