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Wastewater surveillance for COVID and other diseases continue

The declared state of emergency for COVID-19 pandemic may be over, but the virus isn’t totally gone. KPBS Health Reporter Matt Hoffman says a program to track COVID and other virus’ in our wastewater continues.

The declared state of emergency with the COVID-19 pandemic may be over, but the virus is not totally gone. Testing for COVID-19 at home is easy and efficient. However those results are not tracked countywide — that is where sewage comes in.

“Although not everyone takes a test these days or reports a test — everyone poops,” said Rob Knight, director of UC San Diego’s Center for Microbiome Innovation. “We see signals from everybody when it gets into the wastewater.”

Knight pioneered wastewater testing for COVID-19 at UC San Diego (UCSD). It started during the first year of the pandemic, analyzing samples from the Point Loma Treatment Plant before expanding to the Encina and South Bay treatment plants. Knight said the testing has proven to be an early indicator of viral spread, with detection up to two weeks before standard testing. That is because infections first develop in someone’s gut. The sewage testing is continuing in post-pandemic emergencies.


“Although there’s the general feeling that COVID is over — it could be like the flu where new variants arise that are much worse than the variants we have currently,” Knight said. “And if you have to set up the program again from scratch — train all the staff and so on — it’s very difficult to do that. So as an insurance policy, it’s very valuable to keep it going.”

Knight said the amount of COVID-19 in the wastewater is the lowest it has been in about a year. In the past, San Diego County has seen summer and winter surges as the virus evolves. Wastewater testing allows researchers to see within a day or two what strain or variant is dominant, something Knight said is critical.

“You probably remember the omicron spike that caught everyone by surprise and then before that, the delta spike that caught everyone by surprise — we’d really like there to be no more surprises at this point,” Knight said.

San Diego County Public Health Officer Dr. Wilma Wooten said her office is contracting with UCSD to continue wastewater testing for at least five more years.

“I personally view wastewater testing as the future of surveillance in public health,” Wooten said.


The county is also working with partners to look for other diseases in wastewater. In addition to UCSD, samples are sent to WastewaterSCAN, which monitors the sewage for COVID-19, influenza (flu), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), norovirus and mpox (formerly referred to as monkeypox).

“That’s the beauty of wastewater testing is the early detection of viruses,” Wooten said. “It helps you determine that quicker than waiting to diagnose people with a particular disease or infection.”

Samples are taken from wastewater treatment plants twice a week. On UCSD campuses, they have their own testing process that examines samples taken nearly every day from more than 100 locations. Knight said research is underway to see how wastewater data can be used in other ways too.

“What I’m really excited about in the longer run is applying what we know about the microbiome to these wastewater samples and using it for much longer-term predictive health.”

Knight said stool samples can be used to help predict certain health conditions. He referenced the Karelia region of Finland, which he said went from being among the worst areas in Europe for cardiovascular disease to being among the best.

“That sort of potential could be stored right there in these wastewater samples that we are literally flushing down the toilet right now,” Knight said.

Knight said using wastewater to monitor diseases like COVID-19 presents a much less biased picture than just testing results.

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