Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations

Abstract

Wastewater-based epidemiology (WBE) is an emerging approach for community-wide COVID- 19 surveillance. WBE was characterized mostly at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be implemented in a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population 1,471) from January to November 2021. Community testing data showed an average of 0.004% incidence rate in these sewersheds (97% of monitoring periods reported two or fewer daily infections). In 92% of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. COVID-19 cases poorly correlated with SARS-CoV-2 N gene concentrations except for one location where frequent COVID-19 testing was required. Thus, we developed a COVID-19 warning system for high COVID-19 risk when the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (PMMOV) in wastewater is higher than 10-2. This COVID- 19 warning system now identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.5%) with 73% sensitivity and 71% specificity. Importantly, it can discern neighborhood- level outbreaks that would not otherwise be identified by county-scale WBE. We also demonstrated that SARS-CoV-2 variant-specific RT-qPCR assays could be combined with the COVID-19 warning system to identify the introduction of SARS-CoV-2 variants into sewersheds with a low COVID-19 incidence. This new COVID-19 warning system will contribute to effective community-wide disease surveillance when COVID-19 incidence may be maintained at a low level.Graphical abstract