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Omicron has been found in wastewater in California and Texas

AUDIE CORNISH, HOST:

Scientists say they have detected pieces of omicron in wastewater in Houston and two cities in Northern California. That indicates the COVID variant is present in those cities. What does that mean for public health? Raquel Maria Dillon from member station KQED explains.

RAQUEL MARIA DILLON, BYLINE: Last week, researchers flagged four samples from wastewater plants in Sacramento and Merced for genetic mutations that looked like omicron. On Monday, they did another round of tests, or assays, to be more sure, says Stanford environmental engineering professor Alexandria Boehm.

ALEXANDRIA BOEHM: Because we detected it with two different assays that target two different mutations in omicron and since they were both detected, I'm very, very sure that omicron is present in the wastewater samples.

DILLON: So far, the variant isn't showing up in nose swabs in Sacramento and Merced counties, and Boehm is not saying these four positive wastewater samples show community transmission of omicron.

BOEHM: And whether they are meaningful to public health, I think, will depend on whether there is an increasing trend in concentrations or if there's consistent detection over time.

DILLON: Researchers are looking for omicron in wastewater across the country. The fact that they found the variant at all is kind of amazing. Boehm's team can spot tiny fragments of the virus' RNA in giant wastewater plants, like this one in San Jose.

AMIT MUTSUDDY: Every time you flush, think of us.

DILLON: Amit Mutsuddy is deputy director here.

MUTSUDDY: So it serves about 1.4 million people and 22,000 businesses.

DILLON: Underneath the smelly tanks in a dimly lit tunnel, there's a sink where the gooey black sludge that sinks to the bottom comes out of a tap. It goes into collection jars that get sent to the lab daily.

(SOUNDBITE OF WATER GUSHING)

DILLON: If they find the telltale strands of omicron RNA in that gunk, researchers can identify its presence in a community in concentrations as small as 1 or 2 infections out of 100,000 people.

TYSON GRABER: Thankfully, we do know the language.

DILLON: Canadian cell biologist Tyson Graber compares wastewater testing to looking at an alphabet soup of RNA in the sludge and trying to recognize sentences that describe COVID's variance. But the RNA letters are combined with everything else that passes through your body plus last night's pan drippings that got scraped down that kitchen sink times about several hundred thousand other people.

GRABER: It's because of that that we really understand the language of SARS-CoV-2 now at a rate that is unprecedented in biomedical research history.

DILLON: Dr. Sara Cody, the chief health officer in Santa Clara County, says the beauty of wastewater surveillance is that everyone in a given area gets tested because, as the children's book says, everyone poops - even people who are infected but don't have symptoms and don't seek out a lab test, even people taking at-home rapid tests.

SARA CODY: If people aren't going out and getting a PCR test, those results and those cases aren't reported to us, and we won't see them in our case surveillance data. But we will still see it in our wastewater data.

DILLON: Santa Clara County has more than a year's worth of wastewater data to compare with results from PCR lab tests. Cody says they've learned when those lines track one another.

CODY: We started to see an uptick in a number of our sewer sheds just a little bit ago. And now we are beginning to see an uptick in our case count. So I think it gives us information a bit earlier.

DILLON: She says this kind of fast-moving collaboration between engineers, epidemiologists and microbiologists is an important new early warning system to help understand the speed and extent of omicron's spread.

For NPR News, I'm Raquel Maria Dillon in Oakland, Calif.

(SOUNDBITE OF MUSIC) Transcript provided by NPR, Copyright NPR.