Female scientists working with waste water
February 17, 2021 | Molecular Biology

Wastewater monitoring of SARS-CoV-2

Experts answer your top six questions

Last year, several studies showed that people infected with SARS-CoV-2 could pass viral RNA from their feces into sewage and wastewater drainage systems. These studies, including those from the Universities of Arizona, Minnesota and Virginia, demonstrated the usefulness of wastewater testing for detecting the virus and predicting or tracking outbreaks of COVID-19, providing estimates for where and how widespread it was. Experts have now called for comprehensive wastewater testing programs and recognition of their potential as an early-warning system.

While all studies show the benefits of monitoring wastewater, as yet there’s no consensus on best practices. To help drive a gold standard for wastewater monitoring of SARS-CoV-2, QIAGEN invited leading experts in the field of wastewater management and treatment from academia and government to take part in a panel Q&A on November 17, 2020. In particular, we would like to thank Francoise Chauvin, Scott Meschke, Sean Norman and Mami Taniuchi for taking part.

1. Collaboration with public health organizations

Q: Public health departments are apprehensive to partner with a wastewater monitoring project because they feel there isn't enough data to make it “actionably significant” How do we persuade them?

It’s not easy. So far, no one has defined an actionable viral abundance in municipal sewage for whole communities. But there are several examples of targeted sewage testing in, for example, universities. These show sewage viral abundance provides actionable data that can be used for targeted individual-level testing and viral mitigation. Also, the CDC (Centers for Disease Control and Prevention) in the US provides helpful information. Another thing is to be transparent on all analytical aspects – from presenting the details of the analytical method, to how the method is implemented, to any QC issue, to any technical/workload issue. Cooperation relies on being responsive to data requests and sticking to agreed data delivery times, data formats and reporting requests. Just try to get them to designate a point person to inform about monitoring advances and engage with monitoring groups.

2. Sample types contributing to viral RNA in wastewater

Q: The levels of SARS-CoV-2 that can be detected in wastewater from human excretion and oral expulsion (saliva) are yet unknown. Has there been research to analyze public water systems (e.g., sinks, faucets, etc.) in addition to sewage systems, and what about urine tests to replace swab tests?

We’re not aware of drinking water studies, although some groups have done studies on monitoring of environmental surfaces, particularly in food packing plants where they have detected SARS-CoV-2 in bathrooms. Regarding urine tests to replace swab tests, the titer in urine is much lower than in fecal, saliva and nasal samples, which would result in a loss of sensitivity. Also, current literature indicates that the virus is predominantly present in stool, with a much smaller amount found in urine.

3. Data and result sharing

Q: Can you elaborate on how data is shared with the public? Why isn’t more data available: On a global dashboard, only 163 universities and 43 countries are mentioned?

We expect to see dashboard interfaces in the near future to present the information in a way that can be easily interpreted by the public. It’s not always possible because departments of health are often the data owners and sometimes, they feel sharing the data with the public can be counterproductive. They can be unsure how to use the data and worry that public-facing dashboards may lead to confusion, or distrust of public health authorities.

4. Testing in special environments

Q: a). What do you think about monitoring special environments such as natural reservoirs near camping grounds, shorelines near sewage runoffs, cruise ship treatment plants, schools and campuses?

We’re not aware of any major studies yet at reservoirs. There are a few groups monitoring natural waters receiving fecal contamination. Wastewater treatment plants (WWTPs) on cruise ships would be ideal for monitoring. With a higher concentration of people in a limited area, it could be a great way to identify cases and confirm those cases with RT-PCR sample testing. Sampling airline and cruise-ship waste at airports/sea ports would provide a good means of identifying new introductions into an area. In small, well-defined communities (150–200 people), such as a campus, you would most likely be able to detect COVID-19 successfully since human waste is not likely to be diluted as much as in a larger community. We know we can detect a single case in a building with 200–300 people. Wastewater monitoring could be accomplished through composite sampling. However, it might be better to clinically test a population that small. School and nursing-home testing should be very similar to campus dormitories.

b). What’s your view on monitoring schemes? At campuses, schools and nursing homes, for example, they’re collecting regularly for 24 hours then mixing the sample.

A composite sample representing 24 hours is a good approach. Sample stability is adequate if stored at low temperature (4°C) but freezing is not advisable. Sampling in this situation can deliver actionable data that could be coordinated with the local public health authorities. It would be possible to have a clear plan on what to do if positives are detected (i.e., what level of confirmation would trigger specific actions). But be aware with less compositing and a lower probability of sampling during the right moment, the sample might not be representative, and you could miss something even with 24-hour, hourly composites.

