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Wastewater Testing: A Powerful Tool You Should Know About

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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. 

Having lived with COVID-19 since the beginning of 2020, we’ve all come to realize how critical rapid testing and viral surveillance is to our ongoing battle with SARS-CoV-2. What you may not know is how instrumental polymerase chain reaction (PCR) testing, a common laboratory method for amplifying DNA, has been in efforts to accurately diagnose COVID-19, and identify and monitor new areas of community spread through wastewater testing. 

Using PCR to trace pathogens is not a new concept, nor is wastewater testing. Initially deployed in the early 1990s to track and prevent new polio outbreaks, qPCR (quantitative polymerase chain reaction) testing for poliovirus RNA was estimated to be 4-5x more sensitive in predicting outbreaks than simply monitoring communities based on reported cases. In viruses such as polio, where it’s common for some individuals to be asymptomatic, the study of wastewater samples attracted attention for enabling large-scale community surveillance. This groundbreaking work better informed public health officials of the initial prevalence and degree of community spread in addition to increasing/decreasing statistical trends. 

Benefits of wastewater testing for disease surveillance 

The benefits of wastewater testing are numerous, but here are a few of the most prominent:  

  • Cost effective—Wastewater surveillance enables research teams to efficiently survey hundreds to thousands of individuals at one time, which is significantly more cost effective than individual diagnostic tests. 

  • Timely surveying of transmission across entire communities—As noted above, this large-scale effort reduces costs and also saves significant time, when days, if not hours, matter.  

  • Avoids bias often associated with other epidemiological indicators—Although unintentional, when working on a global scale, socioeconomic, geographic, and personal biases can quickly enter the statistical equation. In the case of COVID-19, these biases were especially problematic given that initial disease prevalence monitoring was based on the number of positive counts, yet community access to testing was extremely limited. 

  • Improved warning system—In cases where initial diagnostic testing is unavailable or requires lengthy processing intervals, wastewater testing could provide health officials with closer to real-time insights on disease prevalence. This benefit is critically important in situations where novel viruses are at play, as diagnostic testing development takes time. In the outbreak of 2020, rapid forms of diagnostic testing took many more months to develop, manufacture, and distribute. During this time, wastewater testing filled a critical information gap. 

qPCR wastewater testing for SARS-CoV-2 detection  

Wastewater surveillance experience from prior disease outbreaks prepared scientists for what was to come once it was known 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 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 tests 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. 

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 for research teams on how to handle special considerations like proper sample collection, ideal collection sites, as well as best practices for sample collection frequency, storage, and testing procedures. In addition, in collaboration with the Department of Human Services, they published requirements on how to become a National Wastewater Surveillance System (NWSS).  

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

COVID-19 surveillance solutions 

Can we expect wastewater surveillance to replace other COVID-19 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 methods during infectious disease surveillance offers benefits to our tracking toolbelt. Many teams around the country are already working on projects to build infrastructure in their communities to include this technology in their surveillance systems. In the coming years, expect even more communities to begin next steps on implementing the methodologies used with COVID-19 to supplement infectious disease response plans. 

For more on how IDT can assist with your next PCR project, head on over to our PCR hub or chat with us today