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 associated with increased transmissibility, infectivity, and viral load, making Lambda more lethal.
“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]
The Introduction and Structural context of spike mutations sections (page numbers unavailable) report a moderate infectivity advantage and increased transmissibility associated with D614G. They do not establish increased viral load or that D614G makes the Lambda variant more lethal. (LLM, conf=0.90)
Experimental — accuracy not yet measuredMutations in the spike protein and RBD have been shown to affect antibody neutralisation and thus reduce vaccine-induced immunity.
“Mutations in the spike protein and RBD have been shown to affect antibody neutralisation and thus reduce vaccine-induced immunity [22].”
The paper says Lambda is more resistant to neutralization by convalescent sera and the Alpha variant than the parent D614G spike protein.
“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]
The Variants of interest or concern section discusses modest reductions in neutralization of Alpha (B.1.1.7) by convalescent sera, but does not compare it with Lambda. Searches for Lambda and the claimed 3.3-fold and 4.9-fold comparisons found no passage addressing those results in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredReduced sensitivity of SARS-CoV-2 variants to antibody and serum neutralization has been widely observed.
“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]
The receptor binding domain and N-terminal domain are immunodominant targets of neutralizing antibodies elicited by COVID-19 vaccines or SARS-CoV-2 infection.
“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]
Each pathogen poses a unique set of challenges, including high lethality, rapid mutations, immune evasion, new strains and variants.
“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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Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19
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“Owing to the large number of mutations in the spike protein and elsewhere on the virus (https://covdb.stanford.edu/page/ mutation-viewer/#omicron), there is concern that this variant will exhibit substantial escape from vaccine-elicited immunity 4,5 .”
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“Some of these mutations have also been found in previous variants and are known to lead to increased transmissibility, higher viral binding affinity, and antibody escape.(7,8) For instance, mutations in the residues K417, E484, and N501, which have also been found in Beta (B.”
BackgroundStructural biology of SARS-CoV-2 and implications for therapeutic development
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“…at different time points after vaccina Greater breadth of IgG binding to viral variants following BNT162b2 vaccination compared with infection with Wuhan-Hu-1 SARS-CoV-2 Immune-evasive SARS-CoV-2 variants have spread globally (Harvey et al., 2021; Plante et al., 2021; Röltgen and Boyd, 2021).”
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“Adaptive mutation of the SARS‐CoV‐2 genome can change the infectivity, immune evasion, and phenotypic characteristics of the virus.(13,14,20) The emergence of the Omicron”
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The emergence, genomic diversity and global spread of SARS-CoV-2
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Human genetic and immunological determinants of critical COVID-19 pneumonia
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Neutralization of SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine–elicited human sera
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Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir
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SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies
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Self-citationRapid assessment of SARS-CoV-2–evolved variants using virus-like particles
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“…are not well positioned to identify mutations—single-nucleotide polymorphisms (SNPs), insertions or deletions—carried in SARS-CoV-2 variant lineages 6,17,18 , we wanted to develop a single platform with both diagnostic and surveillance capabilities for comprehensive detection of 26 SARS-CoV-2…”
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Correlates of protection against SARS ‐ CoV ‐2 infection and COVID‐19 disease
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“Antibodies are bifunctional molecules, comprised of (1) two antigen- binding domains (2× Fabs) that provide specificity and can block infection and (2) a constant domain (Fc) involved in directing immune clearing effects via the recruitment of the immune system (Figure 5).”
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Global disparities in SARS-CoV-2 genomic surveillance
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SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19
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“The spread of new mutations in the S-protein can potentially reduce the effectiveness of the immune response to vaccines [57].”
BackgroundSARS-CoV-2 Omicron strain exhibits potent capabilities for immune evasion and viral entrance
Zhang, X., Wu, S., Wu, B., Yang, Q., Chen, A., Li, Y., Zhang, Y., Pan, T. S., Zhang, H., & He, X. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00852-5 · Cited by 265 · see citing works
“Surprisingly, almost half are located in RBD, including the shared K417N, N501Y with Beta, the shared T478K with Delta, as well as the D614G in almost all the VOCs, where T478K has already caused breakthrough infection in vaccinated people.(5) Moreover, mutation of E484A occurs in Omicron while the E484K in Beta, whic…”
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“Vaccination has been reported to significantly drop the COVID-19 infection of emerging VOCs, including Delta (27).”
