Testing Wastewater for COVID-19

The U.S. is in the grips of a third wave of the coronavirus pandemic, and inching toward the possibility of another grim milestone – hitting up to 200,000 cases a day.

It’s a potential reality that makes UNLV researcher Edwin Oh’s work even more urgent: sequencing the RNA of the SARS-COV-2 virus to find targets that make vaccines more effective.

“I can envision a possibility where we create the vaccine, but the virus has mutated to a point in some communities where that vaccine is less effective for people who’ve contracted a different strain,” Oh said, adding, however, that recent vaccine development announcements from Pfizer and Moderna are promising.

Oh’s research program — screening wastewater for the presence of COVID-19 — is made up of postdoctoral fellows and UNLV students. Together with a variety of collaborators in Nevada and in neighboring states, this effort could help inform vaccine development in the future.

But his work has already made inroads in other ways. In August, Oh’s research group was part of a collaboration led by the University of Arizona to screen wastewater in dorms and buildings around campus to determine whether the virus was circulating. The surveillance program picked up two asymptomatic student cases of COVID-19 and helped prevent a potential outbreak at the start of the fall semester.

Oh’s latest endeavor takes it a step further: extract the RNA from the virus and determine if and where different strains of the virus are cropping up in communities around Las Vegas.

“Is the virus that we’re getting in Nevada very, very different from California, or very, very different from Denmark? And over time, how is this virus changing? This would be an inexpensive and efficient program to help us identify communities that might respond far better to certain vaccines that are being developed in the market right now,” said Oh.

Here, Oh explains what his wastewater surveillance program has found to date, how such programs can help prevent disease outbreaks and supplement ongoing public health contact tracing efforts, and why more state and federal agencies should collaborate on and invest in these efforts.

What can we learn from testing wastewater for the presence of COVID-19?

The virus – SARS-COV-2 – is what’s known as an RNA virus. This is a virus that enters through the respiratory system and it’s thought to be shed in fecal matter and in urine, so that’s why we and others had this hypothesis that we would screen sewage for SARS-COV-2. What we see in wastewater can predict what’s going to happen in communities by giving us anywhere between a two- to five-day advance notice of the virus’s presence before symptoms begin to show. That’s a decent amount of time for our public health officials to now contact trace within that community to figure out whether something might have been missed.

This is a substance that we can detect in the lab very easily and measure its potency in two ways. One way is by total amount: is there more, or is there less of it? The assumption is that if there’s more of it, then there’s more people shedding it, then more people in that building have it, and therefore, it could be extremely dangerous.

The other way is to determine the actual sequence that the virus contains. You and I, we have 3 billion nucleotides in our genome and that makes us who we are; for a virus, all of the features it requires to enter a human cell, for it to replicate in a human, is contained within 30,000 nucleotides. It’s a small fraction of the human genome, but that small genome is sufficient to wreak havoc and kill more than 1.3 million people in the world.

How can sequencing the RNA of the COVID-19 virus help in the effort to develop a vaccine?

Sequencing can help determine if there’s a mutation within that 30,000 nucleotides that might make it more infectious.

There’s been a story going around for some time about how the animals on a mink farm in Denmark could contain a mutation that would make this virus potentially more infectious and that could be extremely dangerous for our population for many different reasons.

We are hoping a vaccine will be developed within the next few months. Last week, Pfizer announced that a vaccine that has been studied is now 90% effective in 48 individuals – that’s awesome. And this week, Moderna announced its vaccine is 94% effective.

We’re currently collaborating with University of Nevada, Reno to screen wastewater in northern Nevada. Our collaborator found a very specific change in the virus that seems very, very unique to Reno. It’s unclear why it’s unique to Reno, and so what we want to determine is: could we have detected that change much sooner using wastewater, and, can we now detect any change that might be unique to that community?

This goes back to vaccination and therapeutics – knowing the sequence of the virus will help us determine whether changes in the sequence can lead to a worse outcome, and can also help us identify whether communities might be actually resistant to a vaccine that is currently being developed.

Can you tell us about UNLV’s collaboration with the University of Arizona to screen wastewater for the presence of COVID-19 and the results of that effort? What did it tell us about how wastewater surveillance can prevent the spread of the disease?

