What our poop is telling us about the omicron surge – San Bernardino Sun

Not everyone who comes down with COVID-19 gets tested. And even for those who do, depending on the type of test used, the results may never be counted among official case statistics.

But everyone poops. And because the virus that causes COVID-19 can be shed not just from your nose and mouth but from stool as well, flushing that waste into a sewage system can help public health officials monitor virus levels in your community.

Recently, all of those flushes are adding to the signs officials are seeing that the omicron surge may be peaking in Southern California.

“It seems like, in most locations, concentrations (of the virus in wastewater) are stabilizing, which is very reassuring,” said Kara Nelson, an environmental engineering professor at UC Berkeley who is in charge of the Covid-WEB monitoring program.

Scientists recognized early in the pandemic that they could use wastewater as one tool to monitor a community’s infection levels, and see a lot of promise for using this strategy in the future to keep tabs on the coronavirus as well as other diseases.

Southern California levels

Several wastewater treatment agencies in Southern California are participating in those efforts, including the Los Angeles County Sanitation Districts, the Orange County Sanitation District and the San Bernardino Municipal Water Department. Their data is shared with county and state health departments as well as the Centers for Disease Control and Prevention.

In Los Angeles County, two “sewersheds” that each serve millions of people are being monitored, said Prabhu Gounder, who oversees wastewater testing and other non-case-based surveillance efforts for L.A. County Public Health.

One is in the city of Los Angeles, and the other much larger one monitored by the county stretches from just south of Los Angeles International Airport to Long Beach, and stretches as far east as Pomona, Gounder said.

“The data from L.A. city suggests that case rates are still increasing,” he said. “From L.A. County sanitation, they have started to see a decline in concentrations.”

In San Bernardino County — whose sewershed also includes Loma Linda and part of Highland — coronavirus levels are declining almost as sharply as they rose. From late December to early January, concentrations rose more than 1,300%, but they’ve now fallen about two-thirds of the way back down, according to data provided by UC Berkeley.

Concentrations have been decreasing in Orange County as well, according to a California Department of Public Health spokesperson. The agency was not aware of any wastewater surveillance happening in Riverside County.

Other positive signs

The wastewater data is one of several indications in Southern California that the unprecedented surge in coronavirus infections that started this winter may be peaking:

  • The number of cases reported each day has begun declining in Los Angeles County, and appears to be leveling off in Orange, Riverside and San Bernardino counties.
  • The number of people in the hospital with a confirmed COVID-19 case is just starting to drop in L.A., Orange and San Bernardino counties, and is leveling off in Riverside County.
  • State data shows test-positivity rates are starting to decline in all four counties.

But officials emphasize that it’s too soon for people to relax the precautions they’ve been taking.

“Although these declines are a positive sign, residents should not take them as an indication to forgo common-sense protective measures that will allow these declines to continue,” L.A. County said in a news release Tuesday.

Nelson, from UC Berkeley, said that even though the virus concentrations in wastewater do seem to be stabilizing or decreasing, “We’re still seeing the highest concentrations that we’ve seen in the entire pandemic, so we are not out of this surge yet.

“There’s reason to be optimistic that everything we are doing is working, so we need to keep doing it.”

Early-warning system

To measure those concentrations, a wastewater treatment plant takes samples of its water every few days. Ryan Sinclair, an environmental microbiologist at Loma Linda University who’s been consulting for San Bernardino County during the pandemic, said the San Bernardino plant has a sampler that collects a small amount of water once an hour for 24 hours.

That composite sample is then filtered down to just the solids, and the RNA in those solids is extracted. A lab can then use PCR testing — the same kind you might get from a doctor, although obviously administered differently — to determine how much coronavirus was in the sample. A similar collection and testing method is used in L.A. County.

Wastewater tests can serve as something of an early-warning system when a surge is about to start, Sinclair said. That’s because people start shedding virus before they start feeling symptoms and decide to get tested, so an increase is likely to show up in the wastewater days before it shows up in clinical testing data.

“You can say, OK, we’re seeing a big spike here, so hospitals should be aware they’re going to have another big surge to deal with,” Sinclair said.

It also can help public health officials start getting the message out to the community to make sure they’re following safety guidelines, or determine where to schedule pop-up testing sites, Nelson said.

Gounder pointed out that wastewater data can be somewhat variable, so it’s not always clear that a jump in concentrations means virus levels are rising until other indicators start going up as well.

Other benefits

During a surge, if the clinical testing system gets overwhelmed, wastewater tests can still give officials a current picture, said Colleen Naughton, a civil and environmental engineering professor at UC Merced who is behind the COVID Poops dashboard and Twitter account.

Naughton and Nelson both said wastewater testing helped officials identify when the omicron variant showed up in a community sooner than they would have just from looking at individual clinical tests.

When the samples come from a treatment plant that serves a community with hundreds of thousands or even millions of residents, officials can’t tell precisely where an outbreak is happening.

But that could happen if funding were available to sample wastewater at the neighborhood level. And the technology could be used in smaller residential settings, such as nursing homes, jails and college dorms, to catch even one infection and try to stop it from spreading through the entire facility, Sinclair said. It also would be ideal to monitor disadvantaged communities whose residents might not have adequate access to clinical testing and vaccinations, he said.

Potential for the future

Testing wastewater for pathogens isn’t new; it’s been used for decades to monitor for diseases such as polio and hepatitis.

But its use boomed during the pandemic. The CDC and Department of Health and Human Services have now created a National Wastewater Surveillance System to monitor coronavirus in wastewater. California is participating, and Gounder said he believes the CDC will start posting data publicly online in the next few days.

Scientists say there’s a lot of potential for expanding wastewater testing, not just for coronavirus but for other scourges as well. Naughton said the EPA is looking at whether it could be used more widely to look for antimicrobial resistance, track influenza and other respiratory diseases, and even help measure the use of opioids and other drugs in a community.

Most health officials believe COVID-19 eventually will become an endemic disease — it won’t go away but it will become less disruptive. Wastewater testing could help officials spot outbreaks, in addition to the ways they track diseases now such as by monitoring emergency room visits and specimen tests.

“We’re not going to be able to continue testing at the level we are now, and we will need to have systems in place to understand what’s going on with community transmission and inform our policies,” Gounder said.


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