Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations

Abstract

Curtailing the Spring 2020 COVID-19 surge required sweeping and stringent interventions by governments across the world. Wastewater-based COVID-19 epidemiology programs have been initiated in many countries to provide public health agencies with a complementary disease tracking metric and non-discriminating surveillance tool. However, their efficacy in prospectively capturing resurgences following a period of low prevalence is unclear. In this study, the SARS-CoV-2 viral signal was measured in primary clarified sludge harvested every two days at the City of Ottawa's water resource recovery facility during the summer of 2020, when clinical testing recorded daily percent positivity below 1%. In late July, increases of >400% in normalized SARS-CoV-2 RNA signal in wastewater were identified 48 h prior to reported >300% increases in positive cases that were retrospectively attributed to community-acquired infections. During this resurgence period, SARS-CoV-2 RNA signal in wastewater preceded the reported >160% increase in community hospitalizations by approximately 96 h. This study supports wastewater-based COVID-19 surveillance of populations in augmenting the efficacy of diagnostic testing, which can suffer from sampling biases or timely reporting as in the case of hospitalization census.

Keywords: COVID-19; Resurgence; SARS-CoV-2; Virus; Wastewater-based epidemiology; Wave.

Graphical abstract

Fig. 1

Bird's-eye view of the Ottawa WRRF, with the primary clarifiers identified.

Fig. 2

Ct values of the SARS-CoV-2 N1 and N2 gene regions, and the PMMoV normalization gene (1:10 dilution shown), outlining the low variability of PMMoV, justifying its use as a normalization gene. The 10th and 90th percentile are displayed, along with the median (dotted line inside shapes). The variance of the different targets is also shown at the top.

Fig. 3

Epidemiological metrics and SARS-CoV-2 viral concentrations over the study period; a) COVID-19-caused hospitalizations, b) percent test positivity (7-day mid-point floating average), c) percent test positivity and d) number of new daily cases, along with e) wastewater SARS-CoV-2 N1 and N2 gene copies/PMMoV gene copies. Open data points signify points which were below the limit of quantification. The dotted line in the background represents the number of daily clinical tests/100 K pop. Performed.

Fig. 4

Figure of the new daily cases epidemiological metric (in red) with SARS-CoV-2 viral RNA signal in Ottawa's primary clarified sludge samples, with the precedence of SARS-COV-2 viral signal in wastewater clearly outlined. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)