SARS-CoV-2 Mutations Tracker

Stay up to date re mutation specific antibodies, proteins, assays

SARS-CoV-2 Lineages

B.1.1.529 Lineage / Omicron Lineage

Background B.1.1.529: The South African Institute of Infectious Diseases NICD said Thursday, Nov. 25, 2021, that 22 cases of the new variant B.1.1.529 (Omicron) have been detected in South Africa. The World Health Organization (WHO) is already investigating whether B.1.1.529 should be classified as a concern. Researchers spotted B.1.1.529 in genome-sequencing data from Botswana. The variant stood out because it contains more than 30 changes to the spike protein — the SARS-CoV-2 protein that recognizes host cells and is the main target of the body’s immune responses. Many of the changes have been found in variants such as Delta and Alpha and are linked to heightened infectivity and the ability to evade infection-blocking antibodies.

SARS-CoV-2 omicron lineage is made up of several sublineages, including BA.1 and BA.2, all of which are being monitored by WHO. As of 22.02 the BA.2 virus variant is considered a variant of concern. BA.2 is among the most common, with reported sequences increasing in recent weeks, relative to BA.1, though global circulation of all variants is currently declining. BA.2 differs from BA.1 in its genetic sequence, including some amino acid differences in the spike protein and other proteins. Studies have shown that BA.2 has a growth advantage over BA.1.

Start of 2023, a new Omicron subvariant, XBB.1.5, has been spreading rapidly and is considered by WHO to be the most transmissible variant at this time. A new research result on XBB.1.5 published in bioRxiv revealed a significantly higher hACE2 binding affinity compared to previous dominant variants such as Q.1.1 and XBB/XBB.1. In addition, convalescent plasma samples from BA.1, BA.5 and BF.7 breakthrough infections are significantly bypassed by XBB.1.5.

Mutations: A67V, H69del, V70del, T95I, G142del, V143del, Y144del, Y145D, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

Mutations BA.2: T19I, L24DEL, P24DEL, P26DEL, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S,K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K

Proteins:

XBB and XBB.1.5 Proteins - Omicron Variant

Emerging Omicron Variants

Protein for the following emerging SARS-CoV-2 Omicron Variants: BF.7 - Omicron, BQ.1.1 - , BN.1 - Omicron, BJ.1 - Omicron

BA.2 Sub Lineages Proteins - Omicron Variant

BA.1 Proteins - Omicron Variant

BA.2 Proteins - Omicron Variant

BA.2.75 - Omicron Proteins - Omicron Variant

BA.3 Proteins - Omicron Variant

BA.4 Proteins - Omicron Variant

BA.5 Proteins - Omicron Variant

Antibodies:

Neutralizing antibody CR3022 (ABIN6952467) and MM117 are not affected by omciron mutations.

Click here for more detailed data and information regarding CR3022!

References:

• Alexander Wilhelm, Marek Widera, Katharina Grikscheit, Tuna Toptan, et al., Reduced Neutralization of SARS-CoV-2 Omicron Variant by Vaccine Sera and monoclonal antibodies, preprint, https://doi.org/10.1101/2021.12.07.21267432
• Heavily mutated coronavirus variant puts scientists on alert, Nature News, Internet: https://www.nature.com/articles/d41586-021-03552-w
• https://covdb.stanford.edu/sierra/sars2/by-patterns/report/

B.1.1.7 Lineage / Alpha Lineage

Background B.1.1.7: Initially a UK lineage, associated with a variant of concern with N501Y, P681H and numerous other mutations. Evidence of having higher transmissibility than other lineage resulting in rapid growth in the UK and internationally.¹

Mutations: N501Y, A570D, D614G, P681H, T716I ,S982A, D1118H, D3L (N protein), S235F (N protein), T1001I (orf1ab), A1708D (orf1ab), 2230T (orf1a), Q27 (orf8)

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

N-protein antibodies ABIN6953169 and ABIN6953170 form an antibody pair and are specific for SARS-CoV-2 Nucleocapsid Protein. The pair detects Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Gamma (P.1/P.2) variants of SARS-CoV-2.

