State officials step up testing for Omicron variant

State officials said they’re stepping up variant testing to identify Omicron when it arrives in Oregon.

The new strain, which was first detected last month in Botswana and then South Africa, turned up in California on Wednesday, and on Thursday three new cases emerged in New York, Minnesota and Colorado.

It might only be days before it arrives in Oregon.

The variant is more infectious than the Delta variant, according to the Oregon Health Authority and other sources. If it gains a foothold, it could become the dominant strain as it has in South Africa, experts said.

Health officials say vaccination is the best defense against the new variant and others, though it’s not yet clear whether the current vaccines can ward off Omicron. The first case in the United States occurred in someone who had traveled to South Africa and was vaccinated with two shots. That person only suffered mild symptoms, according to news reports. The Minnesota case was also in a vaccinated person who had a mild infection as well. 

In Oregon, the state has been testing since last spring to detect variants. Oregon Health & Science University, Oregon State University and the University of Oregon have genomic sequencing labs as well. OSU also has a surveillance program testing wastewater at 40 sites around the state to detect Covid-19. Next week, that program will start testing for Omicron, state officials said.

The state public health lab can sequence 200 samples a week, and it is working on expanding that capacity, a spokesman said. The University of Oregon has more capacity: It can sequence 3,000 samples a week at a cost of $19 per test.

The state currently has 11 variants on its radar. The highly infectious Delta variant is the only one listed as of concern. Omicron is not yet listed.

The state’s data dashboard indicates that only a relatively small number of variants are being found. For example, it showed that fewer than 30 variants emerged the week of Nov. 14, the latest date on the dashboard. That week, the state identified more than 6,000 confirmed and presumed Covid-19 cases.

To track variants, Covid-19 samples are tested with a common diagnostic molecular test, called PCR or polymerase chain reaction, that shows when there is a certain mutation in the spike protein that the virus uses to shoehorn itself into cells. When the mutation turns up, the samples are sequenced. Genomic sequencing is laborious and costly; the state only tests high-quality samples to tamp down costs. 

Since the pandemic started, it’s sequenced 7% of Covid-19 samples.