Coronavirus variants and mutations—what do we know?
This content 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. Omicron is currently the only circulating variant of concern (VOC) listed by the World Health Organization. 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, performance of vaccines, diagnostic tools, and infection control measures.
As SARS-CoV-2 mutates, COVID-19 testing labs may have questions about the potential impact of the mutations on current molecular diagnostic tests.
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.
Podcast: BBC interview w Manoj Gandhi, Senior Medical Director for Genetic Testing Solutions, Thermo Fisher Scientific: "The Omicron Variant, Testing Solutions, and the Pandemic Response."
The S gene target failure infographic: Learn more about this COVID-19 testing phenomenon, as well as an advantage that certain Applied Biosystems TaqPath COVID-19 diagnostic solutions* can offer in terms of surveillance for variants of concern.
The effect of mutations on inclusivity of the TaqPath COVID-19 diagnostic 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 uses 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 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.
Different variants have different mutations in the SARS-CoV-2 genome. Currently, only one known mutation—the 69-70del in S gene—is noted in relation to the TaqPath COVID-19 portfolio of tests. It should be noted that none of currently known mutations affect the ability of our Applied Biosystems TaqPath COVID-19 portfolio of assays to detect the virus.*
The 69-70del mutation is a 6-nucleotide deletion (21765–21770) in the spike (S) gene. The 69-70del mutation was initially observed in the B.1.1.7 lineage, designated by the World Health Organization (WHO) as the Alpha variant. The 69-70del mutation is also observed in the SARS-CoV-2 Omicron variant (lineage B.1.1.529, also known as 21M). The Omicron variant is diverse and includes sub-lineages BA.1 (also known as 21K; BA.1 includes multiple sublineages), BA.2 (also known as 21L; BA.2 includes multiple sublineages including BA.2.12.1), BA.3, BA.4, and BA.5. and their descendent lineages. The BQ1 and BQ1.1 sublineages of BA.5 are currently gaining dominance in the US and across Europe. The 69-70del mutation is observed in the BA.1, BA.3, BA.4, and BA.5 lineages and their respective sublineages. The BA.2 lineage does not contain the 69-70del mutation. Since our assays are designed to detect multiple genetic targets, the overall inclusivity of our tests should not be impacted by the currently known variants.
TaqPath COVID-19 diagnostic tests
The TaqPath COVID-19 diagnostic tests use a multi-target (orf1ab, N gene, and 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, also known as the S gene target failure (SGTF). Because of this, the test may signal the presence of the 69-70del.
The SGTF helped detect the Alpha variant, the initial outbreak of the Omicron BA.1/BA.3 variant, as well as the replacement of the BA.1/BA.3 variant with the BA.2 variant. For the Omicron variant BA.2 and other SARS-CoV-2 variants without the spike protein mutations, the TaqPath COVID-19 diagnostic tests detect all three gene targets from the orf1ab, S, and N regions of the virus.
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.
- 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 detecting pathogens, novel mutations, and controlling the associated outbreaks.
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.
- World Health Organization (WHO). Tracking SARS-CoV-2 variants. 2022.
- World Health Organization (WHO). Enhancing response to Omicron SARS-CoV-2 variant. 2022.
- Food and Drug Administration (FDA). SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests. 2021.
- Centers for Disease Control and Prevention (CDC). Science Brief: Omicron (B.1.1.529) Variant. 2021.
- European Centre for Disease Prevention and Control (ECDC). SARS-CoV-2 variants of concern as of 10 November 2022.
* As of May 19, 2022.
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.