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SARS-CoV-2 variants, spike mutations and immune escape
Open accessAbstract
Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of 'variants of concern', that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.
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“D614G is again associated with the increase in transmissibility, infectivity, and viral load, making the Lambda variant even more lethal [55].”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [55]
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“Each pathogen poses a unique set of challenges, including high lethality, rapid mutations, immune evasion, new strains and variants252–258.”
From mRNA vaccines for infectious diseases: principles, delivery and clinical translation (2021) · cites this paper as [252]
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“Mutations in the spike protein and RBD have been shown to affect antibody neutralisation and thus reduce vaccine-induced immunity [22].”
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In the citing paper
“The Lambda variant spike protein is found to be 3.3 times more resistant to neutralization by the convalescent sera than the parent D614G spike protein and 4.9 times to that of the Alpha variant ones.”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [55]
Experimental — accuracy not yet measuredIn the citing paper
“However, reduced sensitivity of SARS-CoV-2 variants to antibody and serum neutralization has been widely observed (18–21).”
From Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization (2022) · cites this paper as [19]
In the citing paper
“both being immunodominant targets of neutralizing antibodies elicited by COVID-19 vaccines or by SARS-CoV-2 infection (5, 6).”
From Neutralization of SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine–elicited human sera (2022) · cites this paper as [6]
In the citing paper
“However, sequencing data of SARS-CoV-2 from patients revealed persistent accumulation of new mutations over the last two years of the Covid19 pandemic, leading to the emergence of new viral strains that can be more transmissible or virulent5,6 or evade vaccines7–9.”
From The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness (2022) · cites this paper as [8]
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COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme
Fasching, C. L., Servellita, V., McKay, B., Nagesh, V., Broughton, J. P., Sotomayor-González, A., Wang, B., Brazer, N., Reyes, K. R., Streithorst, J. A., et al. (2022) · Journal of Clinical Microbiology · doi:10.1128/jcm.00261-22 · Cited by 44
“However, given the 253 rapid emergence and dynamic shifts in the distribution of variants over time (13), it is 254 likely that tracking of key mutations, several of which are suspected to arise by 255 convergent evolution (36), rather than tracking of variants, will be critical for surveillance 256 as the pandemic co…”
BackgroundInfluentialGupta, A., Konnova, A., Smet, M., Berkell, M., Savoldi, A., Morra, M., averbeke, V. V., Winter, F. D., Peserico, D., Danese, E., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci166032 · Cited by 42
Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike
Wrobel, A. G. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102619 · Cited by 48
Choi, J. H., Jun, M. S., Jeon, J. Y., Kim, H.-S., Kim, Y. K., Jeon, C. H., Choi, S. H., Kim, D. S., Han, M., & Oh, J. W. (2023) · Journal of Translational Internal Medicine · doi:10.2478/jtim-2023-0118 · Cited by 44
“[11] Tumors are known to evolve over time as a result of genetic mutations and natural selection, leading to the emergence of increasingly aggressive and treatment-resistant cancer cells.”
Shanmugaraj, B., Khorattanakulchai, N., Panapitakkul, C., Malla, A., Im‐Erbsin, R., Inthawong, M., Sunyakumthorn, P., Hunsawong, T., Klungthong, C., Reed, M. C., et al. (2022) · Vaccine · doi:10.1016/j.vaccine.2022.05.087 · Cited by 42
The Coronavirus pandemic – 2022: Viruses, variants & vaccines
Alexandridi, M., Mazej, J., Palermo, E., & Hiscott, J. B. (2022) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2022.02.002 · Cited by 44
Superimmunity by pan-sarbecovirus nanobodies
Xiang, Y., Huang, W., Liu, H., Sang, Z., Nambulli, S., Tubiana, J., Williams, K. L., Duprex, W. P., Schneidman‐Duhovny, D., Wilson, I. A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111004 · Cited by 43
“SARS-CoV-2 continues to evolve, producing variants with high transmissibility and potential to evade host immunity (Harvey et al., 2021; Karim and Karim, 2021).”
