Citywide wastewater SARS-CoV-2 levels strongly correlated with multiple disease surveillance indicators and outcomes over three COVID-19 waves

Abstract

Public health surveillance systems for COVID-19 are multifaceted and include multiple indicators reflective of different aspects of the burden and spread of the disease in a community. With the emergence of wastewater disease surveillance as a powerful tool to track infection dynamics of SARS-CoV-2, there is a need to integrate and validate wastewater information with existing disease surveillance systems and demonstrate how it can be used as a routine surveillance tool. A first step toward integration is showing how it relates to other disease surveillance indicators and outcomes, such as case positivity rates, syndromic surveillance data, and hospital bed use rates. Here, we present an 86-week long surveillance study that covers three major COVID-19 surges. City-wide SARS-CoV-2 RNA viral loads in wastewater were measured across 39 wastewater treatment plants and compared to other disease metrics for the city of Houston, TX. We show that wastewater levels are strongly correlated with positivity rate, syndromic surveillance rates of COVID-19 visits, and COVID-19-related general bed use rates at hospitals. We show that the relative timing of wastewater relative to each indicator shifted across the pandemic, likely due to a multitude of factors including testing availability, health-seeking behavior, and changes in viral variants. Next, we show that individual WWTPs led city-wide changes in SARS-CoV-2 viral loads, indicating a distributed monitoring system could be used to enhance the early-warning capability of a wastewater monitoring system. Finally, we describe how the results were used in real-time to inform public health response and resource allocation.

Keywords: COVID-19; Hospitalizations; Lead time; Positivity rate; SARS-CoV-2; Syndromic surveillance; Wastewater-based epidemiology.

Graphical abstract

Fig. 1

Positivity rate, COVID-diagnosis ED visit rate, hospital general bed use rate, and ICU bed use rate (left y-axis), and smoothed city-wide wastewater viral load (right y-axis) time series for September 1, 2020 through April 25, 2022. Positivity rate is the daily positivity rate for the City of Houston's 105 zip codes. ED visit rate is the daily rate of COVID-related emergency department visits for the Texas PH Region 6/5S. General and ICU bed rates are the daily rates of general and ICU beds in use for COVID patients for Harris County, respectively. City wastewater is the daily spline-smoothed aggregate viral load for the city of Houston. Grey shading indicates the time period included for each wave in the time-step correlation analysis.

Fig. 2

Pearson correlation coefficients for the cross correlation between disease metrics and daily spline-smoothed wastewater viral load for the city offset between −7 (lagging) and +21 (leading) days. The correlation analyses were performed using the raw daily rates for positivity, ED visit, general bed use, and ICU bed use rates. Triangles indicate correlation coefficients significantly different from zero.

Fig. 3

(A) Heatmap of the week-to-week percent change in wastewater viral load for the city-wide total and each of the 39 wastewater treatment plants. Wastewater treatment plants are ordered by population on the y-axis. Grey boxes indicate no sample was collected. (B) Wastewater viral load trends (splines) for city-wide total (top green line with 95 % confidence band in grey) and individual wastewater treatment plants. As examples, 69th Street is shown in red, Intercontinental Airport in dark orange, and Clinton Park in light orange. Black markers indicate the minimums for the city total and each site leading up to each wave. Dotted line indicates the date of the city-wide total minimum. Grey shaded areas indicate the date ranges corresponding to each wave.