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SARS-CoV-2 mutations, their attributes, and conducting surveillance studies

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 7 Jun 2021 || By Manoj Gandhi, M.D., Ph.D. Shares: Versions of this article Original article. Tags COVID-19, Mutations, QPCR, Sars-cov-2, Surveillance, Variants

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.

Download the free poster

Resources
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For research use only. Not for use in diagnostic procedures.