New SARS-Cov-2 variants identified

Jan. 21, 2021

There is an unsettling development in the COVID-19 pandemic – new variants of SARS-CoV-2, the virus that causes the disease.

According to the Centers for Disease Control and Prevention (CDC), at least two new variants are circulating, and they are:

• 20B/501Y.V1, VOC 202012/01, or B.1.1.7 lineage, which emerged in the United Kingdom in September with an unusually large number of mutations, and this variant has been detected around the world, including in the United States and Canada.

• 20C/501Y.V2, or B.1.351 lineage, which emerged in South Africa independently of the B.1.1.7 lineage but shares some mutations with the B.1.1.7 lineage. In addition to South Africa, where it was identified in October, the variant also materialized in Zambia in late December 2020.

The CDC said that the variant in the United Kingdom, B.1.1.7, is associated with more efficient and rapid transmission than the dominant form of the virus that had been circulating in 2020. Increased transmission can lead to a higher volume of cases, hospitalizations and deaths.

So far, there has not been evidence to suggest that either variant has any impact on disease severity or the efficacy of vaccines, according to the CDC.

The CDC also said that viruses generally mutate over time, leading to new variants, so public health experts were not surprised that this is what happened with SARS-CoV-2. For example, the strain of SARS-CoV-2 that first appeared in China in December 2019 was overtaken by a variant that became the dominant strain throughout the world by April 2020. The CDC also said that SARS-CoV-2 acquires about one new mutation in its genome every two weeks.

The CDC and other public health bodies have taken steps to detect and monitor the presence of new strains of SARS-CoV-2. State and local health departments send out 750 samples per week for sequencing and characterization. Under contract with the CDC, large reference labs also are sending sequencing data to the CDC, while some universities are conducting genomic surveillance.

Meanwhile, the U.S. Food and Drug Administration (FDA) said it is monitoring the potential impact of these viral mutations, particularly B.1.1.7, on authorized SARS-CoV-2 molecular tests. The agency said it is doing so because false negative results can occur with any molecular test if a mutation occurs in the part of SARs-Cov-2’s genome assessed by that test.

However, FDA experts also said they believe the risk that these mutations will impact overall testing accuracy is low. CDC officials concur, noting that polymerase chain reaction (PCR) tests for SARS-CoV-2 generally rely on the detection of multiple regions of the genome, so even if one target is impacted, the test should still be able to uncover the other target(s).

The FDA said there are three currently authorized molecular tests – Mesa Biotech Accula, Thermo Fisher TaqPath COVID-19 Combo Kit, and Linea COVID-19 Assay Kit – that may be impacted by genetic variants of SARS-CoV-2, but the impact appears to be insignificant.

What does this mean for laboratorians? It is important to take note of the latest research on SARS-CoV-2 variants, as well as any information that agencies like the FDA or CDC publish on the impact of the variants on commercially available COVID-19 molecular tests. Of course, the FDA also encourages laboratorians to report any issues with these tests to the agency through MedWatch, which is the FDA‘s safety and adverse-event reporting program.

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