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. 2023 Feb;95(2):e28442.
doi: 10.1002/jmv.28442.

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

Affiliations

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

Nicole Acosta et al. J Med Virol. 2023 Feb.

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.

Keywords: COVID-19; RT-qPCR; hospital-acquired infection; prevalent; variant of concern; wastewater-based surveillance.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Daily census of COVID‐19 hospitalized individuals and SARS‐CoV‐2 RNA in hospital wastewater as a function of each variant of concern (VOC). Absolute concentration of SARS‐CoV‐2 RNA N1 signal (grey area), and the VOC proportion (%) of Delta (R203M mutation, red triangles) or Omicron (R203K/G204R mutation, blue triangles) in wastewater samples from five hospital locations: Hospital‐1, Hospital‐2, Hospital 3A, Hospital 3B; and Hospital 3C. The continuous blue and brown lines drawn through the triangle points are the lines of best fit plotted with the second order smoothing of the proportion of each mutation using GraphPad PRISM. N1 signal is presented in the left y‐axis and both VOC proportion (%) and smooth lines are presented in the first right y‐axis. Red and blue circles denote the weekly mean total number of prevalent cases for each VOC in the hospitals which is presented by the second right y‐axis. Vertical dash lines correspond to days where outbreaks were declared including the total number of individuals (i.e., patients plus health care workers) involved in each outbreak (Table 1). Asterisk denotes that for a specific outbreak more than one unit was involved. Please note that the N1 left Y‐axis scale is different for Hospital 3A. Since data in the left y‐axis is presented on a logarithmic 10 axis, it is not possible to plot nondetermined values (0)
Figure 2
Figure 2
Association between total active COVID‐19 cases and wastewater SARS‐CoV‐2 RNA from hospitals. Heatmap of the Spearman analysis between daily cases (measured as Delta‐specifically, omicron‐specifically or total cases) and wastewater signal obtained with either the N1 assay or N200 assay or VOCs specific assays (i.e., R203M [Delta] or R203K/G204R [Omicron]) from monitored sites: Hospital 1, Hospital 2, Hospital 3A, Hospital 3B; and Hospital 3C. Spearman r value is only shown for those analysis when p < 0.05. VOC, variants of concern
Figure 3
Figure 3
Association between hospital‐acquired (HA) COVID‐19 cases and wastewater SARS‐CoV‐2 signal from hospitals. Heatmap for the Spearman analysis between cases of COVID‐19 attributed to Delta, Omicron VOC and/or all active cases and wastewater signal obtained with either the N1 assay or N200 assay or VOCs specific assays (i.e., R203M [Delta] or R203K/G204R [Omicron]) from five hospital locations: Hospital 1, Hospital 2, Hospital 3A, Hospital 3B; and Hospital 3C. HA cases occurring ± 2 days were compared to wastewater signals. Spearman r value is only shown for those analysis when p < 0.05. VOC, variants of concern
Figure 4
Figure 4
SARS‐CoV‐2 abundance in hospital wastewater as a function of VOC‐related waves. SARS‐CoV‐2 RNA data from the Delta‐wave (i.e., mid‐August to end of November 2021) were compared with samples collected during Omicron‐wave (i.e., January 2022). (A) N1 SARS‐CoV‐2 RNA signal (copies/ml). (B) N1 SARS‐CoV‐2 genomic copies normalized relative to genomic copies of the fecal biomarker PMMoV. Median and interquartile ranges are indicated as the middle, top, and bottom lines of each box. Ends of the whiskers mark the lowest and highest signal determined in each category for each hospital analyzed. Differences were determined using the Mann–Whitney U test. VOC, variants of concern
Figure 5
Figure 5
Aggregate abundance of SARS‐CoV‐2 wastewater signal during Delta or Omicron as a function of outbreak status. Aggregate SARS‐CoV‐2 RNA data from the Delta‐wave (i.e., mid‐August to end of November 2021) or Omicron‐wave (i.e., January 2022) were compared from samples collected during outbreak‐free periods or within 5 days of an outbreak being declared. (A) Combined N1 SARS‐CoV‐2 RNA signal (copies/ml) and (B) Combined N1 SARS‐CoV‐2 genomic copies normalized to genomic copies of the fecal biomarker PMMoV. Median and interquartile ranges are indicated as the middle, top, and bottom lines of each box. Ends of the whiskers mark the lowest and highest signal determined in each category for each hospital analyzed. Differences were determined using the Mann–Whitney U test. VOC, variants of concern

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