The TaqPath COVID-19 Combo Kit*, TaqPath COVID-19 CE-IVD RT-PCR Kit*, and the Accula SARS-CoV-2 Test*, 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 Omicron variant, which was designated a “variant of concern” by the World Health Organization (WHO), 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. This designation and information are leading to renewed travel restrictions and research to examine the variant’s impact on efficacy of existing vaccines and tests. The WHO, the FDA, the CDC, and the European Centers for Disease Control have all reported that using S-gene target failure (SGTF) of PCR assays as a proxy for the variant helped in identifying Omicron, and the CDCs have specifically recognized the TaqPath assay for these findings (1, 2). Cases of the variant were first identified in South Africa and have now been reported in at least a dozen countries around the world.
The 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 out accurate results even in the case where one of the targets is impacted by a mutation. While the S gene target in the test is impacted, the orf1ab 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. As a result, the overall accuracy of the TaqPath COVID-19 assays is not impacted.
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. Thermo Fisher provides both Sanger sequencing and next-generation sequencing solutions for SARS-CoV-2 sequencing.
In addition to the lab-based TaqPath COVID-19 PCR tests, Thermo Fisher Scientific offers the rapid RT-PCR, point of care Accula™ SARS-CoV-2 Test. The Accula test targets a separate part of the genome, the Nucleocapsid (N) gene. Based on sequences published in GISAID database, the Omicron variant contains an ancestral 28881-28883 (GGG to AAC) mutation in the region of the N gene targeted by the Accula test. This mutation has been circulating in SARS-CoV-2 sequences since January 2020 and has been demonstrated to have no impact on Accula SARS-CoV-2 test performance (3).
Specific genotyping assays to detect the Omicron variant are being developed for Thermo Fisher’s TaqMan Mutation Panel**. The panel, which is currently used for research purposes, already has a menu of over 50 assays to assess confirmed COVID-19 cases for the presence of known variants and mutations.
Thermo Fisher is committed to supporting the world’s pandemic response through the monitoring of new SARS-CoV-2 variants and developing and producing innovative, adaptive, and resilient testing solutions using gold-standard PCR technology. This work helps track and subsequently limit the spread of COVID-19, helping communities stay healthy.
For more information about COVID-19 testing solutions from Thermo Fisher Scientific, please visit: https://www.thermofisher.com/covid19
*TaqPath COVID-19 Combo Kit and Accula SARS-CoV-2 Test: For Emergency Use Authorization (EUA) only. For prescription use only. For in vitro diagnostic use.
The Accula SARS-CoV-2 Test has not been FDA cleared or approved. It has been authorized for emergency use by the FDA for use by laboratories certified under the Clinical Laboratory Improvement Amendments (CLIA) of 1988, 42 U.S.C. §263a, that meet requirements to perform high, moderate, or waived complexity tests. The test is authorized for use at the Point of Care (POC), i.e., in patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation. The Accula SARS-CoV-2 Test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens. The emergency use of this test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Federal Food, Drug, and Cosmetic Act, 21 U.S.C. § 360bbb-3(b)(1), unless the declaration is terminated or authorization is revoked sooner.
** For Research Use Only
3) Totten, A. H. et al. Detection of SARS-CoV-2 variants by Mesa Accula. J. Clin. Virol. 141, 104901 (2021).