Omicron COVID variant detected in Sacramento County wastewater last month, officials say

Researchers have detected the omicron variant of COVID-19 in recent wastewater samples in Sacramento.

“Sacramento County Public Health was notified on Friday, December 3 that there were low concentrations detected of the HV69-70 mutation that’s being used as a marker for omicron in a Sacramento sample collected on Tuesday, November 30,” Sacramento County spokeswoman Janna Haynes said in an email.

“These results were confirmed on Monday,” Haynes said in a follow-up statement. “These findings indicate that the Omicron variant is most likely present in Sacramento County. Please note that we have not identified any individual with this variant to date.”

Researchers with the Sewer Coronavirus Alert Network (SCAN) have conducted daily monitoring of SARS-CoV-2 viral materials in sewage across several jurisdictions since late 2020, including at treatment plants in Sacramento, Davis, Merced, the Bay Area and Southern California.

Around mid-2021, those researchers developed methodology to test samples for the presence of genetic variants, such as California’s previously dominant alpha and now-dominant delta.

The World Health Organization on Nov. 26 designated omicron as a variant of concern due to its large number of mutations and rapid spread in some parts of the world.

The SCAN team, made up of researchers from multiple universities including Stanford, quickly fine-tuned a process to monitor and double-check for omicron, said Marlene Wolfe, an environmental microbiologist at Emory University’s Rollins School of Public Health and one of the project’s lead researchers.

“We did find that mutation,” Wolfe said in a phone interview with The Sacramento Bee on Tuesday. “We detected it now on three different days in Sacramento,” beginning in late November.

Wolfe described the amount of omicron detected so far as “just about the minimum amount we can detect with our tests,” calling it consistent with about one to two cases per 100,000 residents.

“It’s likely that this is on the order of perhaps 10 to 20 people who would be shedding (omicron) into wastewater.”

Wolfe said at the 11 plants monitored by SCAN, omicron has been detected three times in Sacramento and once in Merced.

Sacramento’s daily samples recently have bounced between “detect and non-detect.” This is good news, Wolfe explained.

“It’s actually encouraging to see that we don’t detect it (every day). It tells us this hasn’t been here for a while ... we haven’t really missed anything. We’re really at the front edge of understanding what’s happening in these communities.”

What will be critical in monitoring omicron will be whether concentrations of omicron — and of COVID-19 overall — trend upward. With samples on only three non-consecutive days so far, and no cases confirmed yet by clinical labs, it remains too early to draw conclusions or forecast omicron’s potential trajectory in the region.

The wastewater analysis process examines human fecal samples for “SARS-CoV-2 viral genomes in those wastewater solids to then get a sense of how much COVID transmission is happening at a community level,” Wolfe explained in a previous interview with The Bee in July.

SCAN researchers communicate their findings to local health offices and to the California Department of Public Health. Wolfe said Tuesday that, over the course of the wastewater surveillance program, the correlation between rising levels of COVID-19 virus at treatment plants and increases of community case rates has held strong.

Speaking to The Bee over summer, during the surge linked to the delta variant, Wolfe said SCAN researchers were still working to determine whether wastewater surveillance could be used to detect genetic variants.

A few months later, SCAN has developed a process to look for variants that’s now routine.

“Every variant is characterized by the mutations that are most important and most consistently observed in circulation,” Wolfe explained Tuesday. “We choose specific mutations that are characteristic of the variant to look at.”

Wolfe said one of the mutations found in omicron is also found in alpha — the variant that was common in California before delta arrived. This meant SCAN already had a test at the ready to look for preliminary signs of omicron, since alpha is no longer widely circulating in California.

To be sure, the researchers analyzed the three days’ samples for another mutation that is in omicron but not in alpha. All three days returned positive, Wolfe said.

Wolfe also emphasized that these findings represent “the genetic markers of omicron” and do not mean that infectious virus is being transmitted via wastewater.

Wastewater surveillance has advantages and disadvantages compared to traditional PCR testing: it can detect broad, community-wide trends regardless of testing capacity, and it can detect them a few days quicker than those tests. But wastewater testing alone can’t give insight into specific hot spots or outbreaks across different parts of a city served by the same treatment plant.

Omicron had not as of midday Tuesday been detected in Sacramento County via traditional sequencing of a test result.

The first confirmed U.S. case of omicron came in a San Francisco resident who returned from travel in South Africa late last month, state and local health officials announced last week. Omicron has also since been confirmed in Los Angeles and Alameda counties.

Health officials worldwide continue to study omicron to determine whether it is more transmissible than delta; whether it causes more severe or milder illness; and whether it reduces protection from vaccination or prior infection.

“There’s a lot that we still have to learn about the omicron variant,” Sacramento County health officer Dr. Olivia Kasirye said during a Board of Supervisors meeting Tuesday.