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Colorado National Guard member is first in US to have confirmed COVID-19 variant

A second National Guard member is suspected to have the variant
Virus Outbreak Colorado
Posted at 2:28 PM, Dec 30, 2020
and last updated 2020-12-30 14:28:42-05

A day after Colorado officials identified the first known case of COVID-19 variant B.1.1.7 in the United States, public health officials in the state are continuing to work to identify anybody else who may have been exposed and any other potential cases of the variant.

The variant, which had previously been reported in the United Kingdom, was found in a man in his 20s working in Elbert County, officials announced Tuesday. The Colorado Department of Public Health and Environment (CDPHE) said its lab was the first in the country to identify the new variant, but it's unlikely the man is the first person to have it in the U.S.

Dr. Emily Travanty, scientific director with the Laboratory Services Division of the CDPHE, noted a second "highly suspicious" case of B.1.1.7 in the same county, but said the results remain unconfirmed as of 10:30 a.m. Wednesday. Initial testing of this second sample shows most of the same mutations associated with the variant, but analysis is not complete yet, she said.

Both individuals are Colorado National Guard personnel who were deployed to support staffing at the Good Samaritan Society assisted living center in Simla in Elbert County, said Dr. Rachel Herlihy, state epidemiologist with the CDPHE. Their deployment began Dec. 23. They were both tested Dec. 24.

Neither individual has traveled internationally in the weeks prior to the tests. Both are isolating for 10 days — the confirmed case in a home in Arapahoe County and the suspected case in a hotel in Lincoln County. The man with the confirmed case has mild symptoms.

The assisted living center in Simla has an ongoing outbreak, and COVID-19 cases were first detected in mid-December following routine surveillance testing, Herlihy said. To date, 20 of the 34 regular staff — not National Guard members — and all 26 residents have previously tested positive for COVID-19. Four residents have died.

Testing is underway to determine if the variant is affecting residents and Herlihy said preliminary results show no evidence the variant is circulating there, but testing will continue Wednesday.

The National Guard member's infection of B.1.1.7 was confirmed with a PCR test, Travanty said. The variant has a distinct molecular signature, or a specific sequence in the S gene.

PCR tests look to the presence of three COVID-19 genes in each sample. Typically, if they're found, the patient is positive, Travanty explained. A sample of the B.1.1.7 variant results in only two of the genes — it lacks what's called the S gene. The presence of the other two genes means that a person is positive. The S gene is still present in the samples, but it has mutated and is typically undetectable in routine PCR tests. Travanty said this is called the "S drop-out profile" and is a signature marker of this specific COVID-19 variant.

When the state lab learned about this new variant, it set up a screen to capture samples where the two other genes were detected, but the S gene wasn't. Samples that meet this profile were flagged so researchers can do more research, Travanty said.

"Today, we've conducted sequencing on 24 of these suspicious samples and our scientists have found two samples that contain mutations in the S gene," she said.

Another 12 are ready for testing, she said. CDPHE will continue to look for mutations in older samples and future ones.

COVID-19 has many variants and early evidence has shown that B.1.1.7 might spread faster, but doesn't seem to include more severe symptoms, said Dr. Eric France, chief medical officer with the CDPHE. However, there is concern that if it's more transmissible, it could lead to more hospitalizations, more filled ICU beds, and the potential to overwhelm the health care systems, he said.

This story was originally published by Stephanie Butzer at KMGH.