Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments

Abstract

We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1700 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a 10 month time period that overlapped with October 2020 and winter/spring 2021 COVID-19 outbreaks in each municipality. We fit lagged regression models to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Lags of 0 to 1 days resulted in the greatest predictive power for the model. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. The close relationship between case rates and SARS-CoV-2 concentrations demonstrates the utility of using primary sludge samples for monitoring COVID-19 outbreak dynamics. Estimating case rates from wastewater data can be useful in locations with limited testing availability, testing disparities, or delays in individual COVID-19 testing programs.

Keywords: SARS-CoV-2; case rate estimation; lagged regression analysis; primary sludge; quantitative PCR; wastewater-based epidemiology.

Figure 2.

Comparison between COVID-19 case rates by day of clinical specimen collection and estimated case rates using RNA concentrations lagged from 0 to 4 days. The model is depicted by a solid line, measured cases are grey bars, and 95% prediction intervals are shown by shading and the dotted lines.

Figure 1.

(top) Daily SARS-CoV-2 RNA concentrations in primary sludge of the six WWTP's considered in this study. (bottom) Daily COVID-19 cases by date of specimen collection per 100,000 residents for the cities and towns served by the above wastewater treatment plants.