Thermo Fisher: TaqPath COVID-19 Tests Detect SARS-CoV-2 In Samples Containing Omicron Variant

Thermo Fisher Scientific Inc. (TMO) confirmed Monday that its polymerase chain reaction or PCR TaqPath COVID-19 Combo Kit, and TaqPath COVID-19 CE-IVD RT-PCR Kit, which test for the presence of SARS-CoV-2, are not impacted by the emerging B.1.1.529, or Omicron variant, enabling accurate test results.

The World Health Organization or WHO has designated the Omicron variant as a "variant of concern". It has more than 30 mutations in the spike protein alone. The WHO has reported that preliminary evidence suggests an increased risk of transmission compared to other variants of concern.

The WHO and European Centers for Disease Control have both reported that using S-gene target failure or SGTF of the PCR assays as a proxy for the variant helped to identify Omicron. Cases of the variant, which were first identified in South Africa, have now been reported in at least a dozen countries around the world.

The company noted that TaqPath COVID-19 assays detect SARS-CoV-2 infections by identifying the presence of three gene targets from the orf1a/b, S, and N regions of the virus. By surveying across multiple genes, the test can report accurate results even in the case where one of the targets is impacted by a mutation.

The overall accuracy of the TaqPath COVID-19 assays is not impacted, Thermo Fisher noted. While the S gene target in the test is impacted in the presence of Omicron variant mutations, the orf1a/b and N gene targets in the TaqPath COVID-19 tests have been determined to not be impacted by any of the mutations in the Omicron variant, based on assessment of sequences in the GISAID public database.

The Omicron variant has been found to include the 69-70del mutation of the S gene, first identified as a mutation in the Alpha variant. This mutation causes a dropout of the S-gene target in results from the TaqPath test, which could indicate to clinicians and researchers a possible Omicron variant infection. Confirmation must then be performed by sequencing the sample.

Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation (CERI), Stellenbosch University and UKZN, South Africa, said, "The Thermo Fisher test allowed us to detect cases that may contain the new variant by identifying samples exhibiting S-gene dropout. This early identification is very important in helping us track and understand the spread of the B.1.1.529 variant to South Africa and the world."

In addition to the original TaqPath COVID-19 tests, Thermo Fisher has developed the TaqPath COVID-19 2.0 tests with an advanced assay design to compensate for emerging mutations.

The company noted that specific genotyping assays to detect the Omicron variant are being developed for Thermo Fisher'sTaqMan Mutation Panel.

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