UC Berkeley team detects omicron variant in Bay Area wastewater

Photo of a sewage pipe
Alvin Wu/File
COVID Wastewater Epidemiology for the Bay Area detected traces of the COVID-19 omicron variant in Bay Area wastewater, which team members say can help in sequencing the variant.

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A team of UC Berkeley researchers recently detected traces of the COVID-19 omicron variant in Bay Area wastewater.

COVID Wastewater Epidemiology for the Bay Area, or COVID-WEB, has developed methods of detecting the main virus and other variants in wastewater since the beginning of the pandemic, according to Sasha Harris-Lovett, COVID-WEB’s program manager and a postdoctoral fellow at the Berkeley Water Center. Campus professor of civil and environmental engineering Kara Nelson leads the program.

Harris-Lovett said the location where omicron was detected will remain unspecified until the testing is definitive. She explained the results “pretty clearly” point to the omicron variant, but the tests the researchers perform do not account for every mutation.

Additionally, the novelty of the variant means more RNA sequencing will help researchers understand what to look for.

“As omicron gets sequenced more and more, clinically and in wastewater, the understanding of what the mutations are may change,” Harris-Lovett said. “This is kind of a learning process.”

A few times per week, wastewater agencies use auto-samplers that take a small amount of wastewater every set number of minutes over a 24-hour period, according to Harris-Lovett. COVID-WEB researchers then extract the RNA and use a qPCR test, similar to a nasal swab test, to quantify the amount of viral RNA.

One of the advantages to wastewater testing is that it can provide early detection of new variants, according to Lee Riley, campus professor of infectious diseases and division head of infectious disease and vaccinology at the School of Public Health.

“This (testing) is really useful because people shed the virus even if they’re asymptomatic,” Harris-Lovett said. “The wastewater kind of provides a signal for what’s going on in the community as a whole.”

Traces of the virus will appear in the wastewater before community members show symptoms, Riley explained. In addition, wastewater testing can narrow the geographic region of the spread of a variant such as omicron.

Arthur Reingold, campus professor and division head of epidemiology, added wastewater detection can provide information about a whole community, but that large wastewater systems are less precise.

“If someone in the population is excreting the virus, you can detect it without having to go and test huge numbers of people,” Reingold said. “If you can’t pinpoint the community based on where the sample came from, then it’s less information.”

Although wastewater testing offers a broad picture, Harris-Lovett noted that it complements clinical testing in terms of identifying and tracking the virus.

Reingold emphasized that getting vaccinated remains the “single most important message.”

“If you’re not vaccinated, you should get vaccinated; if you’re vaccinated, then the current recommendation is that you should get boosted,” Reingold said.

Contact Riley Cooke at [email protected], and follow her on Twitter at @rrileycooke.