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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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The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges
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Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir
Ullrich, S., Ekanayake, K. B., Otting, G., & Nitsche, C. (2022) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2022.128629 · Cited by 197
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant
Saito, A., Tamura, T., Zahradník, J., Deguchi, S., Tabata, K., Anraku, Y., Kimura, I., Ito, J., Yamasoba, D., Nasser, H., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.10.003 · Cited by 188
The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.751778 · Cited by 201
“Amino acid mutations in the spike protein T19R, G142D, FR156⁃157del, R158G, L452R, T478K, D614G, P681R, D950N (25)”
BackgroundInfluentialCOVID-19 vaccination: The road ahead
Altmann, D. M., & Boyton, R. J. (2022) · Science · doi:10.1126/science.abn1755 · Cited by 198
Mucosal immune response in biology, disease prevention and treatment
Zhou, X., Wu, Y., Zhu, Z., Lu, C., Zhang, C., Zeng, L., Xie, F., Zhang, L., & Zhou, F. (2025) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-02043-4 · Cited by 230
Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections
Farinholt, T., Doddapaneni, H., Qin, X., Menon, V. K., Meng, Q., Metcalf, G., Chao, H., Gingras, M., Avadhanula, V., Farinholt, P., et al. (2021) · BMC Medicine · doi:10.1186/s12916-021-02103-4 · Cited by 185
Engineered Ribosyl-1-Kinase Enables Concise Synthesis of Molnupiravir, an Antiviral for COVID-19
McIntosh, J. A., Benkovics, T., Silverman, S. M., Huffman, M. A., Kong, J., Maligres, P. E., Itoh, T., Yang, H. Y., Verma, D., Pan, W., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00608 · Cited by 185
Implications of diversity in sperm size and function for sperm competition and fertility
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A roadmap to pulmonary delivery strategies for the treatment of infectious lung diseases
He, S., Gui, J., Xiong, K., Chen, M., Gao, H., & Fu, Y. S. (2022) · Journal of Nanobiotechnology · doi:10.1186/s12951-022-01307-x · Cited by 188
“Due to the rapid mutation of the virus, the research and development of anti-SARS-CoV2 drugs has a long way to go [10].”
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The Evolution and Biology of SARS-CoV-2 VariantsPreprint
Telenti, A., Hodcroft, E. B., & Robertson, D. L. (2022) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041390 · Cited by 191
Self-citationOmicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
Cele, S., Jackson, L., Khoury, D. S., Khan, K., Moyo-Gwete, T., Tegally, H., San, J. E., Cromer, D., Scheepers, C., Amoako, D. G., et al. (2021) · Nature · doi:10.1038/d41586-021-03824-5 · Cited by 177
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission
Escalera, A., Gonzalez-Reiche, A. S., Aslam, S., Mena, I., Laporte, M., Pearl, R. L., Fossati, A., Rathnasinghe, R., Alshammary, H., van de Guchte, A., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.01.006 · Cited by 173
Paxlovid (Nirmatrelvir/Ritonavir): A new approach to Covid-19 therapy?
Hashemian, S. M. R., Sheida, A., Taghizadieh, M., Memar, M. Y., Hamblin, M. R., Baghi, H. B., Nahand, J. S., Asemi, Z., & Mirzaei, H. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.114367 · Cited by 184
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The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation
Rajah, M. M., Bernier, A., Buchrieser, J., & Schwartz, O. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167280 · Cited by 188
The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses
Murray, S. M., Ansari, M. A., Frater, J., Klenerman, P., Dunachie, S. J., Barnes, E. J., & Ogbe, A. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00809-x · Cited by 173
Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease
Tan, H., Hu, Y., Jadhav, P. D., Tan, B., & Wang, J. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c00303 · Cited by 170
Targeting stem-loop 1 of the SARS-CoV-2 5′ UTR to suppress viral translation and Nsp1 evasion
Vora, S. M., Fontana, P., Mao, T., Leger, V., Zhang, Y., Fu, T., Lieberman, J., Gehrke, L., Shi, M., Wang, L., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117198119 · Cited by 159
“The recent appearance of variants as well as the history of spontaneous resistance of viruses to conventional antiviral drugs – most notoriously to nucleoside inhibitors – suggests the need for new classes of antivirals (Harvey et al., 2021; Seley-Radtke and Yates, 2018).”