BackgroundPseudoscience and fraudulent products for COVID-19 management
Chavda, V. P., Sonak, S. S., Munshi, N. K., & Dhamade, P. N. (2022) · Environmental Science and Pollution Research · doi:10.1007/s11356-022-21967-4 · Cited by 48
Padhi, A. K., & Tripathi, T. (2022) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2022.09.010 · Cited by 42
Rapid detection of SARS-CoV-2: The gradual boom of lateral flow immunoassay
He, J., Zhu, S., Zhou, J., Jiang, W., Yin, L., Su, L., Zhang, X., Chen, Q., & Li, X. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.1090281 · Cited by 44
“, 2020), and the production of variants (Harvey et al., 2021; Tao et al., 2021) and the increase in asymptomatic infections (Johansson et al.”
BackgroundMinimal Antigenic Evolution after a Decade of Norovirus GII.4 Sydney_2012 Circulation in Humans
Parra, G. I., Tohma, K., Ford-Siltz, L. A., Eguino, P., Kendra, J. A., Pilewski, K. A., & Gao, Y. S. (2023) · Journal of Virology · doi:10.1128/jvi.01716-22 · Cited by 43
Barnes, K. G., Levy, J. I., Gauld, J., Rigby, J., Kanjerwa, O., Uzzell, C. B., Chilupsya, C., Anscombe, C., Tomkins-Tinch, C. H., Mbeti, O., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43047-y · Cited by 43
Alhamlan, F. S., & Al-Qahtani, A. A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26031263 · Cited by 46
“Key mutations in the spike protein include N501Y, which increases binding affinity to the ACE2 receptor, and the deletion of amino acids 69–70 ( ∆ 69–70), which is associated with immune evasion and increased infectivity [6,7].”
InfluentialMolecular dynamics simulations: Insights into protein and protein ligand interactions
Grewal, S., Deswal, G., Grewal, A. S., & Guarve, K. (2025) · Advances in pharmacology · doi:10.1016/bs.apha.2025.01.007 · Cited by 43
Saha, A., Roy, S. G., Dwivedi, R., Tripathi, P., Kumar, K., Nambiar, S. M., & Pathak, R. (2025) · Vaccines · doi:10.3390/vaccines13040424 · Cited by 47
“Moreover, SARS-CoV-2’s high mutation rate, particularly in the spike protein, allows it to evade neutralizing antibodies, contributing to breakthrough infections and reinfections [372,373].”
Cheah, B. C. J., Vicente, C. R., & Chan, K. R. (2025) · Viruses · doi:10.3390/v17070882 · Cited by 61
“…Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), fast-emerging viral strains have been known to be caused by the rapidly changing antigenicity of the spike protein and mutations in the Receptor Binding Domain (RBD), resulting in increased viral infectivity and communal transmission [54,55].”
Lubinski, B., Frazier, L. E., Phan, M. V. T., Bugembe, D. L., Cunningham, J. L., Tang, T., Daniel, S., Cotten, M. L., Jaimes, J. A., & Whittaker, G. R. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01514-22 · Cited by 74
Epidemic spreading under mutually independent intra- and inter-host pathogen evolution
Zhang, X., Ruan, Z., Zheng, M., Zhou, J., Boccaletti, S., & Barzel, B. (2022) · Nature Communications · doi:10.1038/s41467-022-34027-9 · Cited by 44
Carroll, T. D., Fox, D., van Doremalen, N., Ball, E. E., Morris, M. K., Sotomayor-González, A., Servellita, V., Rustagi, A., Yinda, C. K., Fritts, L., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1009914 · Cited by 39
Attia, S., Mausbach, K., Klugar, M., Howaldt, H., & Riad, A. (2022) · Frontiers in Public Health · doi:10.3389/fpubh.2022.846861 · Cited by 43
“, increased transmissibility and immune evasion, while many changes have unclear significance (9, 10).”
