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The science behind COVID genomic sequencing tests

Published: Dec. 1, 2021 at 4:51 PM EST
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PLATTSBURGH, N.Y. (WCAX) - The omicron variant of COVID-19 has not been found in our region yet and there are still plenty of unknowns about its origins. That’s why local health officials are using genomic sequencing tests to keep tabs on omicron or any other variants of concern.

“To try to summarize my understanding of things so far, it appears -- at least preliminarily -- this virus may be more contagious than delta,” said Dr. Keith Collins, an infectious disease specialist at CVPH in Plattsburgh. He says there are more questions than answers because the variant is so new. “I don’t think we yet have to think the sky is falling. We don’t know enough yet.”

Collins says the variant was discovered through sequential testing of positive PCR tests in southern Africa. The way sequence testing is done, groups of random samples of positive test swabs are sent to sequence testing labs to see which variant -- known or unknown -- is the cause of that positive result. “They sequence the entire genome of the entire virus and they can compare the genome of what they sequenced to known variants,” Collins said.

While CVPH does not have the ability to do sequential testing, there are labs across New York working daily to analyze the tests. Omicron is the 5th variant detected across the world and its first U.S. case just surfaced in California. Health experts tell CBS News that the next six to eight weeks will resolve many of the unanswered questions about the new variant.

“Some countries do a lot more sequencing routinely than others. Quite honestly, I think that is one thing that has been lacking on a consistent basis in the United States,” Collins said.

The U.S. is sequencing 80,000 positive PCR tests per week to test for variants but that’s only a small percentage of covid tests. The CDC has promised to increase its sequencing to one in every seven positive tests. And where you live plays a role on when you could see the new strain surface. Larger cities have more samples that are sent to the sequencing labs than smaller rural areas.

“We’re still getting the same proportion of our tests to have the same sequence testing on them to determine what variants are present, it’s just all relevant to your total population,” said Molly Flynn with the Clinton County Health Department.

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