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 . Some recent emerging variants, however, have accumulated significantly more mutations in short periods of time, causing concern around the globe . 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 .
New information is rapidly emerging about SARS-CoV-2 variants, with questions about transmissibility, virulence, immune escape, and more.
Multiple variants have recently made headlines, including a UK variant known as 501Y.V1, VOC 202012/01, or B.1.1.7 lineage, a South African variant known as 501Y.V2 or B.1.351 lineage, a Brazilian variant known as 501Y.V3 or P.1 lineage, California variants known as B.1.427 and B.1.429, and many others. Some emerging variants are believed to be more transmissible and therefore have potential to increase hospitalizations and deaths, especially in areas with already at-capacity healthcare systems [4,5].
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 a 69-70del mutation in the S gene, which is of interest to clinical testing labs as it may have an impact on the pattern of detection when using some molecular diagnostic PCR tests. While B.1.1.7 shows increased transmissibility, preliminary evidence suggested there was no indication it was associated with increased disease severity [5,6]. 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 .
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 . 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 .
P.1 lineage (501Y.V3 or Brazilian variant)
The first report of P.1 came from Japan in January 2021 when the variant was detected in travelers from Brazil. The variant was first detected in Manaus, Brazil, the capital city of the Amazonas state, where sequencing results from December 2020 identified P.1 in 42% of samples tested. A recent study indicates P.1 is associated with increased transmissibility and potential for re-infection. [3,8]
B.1.427 and B.1.429 lineages (California or West Coast variants)
Recent studies indicate that B.1.427 and B.1.429 likely emerged in late spring or early summer of 2020. The two variants carry similar, though slightly different, genetic mutations. Early studies indicated that one mutation, L452R, may be linked to increased infectivity, and new research suggests that B.1.429 and B.1.427 may be more transmissible. 
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 most often associated with, but not limited to, 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 .
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, P.1, B.1.427, B.1.429 are known to affect our TaqPath COVID-19 portfolio of tests.*
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.
Learn more about SARS-CoV-2 mutation surveillance ›
Confirmation of emerging SARS-CoV-2 mutations and variants can be accomplished by real-time PCR or sequencing. Thermo Fisher Scientific offers multiple options for SARS-CoV-2 research isolates.
Featured solution for SARS-CoV-2 mutation detection
Use your current real-time PCR instrumentation to conduct follow-up testing to identify relevant mutations in your SARS-CoV-2 samples with the customizable TaqMan SARS-CoV-2 Mutation Panel.
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.
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.
- European Centre for Disease Prevention and Control 20 Dec 2020 Threat Assessment Brief
* As of March 15, 2021.
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