Surveillance for SARS‐CoV‐2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks

Abstract

Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR.Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.

Wastewater-Based Surveillance of Respiratory Syncytial Virus Epidemic at the National Level in Finland

“…The correlation between viral RNA in wastewater and disease cases, as well as the capability of WBS to predict cases, has also been shown with other viruses in addition to RSV. Multiple studies have shown that the amount of SARS-CoV-2 RNA in wastewater is correlated with the number of COVID-19 disease cases. − The correlation between wastewater and clinical cases has also been found for the influenza virus. ,, In Finland in the same WWTPs, the correlation coefficient of influenza A RNA in wastewater and the incidence of influenza A (CC = 0.427–0.870) were shown to be similar to the RSV correlation measured in our study (CC = 0.412–0.865) . The study was conducted using the same WWTPs used in this study.…”

Is a new COVID‐19 wave coming from China due to an unknown variant of concern? Keep calm and look at the data

“…Thus, it is plausible that the huge amount of cases currently observed in China are due to the Omicron strain and not to any other variants. 13 Moreover, returning to the data on the spread of the variants of concern, from the first published studies, XBB does not seem to have particular aggressiveness or the strength to become dominant in Europe (see Figure 1A). Although both globally present since last September, BQ.1 and XBB have spread very differently in the world population.…”

Spatially-resolved wastewater-based surveillance enables COVID-19 case localization across a university campus, and confirms lower SARS-CoV-2 RNA burden relative to the surrounding community

“…Sample processing and RNA extraction was performed following established workflows. 11, 12, 22, 23 In brief, 40mL of thoroughly mixed wastewater subsamples was added to 50mL falcon tubes prefilled with 9.5 g of sterile NaCl and 400ul of TE buffer and were then spiked with 200µL of Bovine Coronavirus (BCoV) (final concentration: 5×10 5 50% tissue-culture-infective dose (TCID 50 ) per mL) as an internal control and vortexed for 30 seconds. Solids were then removed via vacuum filtration through a 5 µm polyvinylidene difluoride membrane, where samples were filtered directly into 40ml of 70% ethanol.…”

“…In this way, each PID was often counted multiple times in situations where the person visited multiple locations or one location on multiple days during the monitoring period. As the majority of SARS-CoV-2 RNA shedding occurs in the few days before and after symptom onset 12, 22 , the visits ± 2 days of the ‘date of onset of symptoms’ were considered valid, otherwise excluded in the following analysis. Total affected-visits is named ‘number of cases’.…”