References:

• Pengfei Wang, Lihong Liu, Sho Iketani, Yang Luo et al. Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization. bioRxiv preprint posted January 26, 2021. ; https://doi.org/10.1101/2021.01.25.428137doi.
• Reuschl, A.-K., Thome, L. G., Zuliani-Alvarez, L., et al. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. bioRxiv preprint posted January 24, 2021. ; https://dx.doi.org/10.1101%2F2021.01.24.427991.
• Xiaoying Shen, Haili Tang, Charlene McDanal, et al. SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. https://doi.org/10.1016/j.chom.2021.03.002.
• Wilfredo F. Garcia-Beltran, Evan C. Lam, Kerri St. Denis, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Published: March 12, 2021. DOI:https://doi.org/10.1016/j.cell.2021.03.013
• Emily Engelhart, Randolph Lopez, Ryan Emerson, Charles Lin, Colleen Shikany, Daniel Guion, Mary Kelley, David Younger. Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants. Preprint. bioRxiv 2021.04.27.440939; doi: https://doi.org/10.1101/2021.04.27.440939

B.1.351 Lineage / Beta Lineage

Background B.1.351: A lineage first identified in South Africa and defined by new variant of concern 501Y.V2

Mutations: K417N, A570D, D614G, P681H, T716I, S982A, D1118H, L18F, D215G, K417K, E484K, N501Y, A701V, P71L (E protein), T205I (N protein), K1655N (orf1a)

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

N-protein antibodies ABIN6953169 and ABIN6953170 form an antibody pair and are specific for SARS-CoV-2 Nucleocapsid Protein. The pair detects Alpha (B.1.1.7), Beta (B.1.351), Delta (B1.167.2) and Gamma (P.1/P.2) variants of SARS-CoV-2.

References:

• Pengfei Wang, Lihong Liu, Sho Iketani, Yang Luo et al. Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization. bioRxiv preprint posted January 26, 2021. ; https://doi.org/10.1101/2021.01.25.428137doi.
• Mary Hongying Cheng, James M Krieger, Burak Kaynak, et al. Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment. doi: https://doi.org/10.1101/2021.01.10.426143.
• Hoffmann, M., Arora, P., Groß, R., et al. SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. To appear in Cell. DOI: https://doi.org/10.1016/j.cell.2021.03.036.
• Venkata Viswanadh Edara, Carson Norwood, Katharine Floyd, et al. Infection and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. Cell Host & Microbe, Mar 21, 2021. https://doi.org/10.1016/j.chom.2021.03.009.
• Wilfredo F. Garcia-Beltran, Evan C. Lam, Kerri St. Denis, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Published: March 12, 2021. DOI:https://doi.org/10.1016/j.cell.2021.03.013
• Emily Engelhart, Randolph Lopez, Ryan Emerson, Charles Lin, Colleen Shikany, Daniel Guion, Mary Kelley, David Younger. Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants. Preprint. bioRxiv 2021.04.27.440939; doi: https://doi.org/10.1101/2021.04.27.440939

B.1.429 Lineage / Epsilon Lineage

Background B.1.429: A lineage predominantly circulating in California but with exports to other countries.¹

Mutations: L452R, W152C, D5584Y (orf1ab), T205I (N protein)

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

References:

• Wilfredo F. Garcia-Beltran, Evan C. Lam, Kerri St. Denis, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Published: March 12, 2021. DOI:https://doi.org/10.1016/j.cell.2021.03.013
• Emily Engelhart, Randolph Lopez, Ryan Emerson, Charles Lin, Colleen Shikany, Daniel Guion, Mary Kelley, David Younger. Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants. Preprint. bioRxiv 2021.04.27.440939; doi: https://doi.org/10.1101/2021.04.27.440939
• McCallum M, Bassi J, Marco A, Chen A, Walls AC, Iulio JD, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D. SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. bioRxiv [Preprint]. 2021 Apr 1:2021.03.31.437925. doi: 10.1101/2021.03.31.437925. PMID: 33821281; PMCID: PMC8020983.

