Tracking COVID-19 in Wastewater

 SARS-Co-V2 Wastewater Data Dashboard 

Erie County’s COVID-19 / wastewater project is a partnership between the County, the University at Buffalo (UB), and various municipal partners. Starting in September 2020, wastewater samples were collected twice a week at seven (7) locations representing the largest sewer systems within Erie County, and those samples have been sent to a laboratory managed by the UB School of Engineering and Applied Sciences. Beginning in March 2023, an additional three (3) locations for the next largest sewer systems in Erie County were added to this program as part of the “ NYS Wastewater Surveillance Network ”. At UB’s laboratory, the wastewater samples are tested to assist with understanding the prevalence of COVID-19 in our community.

There is a lot that can be learned from human wastes. Doctors order health tests to analyze urine or stool as means of gathering information on the health of their patients. In a similar way, Erie County is using wastewater to gather information on the health of the community.

Research has shown humans “shed” the virus causing COVID-19 (the SARS-CoV-2 virus) in their stool when infected individuals use the bathroom. The used water and wastes from bathrooms (and other sources) in most populated areas in Erie County are ultimately collected in sewer systems. This “wastewater” may be sampled and the amount of SARS-CoV-2 virus in the sample can be quantified. Using these wastewater data, statistical relationships can be formed to help understand the prevalence of COVID-19 in the community.

UB engineers use equipment to process and test the wastewater to detect the number of virus “fragments” in the sample. These virus fragments are genetic material in the form of ribonucleic acid or RNA. Each virus strain has unique RNA characteristics that allows it to be distinguished from other viruses. Using specialized technologies, a virus “signal” is established using quantitative polymerase chain reaction or qPCR techniques, similar to a nasal swab test. The virus signal is used to quantify the amount of the SARS-CoV-2 virus fragments in the sample. Two different sections of the virus gene may be used for detection, with the “N2” region now recommended by the CDC as the standard for comparison for highly sensitive detection of SARS-CoV-2. Prior to spring 2022, both “N1” and “N2” regions were analyzed as part of this project.

Scientists at UB have developed a standard method to detect the SARS-CoV-2 virus from wastewater using best available practices from researchers across the country and knowledge gained from the Erie County project. Wastewater samples are filtered to collect viral RNA and researchers use a bovine coronavirus (BCoV) as a positive control and other commonly found viruses, like Pepper Mild Mottle Virus (PMMoV), to account for the amount of waste present. The viral RNA is then extracted and analyzed using qPCR techniques. The results are reported as copies of the SARS-CoV-2 virus per liter of wastewater analyzed.r

In a sewer system, there are pipes in the ground that collect wastewater from homes, businesses, and other buildings. Pipes from various areas will connect to other pipes, ultimately conveying the combined flows to a centralized location. The overall geographical area serviced by the network of pipes upstream of that centralized location is referred to as a “sewershed”.

A wastewater sample taken at the centralized location provides general information on the individuals in that sewershed. The number of virus fragments in a sample can be used to calculate the “concentration” of virus based on the known volume of the wastewater, expressed as copies of the SARS-CoV-2 virus per liter of wastewater. This concentration may be used to establish a relationship regarding the relative prevalence of COVID-19 in the sewershed. The higher the concentration, the higher rate of COVID-19 infection in the area served by that sewer system.

Let’s be frank, everyone uses the bathroom, but not everyone can be tested for COVID-19. Erie County’s COVID-19 / wastewater project provides widespread, anonymous information on the health of the individuals within an area, without having to perform extensive individual testing. The data collected through the wastewater project captures information on local residents that are both COVID-19 symptomatic (i.e. those exhibiting signs of sickness), as well as those that are asymptomatic (i.e. appear to be healthy, but are infected and could spread the disease). With the increase in frequency of at-home tests for which results often are not reported to authorities, the wastewater project data has become more and more valuable over time to understand COVID-19 trends in the community.

