Wastewater surveillance for SARS-CoV-2: an effective approach for monitoring COVID-19 outbreak dynamics and variants emergence at the community level

Yuehan Ai
Graduate (PhD)
Jiyoung Lee
Food Science and Technology

The global pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) has resulted in more than 2.5 million deaths and 110 million confirm cases globally. Many health authorities around the world have implemented wastewater-based epidemiology as a fast and complementary tool for the COVID-19 surveillance system. In this study, three SARS-CoV-2 target genes (N1, N2, and E) were quantified from influent samples collected at 9 wastewater treatment plants (n=250 from July to December 2020), covering a metropolitan area and 7 other smaller cities in central Ohio. To determine human-specific fecal strength in wastewater samples more accurately, two human fecal viruses (PMMoV and crAssphage) were measured to normalize the SARS-CoV-2 gene concentrations in wastewater. To help estimate new case numbers from the level of SARS-CoV-2 gene, different statistic models were built and optimized. This study demonstrates the effectiveness of wastewater surveillance in COVID-19 trend tracking in various types of communities. From the longitudinal wastewater data, SARS-CoV-2 gene concentration in wastewater strongly correlated with daily new confirmed COVID-19 cases (averaged Spearman’s r = 0.70, p < 0.05). While all three primers/probe sets used in this study showed good performance, the N2 gene was found to be the best predictor of the trend of confirmed cases. In addition, we recommend using averaged daily case numbers to reduce the noise and variation from the clinical screening data. Interestingly, neither of the normalization using PMMoV or crAssphage significantly enhanced the correlation with new case numbers. This is the first study proposing the use of a quadratic polynomial model to track and predict COVID-19 cases from wastewater surveillance data, which can benefit the communities with limited human testing capability. In the later stage of the pandemic, WBE can help evaluate the effectiveness of vaccination and prioritize the distribution of human testing resources. Moreover, D614G variant was detected in our wastewater via whole-genome sequencing, which agrees with the clinical isolate from the community. This finding suggests that wastewater is an ideal matrix for tracking variant emergence and transmission within a community.