B.1.526 Lineage / Iota Lineage

Background B.1.526: The variant that Ho’s team identified in New York, also known as B.1.526, carries a notorious mutation called E484K that has been found in variants identified in South Africa and Brazil. Studies by multiple labs have shown that the E484K change — which is in a portion of the coronavirus spike protein that recognizes host cells — weakens the potency of antibodies that can ordinarily disable the virus.⁷

Mutations: T95I, D253G, L5F, D253G, E484K, D614G, A701V with a smaller fraction having S477N instead of E484K.¹

Proteins:

- Products under development. Get in touch! -

References:

• Annavajhala, M. K., Mohri, H., Zucker, J. E., et al. A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York. doi: https://doi.org/10.1101/2021.02.23.21252259.

B.1.617.1 Lineage / Kappa Lineage

Mutations: E484Q, L452R

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

References:

B.1.617.2 Lineage / Delta Lineage

Background B.1.617.2: A lineage circulating with variants of biological significance S:P681R and S:L452R, first detected in India and international cases with travel history from India.⁸

Mutations: S:P681R and S:L452R

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

N-protein antibodies ABIN6953169 and ABIN6953170 form an antibody pair and are specific for SARS-CoV-2 Nucleocapsid Protein. The pair detects Alpha (B.1.1.7), Beta (B.1.351), Delta (B1.167.2) and Gamma (P.1/P.2) variants of SARS-CoV-2.

References:

• Cherian S. et al. : "SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India" Microorganisms. 2021 doi: 10.3390/microorganisms9071542

B.1.621 Lineage / Mu Lineage

Mutations: T95I, Y144S, Y145N, R346K, E484K, N501Y, D614G, P681H, D950N

Proteins:

B.1.640.2 Variant

Background B.1.640.2: The B.1.640.2 variant was first identified in October and uploaded to Gisaid, a database for disease variants, on Nov. 4. Abdi Mahmud, a Covid incident manager with the W.H.O., told reporters in Geneva on Tuesday that the variant had been on the agency’s radar since November, but added that it did not appear to have spread widely over the past two months.¹

Mutations: 46 mutations and 37 deletions resulting in 30 amino acid substitutions and 12 deletions. Fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions are located in the spike protein.

Proteins:

- will be added -

References:

• Philippe Colson, Jérémy Delerce, Emilie Burel, Jordan Dahan, Agnès Jouffret, et al., Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein, Preprint, https://www.medrxiv.org/content/10.1101/2021.12.24.21268174v1
• (1) https://www.nytimes.com/2022/01/05/world/covid-variant-france.html

P.1 Lineage / Gamma Lineage

Background P.1: A lineage first identified in Brazil with variants of biological significance E484K, N501Y and K417T, described in a recent virological post: here. P.1 lineage is an alias of lineage B.1.1.28.1.¹

Mutations: V1176F, L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I, P80R (N protein), G174C (orf3a), E92K (orf8)

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

N-protein antibodies ABIN6953169 and ABIN6953170 form an antibody pair and are specific for SARS-CoV-2 Nucleocapsid Protein. The pair detects Alpha (B.1.1.7), Beta (B.1.351), Delta (B1.167.2) and Gamma (P.1/P.2) variants of SARS-CoV-2.

References:

• Toovey OTR, Harvey KN, Bird PW, Tang JWW. Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK [published online ahead of print, 2021 Feb 3]. J Infect. 2021;S0163-4453(21)00047-5. doi:10.1016/j.jinf.2021.01.025
• Wilfredo F. G.-B., Evan C. Lam, Kerri St. D., Adam D. N. Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. doi: https://doi.org/10.1101/2021.02.14.21251704.
• Hoffmann, M., Arora, P., Groß, R., et al. SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. To appear in Cell. DOI: https://doi.org/10.1016/j.cell.2021.03.036.
• Wilfredo F. Garcia-Beltran, Evan C. Lam, Kerri St. Denis, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Published: March 12, 2021. DOI:https://doi.org/10.1016/j.cell.2021.03.013

A.23.1 Lineage

Background A.23.1: International lineage with variants of biological significance F157L, V367F, Q613H and P681R, described fully in the preprent: Bugembe et al 2021. Q613H is predicted to be functionally equivalent to the D614G mutation that arose early in 2020.¹

Mutations: F157L, V367F, Q613H and P681R

Proteins:

- Products under development. Get in touch! -

References:

• Bugembe, D. L., Phan, My V.T., Ssewanyana, I., et al. A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic. medRxiv 2021.02.08.21251393; doi: https://doi.org/10.1101/2021.02.08.21251393

B.1.2 Lineage

Background B.1.2: Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively.⁶

Mutations: Q677P

Proteins:

- Products under development. Get in touch! -

References:

• Hodcroft, E. B., Domman, D. B., Snyder, D. J. Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. medRxiv preprint on February 14, 2021. doi: https://doi.org/10.1101/2021.02.12.21251658

Wild Type Protein

We offer a high quality recombinant SARS-CoV-2 wild type protein. Click on the link to find more details.

