A Reference Guide to Notable SARS-CoV-2 Variants

This blog represents the most up-to-date information as of November 16th, 2022.

Viruses constantly mutate leading to the emergence of new variants. SARS-CoV-2 is no exception. Multiple variants of SARS-CoV-2, such as Alpha, Delta, and Omicron, have appeared globally in this pandemic. While changes are inevitable, scientists and public health officials are concerned that some changes, such as the spike protein mutations, could affect pathogen transmissibility, disease severity, clinical management, performances of vaccines, diagnostic tools, and infection control measures [1].

As SARS-CoV-2 mutates, COVID-19 testing labs may have questions about the potential impact of the mutations on current molecular diagnostic tests.

Mutations and the TaqPath COVID-19 portfolio of tests

We are committed to providing our customers with up-to-date, accurate, and efficient molecular diagnostic technology. The TaqPath COVID-19 portfolio of diagnostic tests use a multi-target assay design to compensate for emerging SARS-CoV-2 mutations. Additionally, we actively monitor post-market reports, publications, and public genomic databases to ensure our coronavirus assays continue to meet the highest quality standards. As part of our post-market surveillance efforts, we collect, review, and analyze data on the performance of our tests, including assessing whether any emerging mutations overlap with our assay design.

As our TaqPath COVID-19 portfolio of assays are all designed to detect multiple genetic targets, the overall test sensitivity should not be affected by the currently known SARS-CoV-2 variants [2]*.

Reference guide to notable SARS-CoV-2 variants and the TaqPath COVID-19 tests

The table below lists the variants of SARS-CoV-2 have been named Variants of Concern (VOCs) by the World Health Organization [1][3]during different stages of the pandemic and the currently known impact on the TaqPath COVID-19 tests. Omicron is currently the only circulating variant of concern (VOC) listed by the World Health Organization.

Table 1: SARS-CoV-2 variants designed as Variants of Concern (VOCs) during different stages of the pandemic and their currently known impact on our tests

WHO Label	Pango Lineage	Nexstrain Clade	Earliest Documented Samples	Date of VOC Designation	Associated Phenotype	Currently Known Impact on Our Tests
Alpha	B.1.1.7	20I (V1)	United Kingdom, Sep-2020	18-Dec-2020	Increased transmissibility and mortality.⁴	No known impact on overall test sensitivity. Decreased detection of only the S gene for variants containing 69-70del mutation (S gene dropout) S gene advantage: Observable S gene dropout may signal presence of 69-70del & potentially B.1.1.7
Beta	B.1.351	20H (V2)	South Africa, May-2020	18-Dec-2020	Reduced antibody recognition, associated with vaccine resistance.⁵	No known impact on overall inclusivity of the tests.
Gamma	P.1	20J (V3)	Brazil, Nov-2020	11-Jan-2021	Reduced antibody recognition, associated with vaccine resistance⁶	No known impact on overall inclusivity of the tests.
Delta	B.1.617.2	21A, 21I, 21J	India, Oct-2020	11-May-2021	Increased transmissibility, associated with breakthrough infections among the vaccinated and more severe illness in unvaccinated individuals.^7,8	No known impact on overall inclusivity of the tests.
Omicron*	B.1.1.529	21 M	Multiple countries, Nov-2021	26-Nov-2021	Increased transmissibility, associated with less severe disease in general, associated with breakthrough infections among the vaccinated individuals.⁹	No known impact on overall inclusivity of the tests.
	*Descendent Pango Lineages of Omicron and their Currently Known Impact on Our Tests*
	BA.1 (and all sublineages)	21 K	No known impact on overall inclusivity of the tests. Decreased detection of only the S gene for variants containing 69-70del mutation (S gene dropout). Observable S gene dropout may signal presence of 69-70del and potentially Omicron sublineage BA1, BA3, BA4, or BA5.
	BA.2 (and all sublineages, including BA.2.75, BJ.1, XBB)	21 L (BA.2.75 = 22D)	No known impact on overall inclusivity of the tests. No observable S gene dropout.
	BA.3	–	No known impact on overall inclusivity of the tests. Decreased detection of only the S gene for variants containing 69-70del mutation (S gene dropout). Observable S gene dropout may signal presence of 69-70del and potentially Omicron sublineage BA1, BA3, BA4, or BA5.
	BA.4 (and all sublineages, including BA.4.6)	22A	No known impact on overall inclusivity of the tests. Decreased detection of only the S gene for variants containing 69-70del mutation (S gene dropout). Observable S gene dropout may signal presence of 69-70del and potentially Omicron sublineage BA1, BA3, BA4, or BA5.
	BA.5 (and all sublineages, including BF.7, BF.14, BQ.1, BQ1.1.)	22B	No known impact on overall inclusivity of the tests. Decreased detection of only the S gene for variants containing 69-70del mutation (S gene dropout). Observable S gene dropout may signal presence of 69-70del and potentially Omicron sublineage BA1, BA3, BA4, or BA5.

Learn more
Visit our emerging mutations and variants webpage for more information. If you have questions about the emerging variants and their impact on the efficacy of our portfolio, or if you would like to discuss your specific situation, please contact our technical support team at thermofisher.com/contactus.

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Intended use and regulatory statements of products vary. For specific intended use and regulatory statements please refer to the Instructions for Use (IFU). Product availability by country varies. For product availability in your country, check the associated product webpages.

*November 16th, 2022

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