A Multicenter Study Investigating SARS-CoV-2 in Tertiary-Care Hospital Wastewater. Viral burden correlates with increasing hospitalized cases as well as hospital-associated transmissions and outbreaks

Acosta, Nicole; Bautista, María A.; Hollman, Jordan; McCalder, Janine; Beaudet, Alexander Buchner; Man, Lawrence; Waddell, Barbara J.; Chen, Jianwei; Li, Carmen; Kuzma, Darina; Bhatnagar, Srijak; Leal, Jenine; Meddings, Jon; Hu, Jia; Cabaj, Jason L.; Ruecker, Norma J.; Naugler, Christopher; Pillai, Dylan R.; Achari, Gopal; Ryan, M. Cathryn; Conly, John M.; Frankowski, Kevin; Hubert, Casey RJ; Parkins, Michael D.

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. Between August and December 2020, twice-weekly wastewater samples from three tertiary-care hospitals (totaling >2100 dedicated inpatient beds) were collected. Hospital-1 and Hospital-2 could be captured with a single sampling point whereas Hospital-3 required three separate monitoring sites. 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. 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 the amount of detectable virus and the proportion of samples that were positive, consistent with increasing hospitalizations at those sites with single monitoring points (Pearson's r=0.679, P<0.0001, Pearson's r=0.799, P<0.0001, respectively). Despite increasing hospitalizations through the study period, nosocomial-acquired cases of COVID-19 (Pearson's r =0.389, P<0.001) and unit-specific outbreaks were discernable with significant increases in detectable SARS-CoV-2 N1-RNA (median 112 copies/ml) versus outbreak-free periods (0 copies/ml; P<0.0001). 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.