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

Abstract

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.

Tracking Emergence and Spread of SARS-CoV-2 Omicron Variant in Large and Small Communities by Wastewater Monitoring in Alberta, Canada

“…We confirmed this finding by screening the wastewater samples from this study by using a separate assay that targets a D3L mutation in the nucleocapsid gene of the Alpha variant ( 23 ). We quantified total SARS-CoV-2 levels separately with widely used universal assays targeting the N1 and N2 regions of the nucleocapsid gene in the wild-type virus ( 3 , 4 ) and all other VOCs identified to date. We triplexed N200 assays for Omicron, Delta, and total SARS-CoV-2 together so we could estimate an Omicron-to-Delta ratio in each wastewater sample using the Omicron signal (R203K-G204R assay) and the Delta signal (R203M assay) (M. Fuzzen et al, unpub.…”

“…We applied the same method consistently at a given sampling site throughout the entire study period. We processed wastewater samples from 3 (22). We confirmed this finding by screening the wastewater samples from this study by using a separate assay that targets a D3L mutation in the nucleocapsid gene of the Alpha variant (23).…”

“…Measuring levels of RNA from SARS-CoV-2 in sewage samples began to be used as a complementary surveillance tool early in the pandemic, resulting in hundreds of wastewater COVID-19 monitoring groups and online dashboards around the world, including in Alberta ( https://covid-tracker.chi-csm.ca ), a jurisdiction of 4.5 million persons in western Canada. This strategy is premised on the fecal shedding of SARS-CoV-2 by infected persons ( 1 , 2 ) and modifies quantitative reverse transcription PCR (qRT-PCR) workflows used for diagnosing patients to quantify viral RNA in sewage sampled at wastewater treatment plants or other nodes within the sewer network ( 3 – 5 ) at regular intervals. Teams in Alberta and elsewhere demonstrated during pandemic waves that wastewater is a leading indicator of COVID-19; results typically precede clinically diagnosed cases by 4–6 days ( 6 – 9 ).…”

Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring

“…Omicron and Delta were the only two variants detected in Alberta by clinical screening during the study period (Alberta Health, 2022). Total SARS-CoV-2 levels were quantified with widely used universal assays targeting the N1 & N2 regions of the nucleocapsid gene in the wild type virus (Acosta et al 2021a, b) and all other VOCs identified to date. Omicron, Delta and total SARS-CoV-2 assays were triplexed together enabling an Omicron-to-Delta ratio to be estimated in each wastewater sample using the Omicron signal (R203K-G204R assay) and the Delta signal (R203M assay).…”

“…Measuring levels of RNA from SARS-CoV-2 in sewage samples began being used as a complementary surveillance tool early in the pandemic, resulting in hundreds of wastewater COVID-19 monitoring groups and online dashboards around the world (Naughton et al 2021), including in Alberta (https://covid-tracker.chi-csm.ca). This strategy is premised on the fecal shedding of SARS-CoV-2 by infected individuals (Cevik et al 2021; Yuan et al 2021) and enabled by modifying RT-qPCR workflows used for diagnosing patients to quantify viral RNA in sewage sampled at wastewater treatment plants (WWTPs) or other nodes within the sewer network (Acosta et al 2021a, b; Qiu et al 2022) at regular intervals. Teams in Alberta and elsewhere demonstrated during pandemic waves that wastewater is a leading indicator of COVID-19, with results typically preceding clinical diagnosed cases by 4-6 days (e.g., D’Aoust et al 2021, Medema et al 2020; Nemudryi et al 2020; Randazzo et al 2020).…”