Looking for omicron in S.D.: 1.7% of COVID-19 cases are sequenced for variants

KELOLAND.com Original

SIOUX FALLS, S.D. (KELO) — To find COVID-19 variants, you have to look for them. 

Throughout the COVID-19 pandemic, there hasn’t been a lot of looking for variants in South Dakota, according to a global science initiative that provides access to genomic data.

The search for variants is led by the South Dakota Department of Health, which first reports if any variant cases are detected in the state. The DOH says variant cases of COVID-19 are identified by genomic sequencing performed by the state public health lab, the Centers for Disease Control and Prevention and other partners. 

Once a variant has been identified, state health officials say it indicates wider, or more, transmission within a community. The DOH says the process, called sentinel monitoring, uses a very small proportion of COVID-19 positive tests to look for variants.

According to data from GISAID, South Dakota has shared the fewest COVID-19 positive genomes to be sequenced of all 50 states.  

Since the start of the pandemic, GISAID data shows South Dakota has shared 2,870 genomes, out of more than 168,000 reported cases, to look for COVID-19 variants. GISAID reports 1.7% of COVID-19 cases in South Dakota are sequenced to look for variants. Oklahoma was ranked lowest with less than 1% of total COVID-19 cases being sequenced and Vermont the highest with 18.8% of total cases being sequenced. 

Of South Dakota’s 2,870 sequenced genomes, the DOH reports 1,277 variant cases of COVID-19 have been found – 1,096 of the delta variant, 176 of the alpha variant, three of the gamma variant and two of the beta variant. 

Avera Health assists the DOH with genomic sequencing and Dr. David Erickson said Avera is now setting up to sequence for the omicron variant.

“What’s circulating currently is the delta variant,” Erickson said. “Many are concerned that very quickly this may transition to the omicron variant. We don’t know that yet, but that’s certainly the concern. The only way you’re going to know is if you sequence those viruses and look for it.”

Erickson said there’s a lot of people, including himself, who believe the omicron variant is already in many states in the United States and many countries around world.

“You’re just not able to screen everybody with generic sequencing,” Erickson said. “Most of the experts believe, if it isn’t here, it’ll be here shortly.”

Erickson also noted CDC director Rochelle Walensky said last week the CDC is sequencing 80,000 samples across the country per week looking for variants. That is up from 8,000 samples sequenced per week earlier this year, Walensky said.

The presence of COVID-19 variants also show the importance of getting a COVID-19 test when experiencing any symptoms, Erickson said. Regardless of vaccination status, Erickson said even people with mild symptoms should take a test, and if you are feeling sick, you should stay home.

During Tuesday’s budget address, Gov. Kristi Noem (R-S.D.) suggested lawmakers approve $69 million to be used for building a new state public health lab. You can view Noem’s proposal below.

A study by an engineering company said the public health lab’s needs can no longer be met by the existing 25-year-old building.

Funding for the new the public health lab, which would also include DOH administrative service and training building, would be funded from the American Rescue Plan, which needs federal approval.

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