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COVID-19 Wastewater Surveillance Program Expands to Test for Flu Strains

Local partnership grows to 20 states; monitoring begins in October with implications for future influenza strains

University of Nevada, Las Vegas

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Published:Oct 05, 2021
|4 min read

It’s still nearly 90 degrees in Las Vegas, so it makes sense if thoughts of winter seem far out of the picture.

But University of Nevada, Las Vegas (UNLV) scientists and community partners are staring squarely at the months ahead to keep Nevada’s communities safe and prepared against the coming flu season.

Coupled with continued COVID-19 cases and a gradual return to normal life—businesses open, students back in school—this year’s flu season might be a much different picture than winter 2021.

“Flu, interestingly enough in 2021, went away for the most part in many states,” said Edwin Oh, associate professor in the Kirk Kerkorian School of Medicine at UNLV. “It’s shocking—the numbers were the lowest that I think have ever been reported. But that was the result of multiple lockdowns, of businesses shutting down, and the limiting of human interaction.”

That’s where Oh’s wastewater surveillance program comes in.

He and collaborators at the Southern Nevada Water Authority and the Southern Nevada Health District are gearing up to keep watch for flu strains that are cropping up in wastewater throughout the state to better target future influenza vaccines.

Flu vaccine effectiveness can vary from 40 percent to 60 percent each year, according to the Centers for Disease Control. Oh is hoping their new flu surveillance program—which is building upon the research infrastructure developed last year to inform public health officials of where COVID-19 was circulating—can help bring those percentages up. And what happens here, won’t stay here, as researchers are partnering with roughly 20 other states to share data.

“The central hypothesis of our work is that we’re hoping our wastewater surveillance system can help flu vaccines become more effective,” Oh said. “At this point, there is no good way to predict whether or not vaccines are working real time for the strains that are present.”

How has the wastewater surveillance program helped us get ahead of emerging COVID-19 variants?

The last 12–16 months have really given us the opportunity to develop a toolkit that can detect most pathogens that are present in our community. Our precision in detecting SARS-COV-2, and our precision in sequencing genomes has gone up tremendously.

Through sequencing and the detection program we found the Alpha and Epsilon variants in our wastewater in December 2020. At that point, we were unaware of any human infections in Southern Nevada. However, in January—about a month after we detected the wastewater genomes—we found the Alpha variant and Epsilon variant in humans.

And more recently, the same has been true for the Lambda variant. We found mutations associated with the Lambda variant in the wastewater, and shortly thereafter we found our first three human infections. So there’s clear proof that this wastewater data can predict the human infections that are going to show up here.

Most recently, we have preliminary data that the newest variant called Mu is here in our community. This is evidence that a seven-days-a-week type of surveillance system is really, really key to staying ahead of this curve, with the full intent of helping to keep our businesses open. If we know what variants are coming in, we’ll be able to mobilize our public health resources to those regions.

Where is the COVID-19 surveillance program headed?

We’ve been looking for new ways to integrate clinical and sewage genomes together with testing and vaccination programs. We recently received a $5 million grant in collaboration with the Southern Nevada Health District to develop new ways to operationalize the data that we’ve been collecting. We want to find a way where it can be better used as a service.

Over the last 12 months we’ve had to put the pieces together and hire the best scientists and UNLV graduate and undergraduate students. Now that we and others have been able to do that successfully, how can we do this on a larger scale? The next time a pathogen enters into a community, we’ll be able to mobilize our resources quickly.

For example, we know that COVID-19 is circulating in schools and that more children are showing up in hospitals. One way of operationalizing this data is that we can go around to different schools now and monitor which ones have higher, medium, or low levels of the virus. And if we know which schools have more virus, we can mobilize our testing units to these schools with greater precision as opposed to dispatching them throughout the entire community. A shotgun approach can be difficult to do with limited resources.

Why is it important to share the work of the surveillance program outside Nevada?

Our local partnership with the health district and the water authority has grown on a national scale. We’re now working with 20 other states to sequence their wastewater genomes.

We’re using our expertise to better understand some potential problems with the detection and sequencing of COVID-19 genomes. Given that Las Vegas is an international tourist destination, we want to know if the viral genomes are being brought in from other parts of the world. Or are we just doing a really good job at spreading these genomes within our community? Or potentially both? By studying genomes in California, Arizona, Michigan, and Wisconsin, we’ll have a better idea where our genomes are coming from. That effort has grown to something where we can run this surveillance locally and increase our resolution by looking at other states too.

How will you build upon the COVID-19 research program to monitor for flu strains?

Scientists are anticipating that co-infection of flu and COVID-19 is going to be a really difficult situation in October, November, December. Our biggest fear is that infection of two different viruses might result in a more severe outcome.

So, this partnership with the health district means we can sequence genomes from both clinical cases and wastewater, and tip us off as to what type of flu vaccines are going to be most useful for this season.

Beginning in October we’re going to start examining whether or not flu strains are circulating in our communities by analyzing and sequencing our sewage and comparing the data with other states.

What can this mean for future flu vaccine development?

Flu vaccines are usually developed and predicted the year before the season—six to eight months before strains show up. So there’s a chance that the predictions will be inaccurate.

This system of wastewater analysis is something that’s never been attempted before. One of the tests we’re going to run is to see if we can predict whether the vaccine being distributed is going to work. And I think the answer is going to be yes, because if we can sequence the genomes, we’ll know what influenza strains are going to be present here. Our goal is to increase our precision in developing the vaccines that are going to be relevant in this part of the world.

- This press release was originally provided by the University of Nevada, Las Vegas