5. Procedure after detecting the virus in dormitories

Q: What should be the next step after detecting a positive monitoring result in a dormitory sample? Also, have there been any discrepancies in confirming positive wastewater results by testing?

When we detect a high viral abundance at a university dorm, we send a testing team to target that building to try to identify the positive case. Testing was on a voluntary basis in the past, but that will shift towards mandatory testing. The testing team uses a saliva-based test. The very important decision of determining how to use the data is left to our public health department using CDC guidance. At the University of Arizona, they immediately conduct rapid testing of all residents in a dorm when there’s a positive sample. It doesn’t make sense to test less than the full dorm population contributing to the positive environmental sample. In other places/situations, the response depends on where you are sampling, the intent of the sampling and the sampling scheme.

Regarding testing confirmations, we’ve identified high viral abundance in the sewage of a building that led to targeted testing and identified an infected individual. When that person left, we saw a reduction of the viral abundance in the sewage to below detection. We’ve also had a situation where cases were not identified in a building where viral presence was detected in sewage. But there, testing was on a voluntary basis and the infected individual may have been missed. In truth, positive environmental samples nearly always result in a positive clinical test result. But remember, results depend on your sampling scheme (how often you sample), the time between the environmental positive and clinical testing, and the degree to which the dormitory population is isolated. For example, there could be transient residents, such as staff, who are not captured in the clinical testing.

6. Viral decay and rapid testing

Q: Is there any evidence that sample and wastewater treatment will affect the viability of the virus? Are there antigen detection tests available for wastewater and sewage?

We know that temperature can affect viral decay, so most researchers try to keep wastewater samples cooled throughout the sampling and processing steps. Regarding treatment plants, this is still being investigated. Most of the literature at this time indicates that the virus is not infectious by the time it reaches treatment plants.
The primary tests being used for environmental monitoring are RT-PCR or dPCR tests. dPCR can be used for absolute and accurate quantification, for example, in monitoring trends. By reducing variability and the impact of inhibitors, dPCR enhances sensitivity producing fewer false negatives and detects very low viral load specimens. It can also be used to provide a good recovery control, at the outset, before using other methods. At least one group is working on viral protein detection and a few groups are working on RT-LAMP assays. Sample concentration techniques do not inactivate the virus, but nucleic acid extraction steps do. We’re not aware of anyone isolating viable virus from sewage. Point-of-care rapid testing has well-known advantages and disadvantages, but we have been focused exclusively on wastewater testing. Not all assay types are well suited for environmental testing. Rapid antigen tests may not be sensitive (in terms of LOD) to be useful for environmental sampling. You need to first determine the use case you’re addressing.

Researcher survey

Since this article was published, we have collected the results from two surveys on wastewater monitoring of SARS-CoV-2. Take a look at what’s changing as we compare the opinions of researchers in March 2021 with those of last year by downloading the survey.

Q&A panelists

Francoise Chauvin, Ph.D., Chief of Laboratory Operations, Bureau of Wastewater Treatment, New York City Department of Environmental Protection
Scott Meschke, Ph.D., Associate Chair, Department of Environmental and Occupational Health Sciences, University of Washington
R. Sean Norman, Ph.D., Associate Professor, Department of Environmental Health Sciences, University of South Carolina
Mami Taniuchi, Ph.D., Associate Professor, Division of Infectious Diseases and International Health, University of Virginia
Afif M. Abdel Nour, Ph.D., Customer Solution Manager, dPCR, QIAGEN
Markus Sprenger-Haussels, Ph.D., Head of Sample Technologies Product Development, QIAGEN
Moderator: Dominic O’Neil, Director, Microbiome Product Development, QIAGEN

Dominic O'Neil
Dominic O'Neil

Dominic O'Neil has over 20 years of experience in the biotechnology industry. Before joining QIAGEN, he gained molecular biology expertise at several companies, including three years at the Whitehead/MIT Center for Genome Research in Cambridge, MA, where he participated in the completion of the initial draft of the human genome. Dominic joined Digene (which later became part of QIAGEN) in 2004 to work on new technology research and development, focusing in particular on sample preparation and diagnostic applications. In 2011, he joined the QIAGEN R&D group in Hilden to work on solutions for next-generation sequencing. Starting in 2015, he focused on microbiome extraction and associated workflows, and now leads the R&D group as Director for Microbiome Product Development.