BackgroundTran, T. T., Vaage, E. B., Mehta, A., Chopra, A., Tietze, L., Kolderup, A., Anthi, A. K., König, M. S. S., Nygaard, G. O., Lind, A., et al. (2022) · npj Vaccines · doi:10.1038/s41541-022-00586-7 · Cited by 47
Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants
Meyer, S., Blaas, I., Bollineni, R. C., Delić-Šarac, M., Tran, T. T., Knetter, C. F., Dai, K., Madssen, T. S., Vaage, J. T., Gustavsen, A., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.111995 · Cited by 41
Challenges in the Vaccination of the Elderly and Strategies for Improvement
Soegiarto, G., & Purnomosari, D. (2023) · Pathophysiology · doi:10.3390/pathophysiology30020014 · Cited by 45
Ning, S., Chang, H.-C., Fan, K.-C., Hsiao, P.-Y., Feng, C., Shoemaker, D., & Chen, R. T. (2023) · Applied Physics Reviews · doi:10.1063/5.0146079 · Cited by 42
COVID-19: From emerging variants to vaccination
Senevirathne, T. H., Wekking, D., Swain, J. W. R., Solinas, C., & Silva, P. D. (2023) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2023.11.005 · Cited by 45
Ahmed, S., Khan, S., Imran, I., Mughairbi, F. A., Sheikh, F. S., Hussain, J., Khan, A., & Al‐Harrasi, A. (2021) · Vaccines · doi:10.3390/vaccines9080836 · Cited by 41
“To better understand the effect of genomic variations on the effectiveness of vaccines, both orthodox viruses and pseudo-viruses possessing particular spike mutations (either individually or in combination) and larger sets of mutations representing variants of concern and other circulating spike mutations have been as…”
BackgroundInfluentialCOVID-19 Vaccines and SARS-CoV-2 Transmission in the Era of New Variants: A Review and Perspective
Marcelin, J. R., Pettifor, A. E., Janes, H., Brown, E. R., Kublin, J. G., & Stephenson, K. E. (2022) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofac124 · Cited by 41
“The emergence of new, highly transmissible viral variants in January/February of 2021 [37], complete saturation by the Delta variant by July 2021, and subsequent dominance of the Omicron variant toward the end of 2021/early 2022 with concern for even greater vaccine escape [38] are important factors.”
BackgroundSelective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide
Yamane, D., Onitsuka, S., Re, S., Isogai, H., Hamada, R., Hiramoto, T., Kawanishi, E., Mizuguchi, K., Shindo, N., & Ojida, A. (2022) · Chemical Science · doi:10.1039/d1sc06596c · Cited by 42
Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power
Tonner, P. D., Pressman, A., & Ross, D. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114021119 · Cited by 41
Tarke, A., Coelho, C. H., Zhang, Z., Dan, J. M., Yu, E. D., Methot, N., Bloom, N. I., Goodwin, B., Phillips, E. J., Mallal, S. A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.28.474333 · Cited by 42
“May 2021 period (Harvey et al., 2021; Walensky et al., 2021).”
BackgroundFidan, Ö., Mujwar, S., & Kciuk, M. (2022) · Molecular Diversity · doi:10.1007/s11030-022-10440-6 · Cited by 42
“The mutations resulted in the emergence of new variants, some of which are classified as “variant of concern” due to their increased transmissibility and better viral fitness [3].”
BackgroundThe past, current and future epidemiological dynamic of SARS-CoV-2
Balloux, F., Tan, C. C. S., Swadling, L., Richard, D., Jenner, C., Maini, M. K., & van Dorp, L. (2022) · Oxford Open Immunology · doi:10.1093/oxfimm/iqac003 · Cited by 41
“For SARS-CoV-2, much attention has been paid to mutational changes in the spike protein [239].”
BackgroundYang, W., Yang, S.-L., Wang, L., Zhou, Y., Xin, Y., Li, H., Mu, W., Wu, Q., Xu, L., Zhao, M., et al. (2022) · Virologica Sinica · doi:10.1016/j.virs.2022.07.014 · Cited by 41
“, 2022) that lead to higher viral transmission capacity and immune evasion (Greaney et al., 2021; Harvey et al., 2021).”
