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State lab sequencing to find COVID-19 variants

Updated: Apr. 1, 2021 at 5:23 PM EDT
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CHARLESTON, S.C. (WCSC) - While COVID-19 variants are still being detected in South Carolina, the majority of samples sequenced here are still the original strain of SARS-CoV-2, according to the state health department.

DHEC officials told us it does not appear that the dominant strain has shifted or changed over the course of the pandemic.

“Most samples sequenced continue to be the original strain,” a spokesperson told us in response to questions we submitted via email to the State Emergency Response Team for COVID-19.

The CDC is tracking five “variants of concern” nationwide.

So far, two of the “variants of concern” have been identified in South Carolina: B.1.351 (South African variant) and B.1.1.7 (United Kingdom Variant).

Regular COVID-19 testing shows whether a person is negative or positive for the virus but does not indicate what strain of the virus the person contracted.

Determining the variant or strain requires sequencing of the sample.

“Sequencing is a much more involved process that takes several days to complete between the sequencing process and the data analysis that is needed. Consequently, only a sample of positive tests are sent for sequencing,” the response said.

DHEC’s Public Health Laboratory selects random samples from each region of the state for sequencing, they said. Samples also are sent to the CDC, which works with various private labs for sequencing and sampling.

According to DHEC’s variants dashboard, they have detected 61 cases of the South African variant and 62 cases of the UK variant in South Carolina.

20 samples (32.7%) detecting the South African variant were in the Lowcountry. 18 samples (29.0%) detecting the UK variant were in the Lowcountry.

As the numbers represent samples, not the precise prevalence of the variants, actual numbers are likely higher in the community.

“As we build greater capacity to conduct sequencing, we will be able to have a better sense of the prevalence of different strains,” DHEC said.

Roper St. Francis Express Care Dr. Melissa Ellis- Yarian shared some good news from a CDC study of COVID-19 vaccine effectiveness.

“People have been worried about these variants. And actually, during the time they were monitoring people who’d received the Pfizer and Moderna vaccines, the variants were circulating,” said Dr. Ellis-Yarian. “Especially the one from the UK that’s been here in the United States. And Pfizer and Moderna both are protective against that so far, so that’s really encouraging.”

According to DHEC’s website, the UK variant spreads more easily and quickly than other variants. At this time, however, it says the CDC has no evidence that variants cause more severe illness or increased risk of death.

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