The use of wastewater data for COVID-19 is an emerging area of research. There are some academic studies that suggest the SARS-CoV-2 virus may be shed by infected individuals before they exhibit signs of sickness. This means the wastewater data may be a “leading indicator” of an increase in COVID-19 infections in the community – potentially allowing public health professionals to better deploy resources or services in an attempt to mitigate the spread of the disease before positive cases are reported.

Starting in Spring 2021, a collaboration between scientists in UB Engineering and UB’s Jacobs School of Medicine and Biomedical Sciences led to the development of methods to perform whole genome sequencing of SARS-CoV-2 from wastewater samples collected as part of this project. Wastewater sequencing is performed at UB’s Genomics and Bioinformatics Core and provides a picture of the SARS-CoV-2 variants present in our community. As PCR testing of individuals has decreased and at-home rapid antigen testing has increased, wastewater testing and sequencing has become increasingly important for public health information. This approach also captures health information from a significantly higher number of people than analysis using nasal swabs from individuals.

In Fall 2021, the New York State Department of Health (NYSDOH) announced it was promulgating additional sampling programs across New York State. The NYSDOH has termed this as the “ NYS Wastewater Surveillance Network ” and has developed its own dashboard. Data from Erie County’s program have been incorporated into this Network as well. Having a Statewide system monitoring wastewater for the presence of SARS-CoV-2 will present more comprehensive information on the prevalence of COVID-19. The statewide effort includes SARS-CoV-2 whole genome sequencing from wastewater, to provide information about variants present in different communities. Wastewater samples from across WNY are sequenced at UB and are incorporated into the NYS dashboard.

Finally, in late-January 2022 the Erie County Department of Health commenced a targeted sampling program in small areas within the City of Buffalo to gather additional wastewater data. The goal of this work was to better understand impacts in areas within the larger Bird Island WWTP sewershed that may be more vulnerable to community spread of COVID-19. The results from this sampling program may be found  here .

A custom  dashboard  has been developed to present the results of the sampling and testing performed as part of Erie County’s COVID-19 / wastewater project. The default view shows all data collected as part of this project. On the left side of the dashboard, you may select a sewershed to highlight the area on the map and to display data specific to that location using the “Smoothed Trend” or “Historic RNA Copy” tabs. You may navigate and zoom in/out in the mapping window, select date ranges to view data on the graphs for specific time periods, and more.

The RNA Copies per liter data are actual results from UB’s laboratory testing. RNA level and recent wastewater trend information for each sewershed follow a CDC methodology to represent whether virus copies are increasing or decreasing when compared to past data.

The data collected as part of this project provide the detection of SARS-CoV-2 (presence/absence) and relative trends, but it is not possible at this time to reliably equate the wastewater data to an exact number of individuals or rates of prevalence in the sewershed that are infected. There are too many variables to do so. For example, the rate at which symptomatic and asymptomatic individuals shed the SARS-CoV-2 virus is currently being researched by scientists all over the world and unfortunately, there is not consensus on the rate. The same may be said for those that are vaccinated or have previously been infected with COVID-19 virus. Likely it will vary somewhat from person to person. Additionally, the amount of non-sanitary flow contributors to the sewer system (groundwater/stormwater/etc.) may affect the wastewater data by lowering the concentration of SARS-CoV-2 virus per liter. As a result, weather conditions could influence the data depending on the sewershed.

It is also not possible to pinpoint exact areas within sewersheds where infected individuals reside. There are literally thousands and thousands of miles of sewer within Erie County. The wastewater from various neighborhoods mixes with discharges from other neighborhoods and the sample is ultimately taken at a centralized location. The only way to perform this project in a large-scale, economical manner, is to primarily use existing sampling equipment maintained by sewer service providers at these centralized locations.

In short, decisions cannot be made and definitive conclusions cannot be formed based solely on the wastewater data alone. That said, the COVID-19 / wastewater project is yet another data source – to be used in conjunction with other available information and metrics – to assist in understanding COVID-19 impacts in our community.

*For smoother functionality and visualization, open the dashboard in a separate tab or window.