This blog represents the most up-to-date information as of June 8, 2021.
The importance of lineage in variants
Coronaviruses mutate by making copies of themselves. Because these copies leave a lineage trail, scientists can track the mutations, which is how they become identified and then labeled as a specific viral family.
A variant is a group of coronaviruses that share the same lineage of mutation. If enough mutations accumulate in a lineage, it might change the way the variant functions. These lineages are known as strains. Consequently, COVID-19 is caused by a coronavirus strain known as SARS-CoV-2. One concern is that a number of variants have arisen during the pandemic, which questions vaccine efficacy.
Several new SARS-CoV-2 variants have emerged that range from having increased transmissibility to comparable or even potentially increased severity of disease. New information is rapidly emerging, and scientists are working to learn more about these variants and the mutations within their genomes to better understand how easily they might be transmitted, whether they may confer increased virulence, the effectiveness of currently authorized vaccines against them, and more. These epidemiological surveillance studies are critical for our collective fight to slow the spread of the SARS-CoV-2 virus.
What can you do to stay on top of the mutations?
Surveillance studies are vital for proactively managing pathogens. For labs who want to identify known mutations associated with specific variants in SARS-CoV-2 positive samples, we offer the customizable Applied Biosystems TaqMan SARS-CoV-2 Mutation Panel. You can build your own panel from a menu of 22 verified real-time PCR assays. This scalable solution lets you run a few or hundreds of samples to identify one or many mutations—all on your current real-time PCR instrumentation.
Table of Variants
Below is a table of SARS-CoV-2 mutations and associated significance in order to help you identify key mutations, what we know about them, and which lineage they derived from. We offer assays for each of these mutations so you can build your own custom TaqMan SARS-CoV-2 Mutation Panel [link to webpage] with the mutations that are most important to you.
|Mutation||Gene||Associated Variants||Variant Nickname||Mutation Significance|
|A1708D||ORF1||B.1.1.7||UK variant||Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report |
|A222V||S||B.1.177||Associated with fast growing lineage |
|A570D||S||B.1.1.7||UK variant||Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report |
|A701V||S||B.1.351||South African variant||Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report |
|D215G||S||B.1.351||South African variant||Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report |
|D614G||S||B.1.1.207,P.1, B.1.1.33, B.1.1.7, B.1.177, B.1.258, B.1.351, B.1.525, Mink Variant||Nigerian, UK, South African, Brazilian / Amazonas variant||Ability to spread more quickly with moderate effect on transmissibility |
|D80A||S||B.1.351||South African variant||Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report |
|delH69V70||S||B.1.1.7, B.1.258, B.1.525||UK variant||Conformation Spike Protein located in the N terminal domain of the S gene; Increased ability to evade immune response; Assays targeting S gene may not pick up |
|delY144||S||B.1.1.7||UK variant||Included in CDC Variants of Concern List |
|E484K||S||P.1, B.1.1.33,B.1.351, B.1.525||South African, Brazilian variant
|Mutation in receptor binding domain (RBD) region; Reduces antibody recognition; Interface with hACE2 receptor; Associated with vaccine resistance |
|E484Q||S||B.1.617||Indian variant||May have reduced neutralization against variants with an E484Q mutation |
|K417N||S||B.1.351||South African variant||Mutation to receptor binding domain (RBD) region in South African Variant |
|K417T||S||P.1||Brazilian / Amazonas variant||Defining SNP associated with P.1 lineage in PANGO International Lineage Report |
|L18F||S||P.1, B.1.351||South African, Brazilian / Amazonas variant||Defining SNP associated with P.1 lineage in PANGO International Lineage Report |
|L242_244L||S||B.1.351||South African variant||Deletion associated with the B.1.351 |
|L452R||B.1.617||Indian variant, California Variant||Associated with increased transmissibility, a reduction in neutralization by some (but not all) monoclonal antibody treatments, and a moderate reduction in neutralization in post-vaccination sera in the USA  Classified as a substitution of therapeutic concern by the CDC |
|N439K||S||B.1.258||Impacts ability to evade antibody-mediated immunity; Increased binding affinity to hACE2 receptor and evade some monoclonal antibodies |
|N501Y||S||P.1 , B.1.1.7, B.1.351||UK variant, South African, Brazilian / Amazonas variant||Located within receptor binding domain (RBD) one of 6 key contact residues; Increased binding affinity to hACE2 receptor in cells |
|P681H||S||B.1.1.207, B.1.1.7||Nigerian, UK variant||Near highly variable S1/S2 furin cleavage site; Predicted to enhance systemic infection. Associated with increased transmissibility |
|P681R||S||B.1.617||Indian variant||May enhance binding and subsequent cleavage of the spike protein and enhances systemic infection and
membrane fusion; potentially resulting in enhanced transmission 
|Q27stop||ORF8||B.1.1.7||UK variant||Truncated ORF8 gene; Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report |
|R246I||S||B.1.351||South African variant||Less prevalent mutation associated with the B.1.351 lineage|
|S982A||S||B.1.1.7||UK variant||Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report |
|T20N||S||P.1||Brazilian / Amazonas variant||Defining SNP associated with P.1 lineage in PANGO International Lineage Report |
|T716I||S||B.1.1.7||UK variant||Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report |
|Y453F||S||Mink Variant||Found in Mink. Associated with binding affinity to hACE2 receptor and evades some monoclonal antibodies |
Learn more about monitoring coronavirus mutations using the TaqMan SARS-CoV-2 Mutation Panel.
- “COG-UK / Mutation Explorer.” COG-UK Mutation Explorer, sars2.cvr.gla.ac.uk/cog-uk/.
- “COG-UK Report on SARS-CoV-2 Spike Mutations of Interest in the UK.” COVID-19 Genomics UK Consortium, www.cogconsortium.uk/wp-content/uploads/2021/01/Report-2_COG-UK_SARS-CoV-2-Mutations.pdf.
- “Frequently Asked Questions.” PANGO Lineages, cov-lineages.org/FAQ.html.
- Pereira, Filipe. “SARS-CoV-2 Variants Combining Spike Mutations and the Absence of ORF8 May Be More Transmissible and Require Close Monitoring.” Biochemical and Biophysical Research Communications, vol. 550, 2021, pp. 8–14., doi:10.1016/j.bbrc.2021.02.080.
- RS;, Baric. “Emergence of a Highly Fit SARS-CoV-2 Variant.” The New England Journal of Medicine, U.S. National Library of Medicine, pubmed.ncbi.nlm.nih.gov/33326716/.
- “SARS-CoV-2 – Increased Circulation of Variants of Concern” www.ecdc.europa.eu/sites/default/files/documents/RRA-covid-19-14th-update-15-feb-2021.pdf.
- “SARS-CoV-2 Variants of Concern.” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html.
- Tegally, Houriiyah, et al. “Emergence and Rapid Spread of a New Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2) Lineage with Multiple Spike Mutations in South Africa.” MedRxiv, Cold Spring Harbor Laboratory Press, 1 Jan. 2020, www.medrxiv.org/content/10.1101/2020.12.21.20248640v1.full.
- “Variants: Distribution of Cases Data.” GOV.UK, www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data.
- Wang P, Wang M, Yu J, et al. Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization. BioRxiv 2021. doi: https://doi.org/10.1101/2021.03.01.433466external icon
- “Weekly Epidemiological Update on COVID-19 – 27 April 2021.” World Health Organization, World Health Organization, www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19—27-april-2021.
For research use only. Not for use in diagnostic procedures.