Coronavirus variants and mutations—what do we know?
This content represents the most up-to-date information as of November 29, 2021.
Viruses mutate, and SARS-CoV-2 is no exception. Throughout the current global crisis, SARS-CoV-2 has been mutating regularly. 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 .
Known variants and mutations of SARS-CoV-2
New information is rapidly emerging about SARS-CoV-2 variants, with questions about transmissibility, virulence, immune escape, and more.
A summary guide of notable emerging SARS-CoV-2 variants is available now.
Explore the interactive viewer or download a free poster about the different types of SARS-CoV-2 variants and mutations that are being discovered around the world.
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 most often associated with, but not limited to, B.1.1.529 and B.1.1.7. Since these assays are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted by B.1.1.529 and B.1.1.7 variants .
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.1.1.529 and 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 [1,4]. The WHO and European Centers for Disease Control have both reported that using S-gene target failure (SGTF) of PCR assays as a proxy for the variant helped in identifying Omicron.
The next-generation TaqPath COVID-19 2.0 assays support multiple workflows and compensate for emerging mutations. In order to provide increased confidence in our COVID-19 test results as SARS-CoV-2 continues to mutate, our Applied Biosystems TaqPath COVID-19 2.0 tests employ an advanced assay design that targets 8 sequences across 3 genomic regions (ORF1a, ORF1b, and N gene) to compensate for emerging SARS-CoV-2 mutations. This increased target redundancy ensures accurate results even in the presence of new emerging SARS-CoV-2 mutations, with high sensitivity and specificity, providing confidence in results now and into the future. TaqPath COVID-19 2.0 tests utilize the RNase P gene as an internal control. This design no longer requires the addition of an external extraction control, such as the MS2 bacteriophage for the TaqPath COVID-19 Combo Kit.
None of the mutations in B.1.1.529, B.1.351, P.1, B.1.617.2, B.1.621 are known to affect our TaqPath COVID-19 portfolio of tests.*
- World Health Organization: Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
- African CDC: Prevention’s Statement regarding the new SARS-COV-2 virus variant B.1.1.529
- eCDC: Threat Assessment Brief: Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA
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 and soutions offered from Thermo Fisher Scientific ›
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. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. 2020.
- Centers for Disease Control and Prevention. Science Brief: Emerging SARS-CoV-2 Variants. 2020.
- US FDA. Genetic Variants of SARS-CoV-2 May Lead to False Negative Results with Molecular Tests for Detection of SARS-CoV-2. 2021.
- Horby, P., Huntley, C, et al. Note on B.1.1.7 Severity. 2021.
- Danner, C. What We Know About the New P.1 Strain of the Coronavirus. NY Magazine. 2021.
- Wadman, M. California coronavirus strain may be more infectious—and lethal. Science. 2021.
* As of August 27, 2021.
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