Coronavirus mutations and variants—what do we know?

Viruses mutate, and SARS-CoV-2 is no exception. Throughout the current global crisis, SARS-CoV-2 has been mutating at a rate of about 1–2 mutations per month [1]. Some recent emerging variants, however, have accumulated significantly more mutations in short periods of time, causing concern around the globe [2]. Scientists predict that these mutant lineages of the SARS-CoV-2 strain will not be the only concerning variants that emerge, as continued uncontrolled transmission of SARS-CoV-2 in many parts of the world and selective pressures, such as vaccines, are creating ideal conditions for additional, significant virus evolution [3].



Known mutations and variants of SARS-CoV-2

Multiple variants have recently made headlines, including a new UK variant known as 501Y.V1, VOC 202012/01, or B.1.1.7 lineage and a South African variant known as 501Y.V2 or B.1.351 lineage. Both have multiple mutations in the S gene, though the variants emerged independently [4]. There is no indication that either the B.1.1.7 or B.1.351 lineage is associated with more severe disease, but both are believed to be significantly more transmissible and therefore have potential to increase hospitalizations and deaths, especially in areas with already at-capacity healthcare systems [4,5].

One particular mutation in the S gene, a double deletion at positions 69 and 70 on the spike protein gene (69-70del), is observed in the B.1.1.7 lineage (501Y.V1 or UK variant). The 69-70del is of particular interest to clinical testing labs as it has an impact on the pattern of detection when using some molecular diagnostic PCR tests. While the B.1.1.7 lineage (501Y.V1 or UK variant) includes the 69-70del, the B.1.351 lineage (501Y.V2 or South African variant) does not.

Find out more about these emerging mutations and variants below.

B.1.1.7 lineage (501Y.V1 or VOC 202012/01 or UK variant)

The B.1.1.7 lineage emerged in the UK in late 2020 and has since spread to multiple other countries. It has a large number of mutations throughout the genome, including the 69-70del mutation in the S gene. While B.1.1.7 shows increased transmissibility, preliminary evidence suggested there was no indication it was associated with increased disease severity. [6]. However, more recent studies do indicate that there is a realistic possibility of increased risk of death in patients infected with B.1.1.7. [7].

B.1.351 lineage (501Y.V2 or South African variant)

South Africa reported a new variant, 501Y.V2 (B.1.351 lineage), named for the N501Y mutation in the receptor binding domain (RBD), in late 2020. The N501Y mutation is shared with the B.1.1.7 (UK) lineage, but the two variants are phylogenetically different and emerged independently [4]. While B.1.351 is linked to higher viral load and increased transmission, there is currently no evidence that B.1.351 is associated with increased severity of disease. [6] Read more at the link below.


The effect of mutations on sensitivity of the TaqPath COVID-19 diagnostic tests

We are committed to providing our customers with gold-standard molecular diagnostic technology. 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. Currently, there is only one mutation to be aware of in relation to the TaqPath COVID-19 portfolio of tests—the 69-70del S gene mutation of B.1.1.7. Since these assays are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted by the B.1.1.7 variant. [6].

The TaqPath COVID-19 diagnostic tests use a multi-target (orf1ab, N gene, s gene) design to compensate for emerging SARS-CoV-2 variants and mutations. Furthermore, they are unique among the most commonly used molecular tests in that the design includes an S gene target. If a sample with a variant that has the 69-70del is tested using the TaqPath COVID-19 tests, it will result in an S gene dropout. Because of this, the test may signal the presence of the 69-70del and, potentially, B.1.1.7. The US FDA and European CDC have both noted this could help with early identification of B.1.1.7, thus helping to reduce further spread of infection [2,7].

None of the mutations in B.1.351 (501Y.V2) are known to affect our TaqPath COVID-19 portfolio of tests.* As B.1.351 does not include the 69-70del mutation, an S gene dropout will not be observed.



SARS-CoV-2 epidemiological surveillance—shedding light on our blind spots  


Global epidemiological surveillance is vital for understanding the evolution of viral pathogens and monitoring for changes in transmissibility, virulence, and disease pathology. As such, global surveillance plays a central role in proactively managing pathogens. However, to date, there are only local surveillance efforts in play with limited global coordination of effort to monitor emerging variants—we are flying blind in the face of this coronavirus. Without a robust, coordinated universal effort to identify and characterize emerging variants, societies run the risk of suffering significant setbacks in health care and economy.

Confirmation of emerging SARS-CoV-2 mutations and variants can be accomplished by sequencing. Thermo Fisher Scientific offers multiple options for SARS-CoV-2 research isolates.


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We offer a complete portfolio of COVID-19 testing solutions. All of our assays are designed with mutations in mind, providing confidence in results. Request more info to find the best kit for your needs.

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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




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* As of January 20, 2021.
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.

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