This blog represents the most up-to-date information as of July 20, 2022.
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 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 with the mutations that are most important to you.
Explore the interactive viewer or download a poster about the different types of SARS-CoV-2 variants and mutations that are being discovered around the world.
Mutation | Gene | WHO label | Associated Variants | Earliest Documented Samples | Mutation Significance |
---|---|---|---|---|---|
A13057T | ORF1ab | Mu | B.1.621 | Colombia | SNP associated with Mu Variant of Interest according to WHO [14] |
A1708D | ORF1 | Alpha | B.1.1.7 | United Kingdom | Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report [3] |
A222V | S | B.1.177 | Associated with fast growing lineage [1][2] | ||
A2710T | ORF1a | Omicron | BA.1, BA.1 | Various countries | SNP associated with high percentage of Omicron Variant of Concern [17] |
A28272T | Mu | B.1.621 | Colombia | SNP associated with Mu Variant of Interest according to WHO [14] | |
A570D | S | Alpha | B.1.1.7 | United Kingdom | Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report [3] |
A701V | S | Beta | B.1.351 | South Africa | Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report [3] |
D215G | S | Beta | B.1.351 | South Africa | Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report [3] |
D3N | M | Omicron | BA.5 | Various countries | Defining SNP associated with BA.5 sublineage of the Omicron variant, considered a Variant of Concern by the WHO [26] |
D614G | S | Various | 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, B.1.1.298 | Nigeria, United Kingdom, South Africa, Brazil / Amazon | Ability to spread more quickly with moderate effect on transmissibility [1][2] |
D80A | S | Beta | B.1.351 | South Africa | Defining SNP associated with B.1.351 lineage in PANGO International Lineage Report [3] |
delH69V70 | S | Alpha | B.1.1.7, B.1.258, B.1.525 | United Kingdom | 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 [1][2] |
delL242 | S | Beta | B.1.351 | South Africa | Deleting associated with the B.1.351 [6]; Associated with reduced capacity for binding certain antibodies [22] |
delY144 | S | Alpha | B.1.1.7 | United Kingdom | Included in CDC Variants of Concern List [7] |
E484K | S | Beta, Gamma, Eta | P.1, B.1.1.33,B.1.351, B.1.525 | South Africa, Brazil | Mutation in receptor binding domain (RBD) region; Reduces antibody recognition; Interface with hACE2 receptor; Associated with vaccine resistance [1][2] |
E484Q | S | Delta (absence of this mutation) | B.1.617 | India | May have reduced neutralization against variants with an E484Q mutation [14] |
EFR156-158G | Delta | B.1.617.2 | India | Defining SNP associated with Delta variant [7] | |
F157L | S | A.23 | Uganda | Defining SNP associated with A.23 variant in in PANGO International Lineage Report. Noted as an international lineage with variants of biological significance [3]. | |
F157S | S | Iota | B.1.526 | United States | United States Mutation associated with variant that causes reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment; Reduced neutralization by convalescent and post-vaccination sera [7] |
F2387V | ORF1a | Lambda | C.37 | Peru | Mutation associated with C.37 WHO Variant of Interest [10] |
F888L | S | Eta | B.1.525 | Nigeria | Mutation associated with of interest. Potential reduction in neutralization by some EUA monoclonal antibody treatments. Potential reduction in neutralization by convalescent and post-vaccination sera [8] |
G339D | S | Omicron | B.1.1.529 | Various Countries | SNP associated with Omicron Variant of Concern according to WHO [15] |
H78Y | ORF3a | Omicron | BA.2.9 and all sublineages | Various countries | Mutation associated with BA.2.9 sublineage WHO Variant of Concern Lineage Under Monitoring [10] |
Q5412H | ORF1b | Iota | B.1.526 | United States | SNP associated with B.1.526 lineage |
Q954H | S | Omicron | BA.1, BA.1.1, BA.2, BA.3 | Various Countries | SNP associated with Omicron Variant of Concern according to WHO [15] |
K417N | S | Beta | B.1.351 | South Africa | Mutation to receptor binding domain (RBD) region in South Africa [1][2] |
K417T | S | Gamma | P.1 | Brazil / Amazon | Defining SNP associated with P.1 lineage in PANGO International Lineage Report [3] |
L11F | ORF7b | Omicron | BA.4 | Various countries | Defining SNP associated with BA.4 sublineage of the Omicron variant, considered a Variant of Concern by the WHO [26] |
L18F | S | Gamma | P.1, B.1.351 | South Africa, Brazil / Amazon | Defining SNP associated with P.1 lineage in PANGO International Lineage Report [3] |
L242_244L | S | Beta | B.1.351 | South Africa | Deletion associated with the B.1.351 [6] |
L37F | ORF10 | Omicron | BA.5.1 | Various countries | Characteristic mutation associated with Omicron BA.5.1 sublineage |
L452M | S | Omicron | BA.2.9.1, BA.2.13 | Various countries | Mutation associated with BA.2.9.1 and BA.2.13 WHO Variant of Concern Lineages Under Monitoring [10] |
L452Q | S | Lambda | C.37 | Peru | Mutation associated with C.37 SWHO variant of Interest. Identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health [10] |
L452R | Delta, Epsilon | B.1.617 | India, California | 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 [11] Classified as a substitution of therapeutic concern by the CDC [8] | |
N439K | S | B.1.258 | Impacts ability to evade antibody-mediated immunity; Increased binding affinity to hACE2 receptor and evade some monoclonal antibodies [1][2] | ||