B.1.525 Lineage / Eta Lineage

Background B.1.525: International lineage with variants of biological significance E484K, Q677H, F888L and a similar suite of deletions to B.1.1.7.¹

Mutations: E484K, Q677H, F888L and a similar suite of deletions to B.1.1.7., Q52R, L21F (E protein), I82T (E protein), L471F (orf1ab)¹

Proteins:

Antibodies:

Chimeric MAb ABIN6953206 is a chimeric monoclonal antibody combining the constant domains of the human IgG1 Molecule with mouse variable regions. CR3022 antibody ABIN6952546 not affected by B.1.1.7, B.1.251, B.1.617.1+2 and P.1 Mutations! Click to see detailed data.

CR3022 antibodies: bind to epitope residues in the RBD that are not mutated^2,3,4,5

References:

• Emily Engelhart, Randolph Lopez, Ryan Emerson, Charles Lin, Colleen Shikany, Daniel Guion, Mary Kelley, David Younger. Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants. Preprint. bioRxiv 2021.04.27.440939; doi: https://doi.org/10.1101/2021.04.27.440939

CR3022 not affected by B.1.1.529 / omicron Variant Mutations

One of the looming questions regarding newly emerging variants of SARS-CoV-2 is, whether existing antibody based assays and pharmaceuticals remain useable. In collaboration with Nanotemper we measured the affinity of our S protein RBD antibody CR3022 (ABIN6952546) to the canonical trimeric SARS-CoV-2 S protein and those of the variants of concern B.1.1.7 / alpha, B.1.351 / beta, B.1.617.2 / delta, B.1.617.1 / kappa and P.1 / gamma by microscale thermophoresis (MST). In a second iteration we acknowledged the dominant B.1.1.529 / omicron variant and extended the antibody selection with neutralizing antibodies MM43 (ABIN7036075) and MM117. Discover the results down below.

Click here for more detailed data and information regarding CR3022!

General References

1. Barnes, Jette, Abernathy, Dam, Esswein, Gristick, Malyutin, Sharaf, Huey-Tubman, Lee, Robbiani, Nussenzweig, West, Bjorkman: "SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies." dans: Nature, Vol. 588, Issue 7839, pp. 682-687, (2021) (PubMed).
2. Wibmer, Ayres, Hermanus, Madzivhandila, Kgagudi, Oosthuysen, Lambson, de Oliveira, Vermeulen, van der Berg, Rossouw, Boswell, Ueckermann, Meiring, von Gottberg, Cohen, Morris, Bhiman, Moore: "SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma." dans: bioRxiv : the preprint server for biology, (2021) (PubMed).
3. Garcia-Beltran, Lam, St Denis, Nitido, Garcia, Hauser, Feldman, Pavlovic, Gregory, Poznansky, Sigal, Schmidt, Iafrate, Naranbhai, Balazs: "Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity." dans: medRxiv : the preprint server for health sciences, (2021) (PubMed).
4. Yuan, Wu, Zhu, Lee, So, Lv, Mok, Wilson: "A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV." dans: Science (New York, N.Y.), (2020) (PubMed).
5. Hodcroft, Domman, Snyder, Oguntuyo, Van Diest, Densmore, Schwalm, Femling, Carroll, Scott, Whyte, Edwards, Hull, Kevil, Vanchiere, Lee, Dinwiddie, Cooper, Kamil: "Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677." dans: medRxiv : the preprint server for health sciences, (2021) (PubMed).
6. Garcia-Beltran, Lam, St Denis, Nitido, Garcia, Hauser, Feldman, Pavlovic, Gregory, Poznansky, Sigal, Schmidt, Iafrate, Naranbhai, Balazs: "Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity." dans: Cell, Vol. 184, Issue 9, pp. 2372-2383.e9, (2021) (PubMed).