BackgroundInfluentialEfficacy and Safety of a Recombinant Plant-Based Adjuvanted Covid-19 Vaccine
Hager, K. J., Marc, G. P., Gobeil, P., Diaz, R. S., Heizer, G., Llapur, C. J., Makarkov, A. I., Vasconcellos, E., Pillet, S., Riera, F. O., et al. (2022) · New England Journal of Medicine · doi:10.1056/nejmoa2201300 · Cited by 250 · see citing works
Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies
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“furin cleavage site, which may affect antibody binding and ACE2 binding [87,88].”
BackgroundSARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants
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Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants
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Sequence analysis of the emerging SARS‐CoV‐2 variant Omicron in South Africa
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Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
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SARS-COV-2 Variants: Differences and Potential of Immune Evasion
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The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance
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“…variant, our data indicate that the NTD supersite is immunodominant and that acquiring immune escape mutations in this region is associated with the efficacy of viral dissemination in the human population, which has been proposed in previous reports (Harvey et al., 2021; McCallum et al., 2021).”
InfluentialBeyond neutralization: Fc-dependent antibody effector functions in SARS-CoV-2 infection
Zhang, A., Stacey, H. D., D’Agostino, M. R., Tugg, Y., Marzok, A., & Miller, M. S. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00813-1 · Cited by 212 · see citing works
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“The K417 of spike protein can form salt-bridge interaction with various antibodies, and mutating this residue would cause disrupted RBDantibody interaction that could lead to viral escape from human antibodies [81, 82].”
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“Additionally, mutations T76I, L141F, G142Y, 156–167 deletion, and R158G, located in the NTD region, were noted to affect antibody binding efficiencies and contribute to immune escape.(30) These mutations sites are mapped and shown in Fig.”
BackgroundWaves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe
Thakur, V., Bhola, S., Thakur, P., Patel, S. K. S., Kulshrestha, S., Ratho, R. K., & Kumar, P. (2022) · Infection · doi:10.1007/s15010-021-01734-2 · Cited by 210 · see citing works
“D614G is again associated with the increase in transmissibility, infectivity, and viral load, making the Lambda variant even more lethal [55].”
BackgroundNeutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum
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SARS-CoV-2 biology and host interactions
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“Specifically, several SARS-CoV-2 variants of concern exhibited improved human-to-human transmission, evasion of previously acquired immunity or changes in disease virulence 5,6 .”
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Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale
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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
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Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant
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The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape
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“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 195 · see citing works
Mucosal immune response in biology, disease prevention and treatment
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Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections
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Engineered Ribosyl-1-Kinase Enables Concise Synthesis of Molnupiravir, an Antiviral for COVID-19
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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
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“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
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Self-citationOmicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
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Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission
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Paxlovid (Nirmatrelvir/Ritonavir): A new approach to Covid-19 therapy?
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The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation
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The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses
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Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease
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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 · see citing works
“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).”
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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 158 · see citing works
“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 142 · see citing works
“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 154 · see citing works
“1 3 emerging evidence of reduced neutralization of some SARSCoV-2 variants [22].”
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“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 150 · see citing works
“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., Katzourakis, A., & Stilianakis, N. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00722-z · Cited by 127 · see citing works
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 145 · see citing works
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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 · see citing works
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 · see citing works
“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 144 · see citing works
“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 135 · see citing works
Scientific rationale for developing potent RBD-based vaccines targeting COVID-19
Kleanthous, H., Silverman, J., Makar, K., Yoon, I., Jackson, N. A. C., & Vaughn, D. (2021) · npj Vaccines · doi:10.1038/s41541-021-00393-6 · Cited by 137 · see citing works
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
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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 · see citing works
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 126 · see citing works
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 132 · see citing works
“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…”
BackgroundIslam, S., Islam, T., & Islam, M. R. (2022) · Clinical Pathology · doi:10.1177/2632010x221075584 · Cited by 130 · see citing works
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 127 · see citing works
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, A. N., Rambaut, A., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01504-w · Cited by 129 · see citing works
Self-citationTzou, P. L., Tao, K., Pond, S. L. K., & Shafer, R. W. (2022) · PLoS ONE · doi:10.1371/journal.pone.0261045 · Cited by 124 · see citing works
“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 125 · see citing works
“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 · see citing works
- 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 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1
- 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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