BackgroundShan, S., Luo, S., Yang, Z., Hong, J., Su, Y., Ding, F., Fu, L., Li, C., Chen, P., Ma, J., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2122954119 · Cited by 157
SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines
Thakur, S., Sasi, S., Pillai, S. G., Nag, A., Shukla, D., Singhal, R., Phalke, S., & Velu, G. S. K. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.815389 · Cited by 167
“The first fitness-enhancing mutation on the spike protein was identified just a few months into the evolution of SARS-CoV-2 (9).”
BackgroundInfluentialStructural and functional impact by SARS-CoV-2 Omicron spike mutations
Zhang, J., Cai, Y., Lavine, C. L., Peng, H., Zhu, H., Anand, K., Tong, P., Gautam, A. K., Mayer, M. L., Rits‐Volloch, S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110729 · Cited by 145
“The latest surge of new infections is caused by the Omicron variant (Organization, 2021), which has acquired an unusually large number of mutations, particularly in its spike (S) protein ( 40 residue changes versus 10 on average in all the previous dominant variants; Harvey et al., 2021).”
Could SARS-CoV-2 Spike Protein Be Responsible for Long-COVID Syndrome?
Theoharides, T. C. (2022) · Molecular Neurobiology · doi:10.1007/s12035-021-02696-0 · Cited by 156
“1 3 emerging evidence of reduced neutralization of some SARSCoV-2 variants [22].”
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Chakraborty, C., Sharma, A. R., Bhattacharya, M., & Lee, S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.801522 · Cited by 154
“Some specific mutation helps to achieve the process of immune escape, and these mutations are called immune escape mutations (5, 15, 34, 35).”
BackgroundMethodInfluentialMutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics
Domingo, E., García‐Crespo, C., Lobo-Vega, R., & Perales, C. (2021) · Viruses · doi:10.3390/v13091882 · Cited by 161
“In addition to single nucleotide mutations, insertions, and deletions—very abundant among SARS-CoV-2 isolates from patients, as compared with other pathogenic RNA viruses—may also be favored by Exo N as part of its recombination-promoting activity [21,105].”
BackgroundAntigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity
Markov, P. V., Katzourakis, A., & Stilianakis, N. I. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00722-z · Cited by 149
Antibody-mediated neutralization of SARS-CoV-2
Gruell, H., Vanshylla, K., Weber, T., Barnes, C. O., Kreer, C., & Klein, F. (2022) · Immunity · doi:10.1016/j.immuni.2022.05.005 · Cited by 150
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Equitable access to COVID-19 vaccines makes a life-saving difference to all countries
Ye, Y., Zhang, Q., Wei, X., Cao, Z., Yuan, H., & Zeng, D. D. (2022) · Nature Human Behaviour · doi:10.1038/s41562-022-01289-8 · Cited by 146
Emergence of Omicron third lineage BA.3 and its importance
Desingu, P. A., Nagarajan, K., & Dhama, K. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27601 · Cited by 144
“This is likely due to differences in mutations in the spike protein required for virus transmission and host cell entry.(7,8) We analyzed whether there were any specific mutations in the spike protein required for virus transmission and entry in these three”
BackgroundApplications of Molecular Dynamics Simulation in Protein Study
Sinha, S., Tam, B., & Wang, S. M. (2022) · Membranes · doi:10.3390/membranes12090844 · Cited by 154
“We also applied MD Simulations to study the effects of SARS-CoV-2 mutations on RBD domain binding affinity with ACE2.”
