Wastewater Detection of COVID-19

When faced with a pandemic such as SARS-Coronavirus-2 (SARS-CoV-2), the virus responsible for COVID-19, timely risk assessment and action are required to prevent public health impacts to entire communities. Because infected individuals may not have access to testing or may be asymptomatic and contraction can mean death, a proactive approach to detect the virus is needed to develop public health strategy to mitigate virus spread. Recent studies have detected SARS-CoV-2 genetic material in sewage and demonstrate a positive correlation between the concentration of viral markers and reported cases. The Coronavirus Sewershed Surveillance Project (CSSP) was a collaborative effort to monitor sewersheds for genetic indicators of COVID-19 in wastewater to provide additional, population-level information about virus circulation that is not captured by clinical testing. Untreated wastewater (influent) samples were screened weekly from select sewersheds and targeted micro-sewersheds for detection and "true" prevalence. Congregate facilities provided unique opportunities for study because they are controlled populations where the precise number and timing of infections can be defined. Detailed monitoring of congregate facilities will be utilized to define the precise per patient contribution and longevity of SARS-CoV-2 RNA to wastewater by 1) increasing the number of facilities tested, 2) altering the frequency at which samples are collected, and 3) comparing sewershed data collected to clinical patient case data. Although SARS-CoV-2 contribution/patient varies among communities, there have been clear outlier communities that produce little or no genetic material in the wastewater despite the presence of known outbreaks. The reason for this lost signal is not known, so factors that contribute to SARS-CoV-2 signal suppression in wastewater were defined by 1) defining the physical nature of the genetic material in the sewershed to better understand the types of factors that could suppress signal, 2) expanding testing within sewersheds with suppressed signal as well as from additional facilities with similar population and industry demographics as those with suppressed signal to narrow the sources of signal suppression, 3) performing exhaustive chemical characterization comparing wastewater from locations that are suppressed to those that are not to identify candidate compounds that could be causing suppression, and 4) obtaining or generating candidate inhibitors and testing their ability to suppress signal from viral genetic material in a controlled experimental setting. The utility of using wastewater RNA to determine what viral variants are circulating in a community was further examined. Towards this the research team: 1) evaluated different methods for characterizing genetic material in wastewater such as variant specific qPCR and targeted high throughput sequencing, 2) developed methods for evaluating existing and emerging variants from wastewater, and 3) designed platforms for communicating wastewater variant results to the public.