Our collaborators at the University of Arizona screened the wastewater of dormitories, buildings, and various centers on campus for the presence of COVID-19. We found a positive hit at two different buildings, and this was really interesting because students had just returned to campus, and a condition for returning to campus for the students was to have received a test result of “negative” before coming back.

Two dormitory residents who initially tested negative later tested positive, even though they  were asymptomatic. These individuals must have contracted this virus during the couple of days that they were on campus.

The realization is that none of this would have potentially been detected if we did not have this surveillance program in play. As a result, these students were isolated and quarantined and they’ve since recovered. A case like this has led to many other similar efforts across the nation, where wastewater surveillance has led to the identification of students and faculty members who had the virus but were asymptomatic. I think that’s the key here. When someone is asymptomatic, it’s so difficult to know.

An interesting caveat to our surveillance program is that we were unable to directly match the viral genomes found in the wastewater to the viral genomes in the asymptomatic students. This is important since we cannot be sure whether an infected out-of-state parent or friend visited the premises for the day and then left. However, our program was not set up to address such challenges and we are now working on the technology to provide more clarity.

The University of Arizona case was the perfect principle that this could be done, and that the surveillance program could lead to actionable public health decisions.

Can you talk about your recent surveillance collaboration with the Southern Nevada Water Authority? What has your research found to date?

We’re working with fantastic collaborators at the Southern Nevada Water Authority who have been collecting wastewater since March to determine the presence or absence of COVID-19. We’re screening major wastewater plants across Las Vegas and Henderson, and we’ve been working together to increase the resolution of our screening. 

Up to this point, we’ve been juxtaposing clinical samples from Southern Nevada public health labs with the wastewater samples. We’ve sequenced around 300 samples, and we’re comparing that to six wastewater samples. It’s a very randomized analysis, and we’ve been observing that the variants, or mutations, we’re seeing in wastewater, you also see in humans, which is very striking. We think our research is going to show that so few samples can predict what was going on in a large community.

Where do you see this headed in the future?

We want to go closer and closer to communities. We want to be in a position where we can go to a nursing home, and extract sewage water from the nursing home, and help that nursing home know that they either have clients or employees with COV-2 and they therefore need enhanced screening at the facility.

We also want to get closer to the Strip. We want to know what type of strains are coming into the Vegas Valley from neighboring states and international destinations.

We’re also using our surveillance program to monitor influenza. We want to know the types of influenza strains are present and how widespread these different strains are.

Can you provide an example of how wastewater surveillance has helped in other diseases?

Back in the 1990s, wastewater surveillance was effective in helping communities determine whether polio was present or not. When you vaccinate a community, you want to know that that community is now going to be immune. So rather than going back and screening people, you can complement other public health measures and take a few samples of wastewater to determine whether it’s still circulating in your community.

With our research in relation to COVID-19, we wanted to take this one step further and ask: how is this virus changing over time?

We’ve heard of some efforts nationwide to look at wastewater for signs of COVID-19. How is this work similar to and different from what’s out there?

So right now, a lot of different countries and facilities are implementing wastewater surveillance, and the nature of that surveillance is focused primarily on a binary outcome: is it there, is it not there?

But I believe our work will lead to a determination of many flavors of the virus. This kind of effort hasn’t been done at a high frequency because extracting the complete RNA genome for the virus from sewage is extremely difficult. The COVID-19 virus is prone to degradation when exposed to various chemicals. We’ve taken a lot of time to optimize the procedure, and we think we now know how to do this quite well, and we can reproduce the method.

What are the next steps as the pandemic rages on and the country continues to wait for a vaccine?

The next step is to do this at a larger scale and bring our sequencing program to additional states. We’re working with collaborators as close as New Mexico, and as far away as Israel.

We’re currently applying for a NIH (National Institutes of Health) grant to harmonize best practices with other U.S. institutions, so as to show that our technique can be reproduced. We’ve been using startup funding to get this project going, and we’re hoping that our upcoming research publications will show the world how this can be done in a very standardized fashion.

We’re in the third wave of the pandemic right now. With every new wave you see that the number of infections is two or three times more than what it was before. That’s why this work is so important right now.