A community’s sewage holds clues about its COVID-19 burden. Over the course of the pandemic, wastewater surveillance has become an increasingly popular way to try to understand local infection trends.
Microbiologists Susan De Long and Carol Wilusz met and became wastewater aficionados in April 2020 when a grassroots group of wastewater treatment plant operators asked them to develop and deploy a test to detect SARS-CoV-2 in samples from the sewers of Colorado. De Long is an environmental engineer who studies useful bacteria. Wilusz’s expertise is in RNA biology. Here they describe how wastewater surveillance works and what it could do in a post-pandemic future.
How is wastewater monitored for SARS-CoV-2?
Wastewater surveillance takes advantage of the fact that many human pathogens and products of human drug metabolism end up in urine, feces or both. The SARS-CoV-2 virus that causes COVID-19 shows up in surprisingly large quantities in feces of infected people, even though this is not a major route of disease transmission.
To figure out whether any pathogens are present, we first need to collect a representative sample of wastewater, either directly from the sewer or at the point where what engineers call “influent” enters a treatment plant. We can also use solids that have settled out of the wastewater.
Technicians then need to remove large particles of fecal matter and concentrate any microbes or viruses. The next step is extracting their nucleic acids – the DNA or RNA that holds the pathogens’ genetic information.
The sequences contained in the DNA or RNA act as unique bar codes for the pathogens present. For instance, if we detect genes that are unique to SARS-CoV-2, we know that the coronavirus is in our sample. We use PCR-based approaches, similar to those used in clinical diagnostic tests, to detect and quantify SARS-CoV-2 sequences.
A lab technician prepares to process wastewater samples for SARS-CoV-2 detection at Colorado State University.
John Eisele/Colorado State University
Characterizing the nucleic acid sequence in more detail can provide information about viral strains – for instance, it can identify variants like omicron BA.2.
Currently, the vast majority of wastewater surveillance efforts are focused on SARS-CoV-2, but the same techniques work with other pathogens, including poliovirus, influenza and noroviruses.
Before the pandemic, one application was monitoring for rare poliovirus outbreaks in areas where polio vaccination is ongoing. Wastewater can also be monitored for signs of various drugs to give insights into the level and type of drug use in a population.
Where does the data go?
During the pandemic, the U.S. Centers for Disease Control and Prevention developed the National Wastewater Surveillance System specifically to track SARS-CoV-2 across the country. Over 800 sites report data to this NWSS system, but not all states and counties are…