How researchers are testing the omicron variant


Washington has been one of the best states in the country to detect variants by genomic sequencing since the start of the pandemic.

SEATTLE – As scientists around the world rush to detect cases of the novel omicron variant of the coronavirus, researchers at a UW medical lab are leading the way.

The laboratory at Department of Laboratory Medicine and Pathology is currently able to do 2,000 genetic tests per week. By Thursday, the lab was on track to making about 90%.

“The holidays and the supply chain issues have made a difference, but we are confident that we will make it happen next week,” explained Dr Pavitra Roychoudhury, Associate Researcher in the Division of Infectious Diseases in the Department of Laboratory Medicine. and pathology.

Given their testing capabilities, UW Medicine receives samples from across the country, and often up to 20,000 in a single day.

Regular PCR and rapid tests cannot detect COVID-19 variants, so more testing and genome sequencing is needed to detect the omicron variant.

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The process begins with testing positive cases of COVID-19.

Roychoudhury said this has been a bit of a problem. Since Washington state has a low positivity rate, it might need 10,000 tests to get 300 or 400 positive cases.

When researchers find a positive case, they extract the genetic material that makes up the virus to eventually sequence the entire viral genome.

“By getting this information, you can look at the mutations that occur in the genome of this virus, compare it to all the other viral genomes that exist for this virus, and tell which variant you are likely to have,” Roychoudhury explained.

Genetic sequencing is time consuming and given the sense of urgency to detect the omicron variant. Researchers are also performing other tests to look for mutations in the virus’s signature pattern. In the case of the omicron, it is the S.

In a briefing Monday, Dr Alex Greninger, assistant professor in the Department of Laboratory Medicine and Pathology, said almost all molecular tests performed in the state “have at least two targets, so even though there are had some sort of mutation in one of these variants affecting one of the targets, the other target would pick it up. Due to the multiple targets, each molecular test has some sort of “insurance policy” that the variant would have been detected.

Greninger said almost all COVID-19 antigen tests target the virus’s core protein, which “is not highly mutated.” Most of the omicron variant mutations are found in the spike protein.

The omicron variant has “sort of the same characteristic” as the alpha variant, which is a “small deletion in the spike protein,” Greninger explained. This makes the rapid screening of candidate omicron variants possible because it is variant specific.

Researchers at the UW lab said they were ready to detect the omicron variant, but were also concerned about how many unknowns still on the table.

“Every day I check the South Africa case numbers to see how it’s spreading in South Africa just to get a feel for what’s going on in the future,” Greninger told KING 5.

Roychoudhury said if omicron is detected, the first step is to alert state health officials. The lab would also keep the sample to continue testing, even sending it to other labs to see what they find.

The new variant of COVID-19 was first confirmed in the United States on December 1. Since then, she has been identified in several states.

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