A technique developed at UC San Diego and Scripps Research to detect the COVID-19 virus in wastewater is now being used around the world. That's the message of an article in Thursday's online edition of the magazine Nature. Researchers say the process is cheaper and faster than clinical COVID-19 testing and has the potential to keep up with and identify emerging variants.
Dr. Chris Longhurst, chief medical officer and chief digital officer at UC San Diego Health, joined Midday Edition to talk about the benefits of the wastewater surveillance program. The conversation transcribed below has been lightly edited for clarity.
What are the current levels of COVID-19 in San Diego's wastewater?
Longhurst: Interestingly, we're seeing that the wastewater levels of COVID-19 have actually leveled off over the last couple of weeks. But of course, we're seeing case rates increase. And that's probably a reflection of the fact that it takes a week or two once you get infected to really become symptomatic and sick. We know with BA.4 and BA.5, which are now the predominant lineages in San Diego, that these are more likely to have immune escape, meaning people who have been previously infected or vaccinated are more likely to get this than they were with prior variants. So, while the wastewater is level, the cases are going up and our hospitalizations are also going up.
What does the wastewater information tell you about the virus levels in the community?
Longhurst: Well, what's really neat about the wastewater is that it's not biased by who is testing. So with wastewater, we know when these circulating levels of COVID are increasing, when they're decreasing, regardless of whether or not people are coming to health systems or doing home testing. In fact, we estimate now that 90% of cases are discovered with home testing, which is great. That's how we want people to test, which is conveniently, frequently, cheaply in their homes. But the wastewater gives us a really good understanding of how the virus is circulating in our community. This is the first time that we've done really broad wastewater surveillance for a virus with COVID, but it's possible with a number of other viruses. In fact, just recently we heard stories in the United Kingdom of discovering some circulating virus that was concerning and required further investigation.
How does wastewater testing speed up the process of identifying new variants?
Longhurst: What's great about wastewater is that we can detect with high resolution sampling really small numbers of new variants. And so the paper that was just published in Nature (Thursday) by Dr. Rob Knight and colleagues — I was fortunate to be part of this effort — and it showed that the wastewater surveillance preceded our discovery of variants in clinical cases by two to three weeks. In fact, you remember when omicron was first announced in South Africa, which was right after Thanksgiving last year. We actually found evidence in our wastewater here in San Diego of omicron before the announcement was made by South Africa.
Now, how has learning about levels of COVID-19 in wastewater, how has that affected public health strategies against the COVID-19 virus?
Longhurst: The wastewater genomics data is incredibly valuable because it is an early indicator. We know when the wastewater levels go up, that precedes the cases going up, which then proceeds the hospitalizations. We showed with the delta surge last summer that the wastewater actually predicted it by three weeks. So it helps us to put in place mitigation techniques. In fact, here at UC San Diego, a couple of weeks ago, when the wastewater was increasing, we moved to our local red tier. We asked all employees on site to test in a mandatory fashion, and we shifted the pre-procedure testing for all of our patients. And so that was really valuable for us because it gave us a bit of a crystal ball looking into the future.
It seems like this wastewater testing started out about two years ago on the UC San Diego campus, and now it's being used around the world. Is that right?
Longhurst: We can't take credit for being the first to ever do wastewater testing. It's been around for about 20 years, but it really hasn't been broadly used. We're certainly one of the first colleges to use this to find cases, and that was extraordinarily helpful for us as part of our Return to Learn program. And we're partnered here at UC San Diego with the County of San Diego to do the wastewater monitoring, not only at the Point Loma wastewater treatment plant where we've been doing it now for over a year, but now also at the Encina and other wastewater treatment plants locally. And so this gives us really tremendous insight that not all counties in California have, even though this is part of Governor Gavin Newsom's recommendation and SMARTER plan.
The reason that it has caught on so well, at least one of the reasons, is because it is so much faster and economical than the usual form of monitoring for COVID-19. Isn't that right?
Longhurst: That's absolutely correct. I can't quote you the number, but every one of our wastewater tests is in the, let's say hundreds of dollars, whereas testing a clinical sample to find out, let's say if I'm COVID positive which genomic variant I'm carrying, it's much more expensive, but it's also not clinically valuable in an individual. We don't treat you differently or give you a different medicine because you have a different variant. But, understanding what variants are circulating the population helps us to plan things like vaccination strategies and antiviral availability and prevention and mitigation techniques.
Can you explain how the level of COVID-19 in sewage translates to the number of infections in the community?
Longhurst: That's part of this paper that was just published in Nature. We're working hard to be able to correlate those wastewater viral levels with number of cases. It's not always easy because different variants can actually shed different amounts of particles in the gut. And so a single surge is comparable within itself, but not always to other surges. Now they're not exponentially different, so we can make some estimates, but we have to learn with each surge and each variant how those wastewater particles behave.
Have institutions such as the CDC and the World Health Organization promoted wastewater testing as sort of an official diagnostic tool for communities?
Longhurst: It's really gaining a lot of steam. So the Center for Disease Control has made this a strong recommendation that communities begin wastewater testing. As I mentioned, the governor made this a requirement as part of the SMARTER plan for the state of California. But it requires substantial infrastructure. You have to have testing facilities. You have to have the ability to monitor this on a regular basis. We're partnered closely with Dr. Seema Shah in the county of San Diego Public Health to make sure that we're getting these samples in a timely fashion. And then we're shortening that turnaround time from when we get the samples at UC San Diego to when we produce those results. And you'll see that on the search website where we now have results as quickly as three to seven days from time of sampling.
