Scientists in Oregon are searching for the Omicron variant somewhere you may not expect. In collaboration with Oregon State University (OSU), Oregon Health Authority’s wastewater surveillance program monitors sewage for variants of the SARS-CoV-2 virus. The program launched in September 2020 tests wastewater for COVID-19 in more than 40 communities throughout the state, covering more than 60 percent of Oregon’s population. All positive wastewater samples are sequenced to determine trends (increasing, decreasing, plateau) and which variants are circulating in communities.  

“It is something that’s really pretty unique to Oregon,” said Dr. Melissa Sutton, the Oregon Health Authority’s medical director of viral pathogens.  “You can find it in other jurisdictions, but not typically at the same scale.”

Starting this week, the team will begin testing wastewater for the Omicron variant. Wastewater surveillance has previously identified emerging variants, including Delta. When samples in wastewater test negative, it means the level of the virus is too low to be detected in the sample provided. That does not mean, however, the virus is not present in the community.  

Samples of wastewater have been tested through Nov. 23 and have all been found negative for the Omicron variant. More recent samples are undergoing testing now. The wastewater monitoring dashboard is updated every Wednesday.

“Once Omicron is circulating in communities, we expect to detect it in wastewater,” Sutton said.

Oregon also sequences clinical specimens from positive COVID-19 molecular tests to detect SARS-CoV-2 variants in the community. To date, Oregon has sequenced 7.1 percent of all positive molecular specimens, and ranks 11th in the country in sequencing volume.

“That might not sound like a lot, but it’s actually a really large number,” said Sutton. “You really only need to sample a small proportion of all individuals to provide accurate estimates of variants in our population.” Wastewater surveillance complements individual-level surveillance testing. It offers several advantages over individual-level sequencing—it is cost-effective and detects infections that may be asymptomatic or occur in people who haven’t been tested.