BackgroundInfluentialDrivers of adaptive evolution during chronic SARS-CoV-2 infections
Harari, S., Tahor, M., Rutsinsky, N., Meijer, S. E., Miller, D., Henig, O., Halutz, O., Levytskyi, K., Ben‐Ami, R., Adler, A., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01882-4 · Cited by 139
Scientific rationale for developing potent RBD-based vaccines targeting COVID-19
Kleanthous, H., Silverman, J. M., Makar, K. W., Yoon, I.-K., Jackson, N. M., & Vaughn, D. W. (2021) · npj Vaccines · doi:10.1038/s41541-021-00393-6 · Cited by 139
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
Sun, C., Xie, C., Bu, G., Zhong, L., & Zeng, M. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01039-2 · Cited by 149
Sokal, A., Spaeth, G. B., Fernández, I., Broketa, M., Azzaoui, I., Selle, A. D. L., Vandenberghe, A., Fourati, S., Roeser, A., Meola, A., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.09.011 · Cited by 135
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Laiton‐Donato, K., Franco-Muñoz, C., Álvarez-Díaz, D. A., Ruiz-Moreno, H. A., Usme-Ciro, J. A., Prada-Cardozo, D., Reales-González, J., Corchuelo, S., Herrera-Sepúlveda, M. T., Naizaque, J., et al. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.105038 · Cited by 123
Heterologous infection and vaccination shapes immunity against SARS-CoV-2 variants
Reynolds, C. J., Gibbons, J. M., Pade, C., Lin, K., Sandoval, D. M., Pieper, F. P., Butler, D. K., Liu, S., Otter, A. D., Joy, G., et al. (2022) · Science · doi:10.1126/science.abm0811 · Cited by 130
SARS‐CoV‐2 variants and vulnerability at the global level
Chavda, V. P., Patel, A., & Vaghasiya, D. D. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27717 · Cited by 135
“The RBD of the spike protein is perhaps the most important portion since it is crucial for connecting the SARS‐CoV‐2 virus toward the human ACE2 proteins on certain cells, allowing the virus to invade those cells.(79) This variant is made up of a mutation in the gene−gene that expresses the SARS‐CoV‐2 spike protein, w…”
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Dhawan, M. K., Saied, A. A., Mitra, S., Alhumaydhi, F. A., Emran, T. B., & Wilairatana, P. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.113522 · Cited by 130
RetractedSARS-CoV-2 evolution in the Omicron era
Roemer, C., Sheward, D. J., Hisner, R., Gueli, F., Sakaguchi, H., Frohberg, N., Schoenmakers, J., Sato, K., O’Toole, Á., Rambaut, A., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01504-w · Cited by 130
Self-citationTzou, P. L., Tao, K., Pond, S. L. K., & Shafer, R. W. (2022) · PLoS ONE · doi:10.1371/journal.pone.0261045 · Cited by 126
“The SARS-CoV-2 RBD is the main target of neutralizing antibodies [6, 7].”
BackgroundNoske, G. D., Silva, E. D. S., de Godoy, M. O., Dolci, I., Fernandes, R. S., Guido, R. V. C., Sjö, P., Oliva, G., & Godoy, A. S. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.103004 · Cited by 130
“Although most polymorphisms are not expected to generate a variant of concern (16), World Health Organization is constantly monitoring the emergence of SARS-CoV-2 mutations, since recent variants have exhibited more transmissible and infectious properties and can affect vaccines effectiveness (17, 18).”
High Rate of Asymptomatic Carriage Associated with Variant Strain OmicronPreprint
Garrett, N., Tapley, A., Andriesen, J. G., Seocharan, I., Fisher, L. H., Bunts, L., Espy, N., Wallis, C. L., Randhawa, A. K., Ketter, N., et al. (2021) · medRxiv · doi:10.1101/2021.12.20.21268130 · Cited by 125
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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