Assessing COVID-19 vaccine hesitancy and barriers to uptake in Sub-Saharan Africa
Wollburg, P. R., Markhof, Y. V., Kanyanda, S. S. E., & Zezza, A. (2023) · Communications Medicine · doi:10.1038/s43856-023-00330-9 · Cited by 41
“Low COVID-19 vaccination rates in this region compound the risk of continued mutation of the virus 4,5 .”
BackgroundSARS-CoV-2-associated lymphopenia: possible mechanisms and the role of CD147
Shouman, S., Elkholy, N., Hussien, A. E., El-Derby, A. M., Magdy, S., Abou‐Shanab, A. M., Elmehrath, A. O., Abdelwaly, A., Helal, M. A., & El‐Badri, N. (2024) · Cell Communication and Signaling · doi:10.1186/s12964-024-01718-3 · Cited by 47
“Some of these variants exhibited changes in transmissibility, severity, and in some cases, resistance to immunity caused by prior infection or vaccination [1, 2].”
BackgroundMantena, S., Pillai, P. P., Petros, B. A., Welch, N. L., Myhrvold, C., Sabeti, P. C., & Metsky, H. C. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02422-w · Cited by 40
“The six SNPs include four associated with antimicrobial resistance in Plasmodium falciparum (Pfcrt K76T, Pfdhps A437G, Pfk13 C580Y and Pfmdr1 Y184F), one associated with micro-cephaly in Zika virus (PrM S139N) and one associated with immune evasion in SARS-CoV-2’s spike protein (K417N/K417T) 28–34 .”
Triveri, A., Serapian, S. A., Marchetti, F., Doria, F., Pavoni, S., Cinquini, F., Moroni, E., Rasola, A., Frigerio, F., & Colombo, G. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00857 · Cited by 38
The Development of mRNA Vaccines for Infectious Diseases: Recent Updates
Nitika, Wei, J., & Hui, A. (2021) · Infection and Drug Resistance · doi:10.2147/idr.s341694 · Cited by 42
“The first one to emerge was spike mutation D614G, which enhanced the spike binding to ACE2 receptor.(81) The next”
Background
Metadata
- Authors
- Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, Peacock, S. J., & Robertson, D. L.
- Affiliations
- MRC University of Glasgow Centre for Virus Research (GB)
- University of Cambridge (GB)
- University of Edinburgh (GB)
- Wellcome Sanger Institute (GB)
- University of Glasgow (GB)
- Corresponding author
- Robertson, David L.
- ORCID
- Venue
- Nature Reviews Microbiology
- Published
- 2021-06-01
- Volume
- 19
- Issue
- 7
- Pages
- 409-424
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC8167834
- OpenAlex
- W3165479483
- Cited by
- 3,528
- References
- 103
- Citations by year
- 2026: 220 · 2025: 310 · 2024: 475 · 2023: 801 · 2022: 1283 · 2021: 420
- FWCI
- 87.86
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion, cc-by-sa)
- Northumbria Research Link (Northumbria University) (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Wellcome Trust (Z/17/Z, 206298/Z/17/Z, 220977/Z/20/Z, 220977/Z/20/Z, 206298/Z/17/Z, 206298)
- UK Research and Innovation (MR/W005611/1/, MC_PC_19027)
- National Institute for Health and Care Research
- Academy of Medical Sciences (AMS-CSF4-Torok)
- University of Glasgow
- Directorate for Biological Sciences
- Medical Research Council (MC_UU_12014, MC UU 12014/12, MC_PC_19026, MR/W005611/1, MR/S00291X/1, COVID-19, MR/R024758/1)
- Biotechnology and Biological Sciences Research Council (BB/R012679/1)
- H2020 European Research Council (725422)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein mutations, variants of concern, immune evasion, antigenicity, neutralizing antibodies, vaccine effectiveness, vaccine update, viral evolution, mutation frequency, COVID-19 pandemic
- MeSH terms
- COVID-19, SARS-CoV-2, COVID-19 Vaccines, Amino Acids, Epitopes, Antigenic Variation, Humans, Mutation, Protein Conformation, Immune Evasion, Spike Glycoprotein, Coronavirus
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