Wastewater Testing: A Powerful Tool You Should Know About

There are many dirty jobs researchers around the world take on for our greater good. While this work often occurs behind the scenes, one in particular is making its way into news stories and local infectious disease surveillance protocols: wastewater testing.  

As COVID-19 showed, rapid testing and viral surveillance are critical tools that help support public health and safety. But what are the powerhouses behind rapid testing and viral surveillance initiatives? Polymerase chain reaction (PCR) and next generation sequencing (NGS).  

Using PCR to trace pathogens is not a new concept, and neither is wastewater testing. A related method, quantitative polymerase chain reaction (qPCR), was deployed in the early 1990s to track and prevent new outbreaks of polio. Using qPCR to test for poliovirus RNA was estimated to be as much as five times more effective in predicting outbreaks than simply monitoring communities based on reported cases. Using qPCR to test for polio enabled large-scale community surveillance in a way that reported cases analysis could not, as it is common for some individuals afflicted with the ailment to be asymptomatic. This groundbreaking work better informed public health officials of the initial prevalence and degree of community spread as well as whether prevalence was rising or falling. 

NGS has also played a significant role in expanding wastewater testing and therefore, also the adoption of this tool by additional organizations. In recent years, we’ve seen broader use by public health organizations, colleges and universities, as well as environmental surveillance groups. The heightened accessibility of NGS has undoubtedly provided these researchers with a powerful tool to identify, track, and trace complex microbial challenges.  

Benefits of wastewater testing for disease surveillance  

There are many benefits to wastewater testing. Some of the most prominent include:   

Wastewater surveillance experience from prior disease outbreaks prepared scientists for what was to come once it was determined that SARS-CoV-2 could be detected in fecal matter. Unlike other viruses that break down quickly after exiting the body, the SARS family of viruses thrives in environments such as wastewater. While it is true that the virus breaks down during the digestive process, researchers quickly found that biomarkers remained in fecal samples for up to two weeks. Subsequent investigation also informed researchers of SARS-CoV-2 RNA’s ability to withstand temperature and chemical changes throughout the sewage system—making the virus a perfect candidate for deploying wastewater testing.  

Findings from a study published in Nature Biotechnology describe how a team of researchers in Connecticut used a form of qPCR testing called reverse transcription quantitative PCR (RT-qPCR) to supplement local and national health officials’ COVID-19 response plans. During the surveillance project, the team extracted nucleic acids from concentrated sewer sludge found in wastewater facilities, and then analyzed the samples using RT-qPCR to calculate the N1 and N2 gene targets of SARS-CoV-2. The result? Additional lead time that allowed local teams to track COVID-19 cases and hospitalizations during the early weeks of the outbreak in New Haven. These data were especially critical at the start of the pandemic, when diagnostic testing supply and distribution challenges limited health officials’ ability to respond to cases and outbreaks quickly. 

There are other notable instances where wastewater testing enabled early COVID-19 escalation warnings: In the fall of 2020, the University of Arizona was able to stop the spread of COVID-19 within the student body by testing fecal samples from the dorms. When results indicated concerning levels of SARS-CoV-2, university officials were able to test students. The findings confirmed what was found in the wastewater analysis when several asymptomatic students tested positive for the virus. Later, the Ohio Department of Public Health was able to issue a public proclamation warning residents of increased community spread based on wastewater testing results that showed high levels of SARS-CoV-2 in samples from local treatment plants. 

Interested in learning more about virology research? Watch IDT’s webinar, xGen™—made for virology research. This webinar shows how xGen can be leveraged to help assess novel variants of known viral pathogens and more. 

Using NGS to detect changing SARS-CoV-2 variants in wastewater samples 

With assistance from IDT’s xGen™ NGS solutions for SARS-CoV-2, Dr. Arvind Varsani, PhD, and his research team at Arizona State University applied high-throughput NGS methods to sequence viral genomes from wastewater to not only investigate community spread during the global COVID-19 pandemic, but also to pinpoint changing viral strains that may not be reported in human cases. This work sets the stage for how the research community can arm public health organizations and healthcare facilities with early indicators of upcoming clinical infestation. 

As we look to the future, Dr. Varsani’s approach of combining NGS technology with traditional virology, microscopy, and molecular and cellular biology techniques to understand the evolution and geographic spread of viruses in their natural habitat may be used to provide insights on novel pathogens and/or variants of concern before widespread infection occurs.

Hear more on Dr. Varsani’s first-hand account of his approach and how IDT aided his research efforts in this short video.

Centers for Disease Control (CDC) offers wastewater surveillance testing guidance  

Given the expanded use cases highlighted during the COVID-19 pandemic, the CDC issued guidelines to research teams on how to handle special considerations like proper sample collection, ideal collection sites, and best practices for sample collection frequency, storage, and testing procedures. In addition, in collaboration with the Department of Human Services, CDC published requirements on how to deploy new National Wastewater Surveillance System standards in a community. 

The goal of these efforts is simple: help health departments respond with increased speed during situations where swift action is imperative. 

Infectious disease surveillance solutions  

Can we expect wastewater surveillance to replace other surveillance efforts? Not likely. Given the vast differences in wastewater processing protocols and variable virus load within individuals, using this method alone would be ineffective. While more research needs to be done to determine how beneficial wastewater testing is as an early warning system for viral community spread, there’s no doubt deploying qPCR and NGS methods during infectious disease surveillance adds to our identification and tracking toolbelts. Many teams around the country are already working on projects to build infrastructure in their communities that includes this technology in their surveillance systems. In the coming years, expect even more communities to take steps to implement these methods to supplement infectious disease response plans. 

For more on how IDT can assist with your next PCR or NGS project, head over to our PCR and xGen™ NGS hubs!