N501Y | S | Alpha, Beta, Gamma | P.1 , B.1.1.7, B.1.351 | United Kingdom, South Africa, Brazil / Amazon | Located within receptor binding domain (RBD) one of 6 key contact residues; Increased binding affinity to hACE2 receptor in cells [1][2] |
P151S | N | Omicron | BA.4 and all sublineages | Various countries | Mutation associated with BA.4 sublineage WHO Variant of Concern Lineage Under Monitoring [10] |
P681H | S | Alpha | B.1.1.207, B.1.1.7 | Nigeria, United Kingdom | Near highly variable S1/S2 furin cleavage site; Predicted to enhance systemic infection. Associated with increased transmissibility [1][2] |
P681R | S | Delta | B.1.617, B.1.617.2, B.1.617.3 | India | May enhance binding and subsequent cleavage of the spike protein and enhances systemic infection and membrane fusion; potentially resulting in enhanced transmission [14] |
Q27stop | ORF8 | Alpha | B.1.1.7 | United Kingdom | Truncated ORF8 gene; Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report [3][4] |
Q498R | S | Omicron | B.1.1.529 | Various Countries | SNP associated with Omicron Variant of Concern according to WHO [15] |
Q52R | S | Eta | 1.525 | Mutation associated with Eta variant that causes potential reduction in neutralization by some Emergency Use Authorization (EUA) monoclonal antibody treatments, and potential reduction in neutralization by convalescent and post-vaccination sera [8] | |
Q677H | S | Eta | 1.525 | Mutation associated with Eta variant that causes potential reduction in neutralization by some Emergency Use Authorization (EUA) monoclonal antibody treatments, and potential reduction in neutralization by convalescent and post-vaccination sera [8] | |
R246I | S | Beta | B.1.351 | South Africa | Less prevalent mutation associated with the B.1.351 lineage [9] |
R346K | S | Mu | B.1.621 | Colombia | SNP associated with Mu Variant of Interest according to WHO [14] |
S13I | S | Epsilon | B.1.427, B.1.429 | California | Mutation associated with Epsilon variant that causes~20% increased transmissibility and reduced neutralization by convalescent and post-vaccination sera [8] |
S477N | S | Iota | B.1.429 | New York | Associated with that results in reduced susceptibility to certain monoclonal antibody treatments and reduced neutralization by convalescent and post-vaccination sera [8] |
S2519P | ORF1a | Omicron | BA.2.11 | Various countries | Mutation associated with BA.2.11 WHO Variant of Concern Lineage Under Monitoring [10] |
S982A | S | Alpha | B.1.1.7 | United Kingdom | Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report [3] |
T1055A | Mu | B.1.621 | Colombia | SNP associated with Mu Variant of Interest according to WHO [14] | |
T13195C | S | Omicron, BA.1 | B.1.1.529 | Various Countries | SNP associated with Omicron Variant of Concern according to WHO [15] |
T16176C | Alpha | B.1.1.7 | United Kingdom | Mutation associated with B.1.1.7 lineage | |
T19R | S | Delta | B.1.617.2 | India | Mutation associated with Delta variant that is associated with increased transmissibility, potential reduction in neutralization by some EUA monoclonal antibody treatments, and potential reduction in neutralization by post-vaccination sera [8] |
T20N | S | Gamma | P.1 | Brazil / Amazon | Defining SNP associated with P.1 lineage in PANGO International Lineage Report [3] |
T376A | S | Omicron, BA.2 | B.1.1.529 | Various Countries | Defining SNP associated with BA.2 sub lineage of the Omicron variant, considered a variant of Concern by the WHO. Assay designed to differentiate between BA.2 and BA.1 strain [16] |
T478K | S | Delta | B.1.617.2 | India | Mutation associated with Delta variant that is associated with increased transmissibility, potential reduction in neutralization by some EUA monoclonal antibody treatments, and potential reduction in neutralization by post-vaccination sera [8] |
T547K | Omicron, BA. 1 | B.1.1.529 | Various Countries | SNP associated with Omicron Variant of Concern according to WHO [15] | |
T716I | S | Alpha | B.1.1.7 | United Kingdom | Defining SNP associated with B.1.1.7 lineage in PANGO International Lineage Report [3] |
T95I | S | Iota | B.1.526, B.1.621.1 | United States | Mutation associated with variant that causes reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment; Reduced neutralization by convalescent and post-vaccination sera [7] |
V1176F | S | P.2 | Brazil | Defining mutation associated with the P.2 Brazil associated with potential reduction in neutralization by some EUA monoclonal antibody treatments. Reduced neutralization by post-vaccination sera [8] | |
V213G | Omicron, BA.2 | B.1.1.529 | Various Countries | Defining SNP associated with BA.2 sub lineage of the Omicron variant, considered a variant of Concern by the WHO. Assay designed to differentiate between BA.2 and wt strain | |
W152C | S | Epilson | B.1.427, B.1.429 | United States | SNP associated with B.1.427 and B.1.429 lineages |
W152L | S | R.1 | SNP associated with R.1 lineage in PHE Technical Briefing. Considered variant under monitoring. [5] | ||
Y145H | S | Delta + | AY.4.2 | India | Defining SNP associated with Delta Plus variant. Mutation located in the spike protein. Selective advantage of mutation still under investigation, but may lead to increased immune evasion |
Y453F | S | B.1.1.298 | Found in Mink. Associated with binding affinity to hACE2 receptor and evades some monoclonal antibodies [1][2] |
Learn more about monitoring coronavirus mutations using the TaqMan SARS-CoV-2 Mutation Panel.
Resources
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- Rosalind Tracker, https://tracker.rosalind.bio/dashboard?number-of-days=30&graph-display=count
For research use only. Not for use in diagnostic procedures.