Q+A on wastewater testing
Since early on in the COVID-19 pandemic, civil and environmental engineering professor Kara Nelson and assistant research engineer Rose Kantor (Ph.D.’16 Microbiology) have led a campus effort to test wastewater samples from across the Bay Area for the SARS-CoV-2 virus. Their team not only developed a novel method to detect the virus, but also worked closely with wastewater agencies and public health departments to monitor samples for infection levels and the presence of new variants. Next up: improving pandemic preparedness and health equity through wastewater-based epidemiology, thanks to a new multimillion-dollar research grant from the University of California.
RK: People have used wastewater to track down typhoid and polio, but it was never applied wide-scale. Fast forward to this pandemic, it became apparent early on that it could be a useful tool because of some of the aspects of COVID-19, including a lot of asymptomatic cases and the lack of availability of clinical testing.
KN: One of the amazing benefits is that, from a single sample, we can get information on thousands to millions of people. It’s efficient, convenient and non-invasive — and it’s not biased by who is able to get tested. There has been concern among public health agencies that they’re missing cases, so our data is complementary to the clinical data that helps authorities make important decisions.
What were some of the biggest challenges?
KN: When the pandemic started, many of my graduate students and postdocs pivoted away from their regular research to work on this, and then students from other disciplines joined our team. But even though my group had experience measuring pathogens in wastewater, we had never looked for SARS-CoV-2. The virus is different than the viruses we were used to because of its structure, so we had to develop new approaches to detect it.
RK: On top of that, everything had shut down, and there were supply chain issues. We needed a method that was really sensitive but also readily available. We overcame a lot of barriers by working with a student who had proposed a novel method. So by using table salt, ethanol and a silica-based column, we found something that was sensitive, fast and safe — and didn’t require materials that were hard to get, which ultimately made it cheaper.
How does your partnership with public agencies work?
KN: In early 2020, I was contacted by our local water agencies to ask if we could partner together to do this. They were eager to support the pandemic response and began collecting samples for us. We process the samples and provide results. As part of our routine analysis, we also test for variants of concern, like Omicron, which we were able to track before it was seen in clinical samples. Our results are posted to a public dashboard, and we have a website with information for our public health partners. We also provide the information to the California Department of Public Health. We now have funding to transition the routine monitoring to the state. We are close to finishing that transition, and the state will take on wastewater monitoring as part of their long-term public health surveillance.
What’s next for wastewater testing? Where might we see innovation?
KN: The holy grail is an untargeted method: being able to analyze each wastewater sample and use sequencing approaches to identify all of the viruses that are present without knowing what they are. That’s the tool that we need to have to detect the arrival of a new virus. A large emphasis of this new grant is developing untargeted detection methods that we can use for detecting the next pandemic virus and get early warning. The other areas that we are emphasizing is how to better understand the health disparities that exist and plan for how to minimize them in the future.
RK: I think we’ll continue monitoring wastewater for Covid-19 and for new strains, including those that might be missed by clinical testing. But we’ll also see a new focus on health equity and on using wastewater testing to monitor public health in a more unbiased fashion than previously, when we relied on the access to healthcare. I’m excited to see how wastewater testing can be used with other public health data to focus resources where they’re most needed.