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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]
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“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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“With SARS-CoV-2, the spike protein appears reasonably conserved across variants (76), and has allowed the design of vaccines that can generate antibodies with pansarbecovirus neutralizing activity (77, 78).”
BackgroundACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner
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“Severe acute respiratory syndrome coronavirus 2 is an enveloped single-stranded RNA virus that belongs to the genus β-coronavirus (Harvey et al., 2021).”
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“The impact of mutations in the S protein of VOCs has been the focus of many studies (Harvey et al, 2021; Jangra et al, 2021; Planas et al, 2021; Pastorio et al, 2022).”
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Free Zinc as a Predictive Marker for COVID-19 Mortality Risk
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“The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1].”
BackgroundSingle-Domain Antibodies Efficiently Neutralize SARS-CoV-2 Variants of Concern
Favorskaya, I. A., Shcheblyakov, D. V., Esmagambetov, I. B., Dolzhikova, I. V., Alekseeva, I. A., Korobkova, A. I., Voronina, D. V., Ryabova, E. I., Derkaev, A. A., Витальевна, К. А., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.822159 · Cited by 36
“The reduction of neutralization by antibodies is 58 caused by mutations in S glycoprotein, including K417N/T, L452R, T478K, E484K and N501Y 59 substitutions (15, 16).”
BackgroundMohandas, S., Yadav, P. D., Sapkal, G. N., Shete, A. M., Deshpande, G. R., Nyayanit, D. A., Patil, D. Y., Kadam, M., Kumar, A., Mote, C., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.103997 · Cited by 39
“40 It harbours N501Y, K417N, T478K, E484A which are amino acid substitutions linked with immune escape.”
Metabolite, protein, and tissue dysfunction associated with COVID-19 disease severity
Rahnavard, A., Mann, B. T., Giri, A., Chatterjee, R., & Crandall, K. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-16396-9 · Cited by 36
Brunner, F. S., Brown, M. R., Bassano, I., Denise, H., Khalifa, M. S., Wade, M. J., van Aerle, R., Kevill, J. L., Jones, D. L., Farkas, K., et al. (2022) · Water Research · doi:10.1016/j.watres.2022.119306 · Cited by 35
Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic
González-Vázquez, L. D., & Arenas, M. (2023) · Genes · doi:10.3390/genes14020407 · Cited by 44
“During the pandemic, the genome of SARS-CoV-2 evolved, producing variants that displayed different infective and immunological properties [9,10], which caused a series of epidemiological waves around the world.”
BackgroundThe Repeated Setbacks of HIV Vaccine Development Laid the Groundwork for SARS-CoV-2 Vaccines
Harris, J. E. (2021) · National Bureau of Economic Research · doi:10.3386/w28587 · Cited by 37
Cheng, S. M., Mok, C. K. P., Chan, K. C., Ng, S. S., Lam, B. H., Luk, L. L., Ko, F. W., Chen, C., Yiu, K., Li, J. K., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.18.2200178 · Cited by 31
The Omicron variant of concern: The genomics, diagnostics, and clinical characteristics in children
Setiabudi, D., Sribudiani, Y., Hermawan, K., Andriyoko, B., & Nataprawira, H. M. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.898463 · Cited by 37
Quintero, A., Eisner, M., Sayegh, R., Wright, T., Ramilo, O., Leber, A. L., Wang, H., & Mejías, A. (2022) · Emerging infectious diseases · doi:10.3201/eid2811.220577 · Cited by 35
The E3 ligase TRIM22 restricts SARS-CoV-2 replication by promoting proteasomal degradation of NSP8
Fan, L., Zhou, Y., Wei, X., Feng, W., Guo, H., Li, Y., Gao, X., Zhou, J., Wen, Y., Wu, Y., et al. (2024) · mBio · doi:10.1128/mbio.02320-23 · Cited by 36
Liu, Z., Xu, W., Chen, Z., Fu, W., Zhan, W., Gao, Y., Zhou, J., Zhou, Y., Wu, J., Wang, Q., et al. (2021) · Protein & Cell · doi:10.1007/s13238-021-00871-6 · Cited by 38
“2 (Delta, WHO label) identified in the United Kingdom, South Africa, Brazil and India, respectively, have posed a new challenge (Grubaugh et al., 2021; Harvey et al., 2021; Lopez Bernal et al., 2021; Planas et al., 2021; Supasa et al., 2021; Xie et al., 2021; Wang et al., 2021b).”
InfluentialPotential Anti-SARS-CoV-2 Activity of Pentosan Polysulfate and Mucopolysaccharide Polysulfate
Zhang, F., He, P., Rodrigues, A. L., Jeske, W. P., Tandon, R., Bates, J. T., Bierdeman, M. A., Fareed, J., Dordick, J. S., & Linhardt, R. J. (2022) · Pharmaceuticals · doi:10.3390/ph15020258 · Cited by 37
Emergence of SARS-CoV-2 Spike Mutations during Prolonged Infection in Immunocompromised Hosts
Ko, K. K. K., Yingtaweesittikul, H., Tan, T. T., Wijaya, L., Cao, D. Y., Goh, S. S., Rahman, N. B. A., Chan, K. X. L., Tay, H. M., Sim, J. H. C., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00791-22 · Cited by 37
Korobova, Z. R., Arsentieva, N. A., Liubimova, N. E., Dedkov, V. G., Gladkikh, A. S., Sharova, A. А., Chernykh, E. I., Кащенко, В. А., Ratnikov, V. A., Gorelov, V. P., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23169058 · Cited by 35
von Wintersdorff, C. J. H., Dingemans, J., van Alphen, L. B., Wolffs, P. F. G., van der Veer, B. M. J. W., Hoebe, C. J. P. A., & Savelkoul, P. H. M. (2022) · Scientific Reports · doi:10.1038/s41598-022-18279-5 · Cited by 45
Reis, H. Ç., & Turk, V. (2022) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2022.102427 · Cited by 40
“The S-glycoprotein is initially closed, where the virus must first become on/activated before it can infect the human cell [6].”
BackgroundZhou, G., Dael, N., Verweij, S., Balafas, S., Mubarik, S., Oude Rengerink, K., Pasmooij, A. M. G., van Baarle, D., Mol, P. G. M., de Bock, G. H., et al. (2025) · European Respiratory Review · doi:10.1183/16000617.0222-2024 · Cited by 34
Nguyen, D. V., Peter Simmonds, K., Steenhuis, M., Wouters, E., Desmecht, D. J.-M., Garigliany, M., Romano, M., Barbezange, C., Maes, P., Holm, B. V., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.27.2100568 · Cited by 34
“These data are consistent with previously published observations that the spike mutations in Beta, and to a lesser extent also in Alpha, variants are associated with reduced susceptibility to neutral-ising antibodies [13-15].”
Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine
Wu, Y., Wang, S., Zhang, Y., Yuan, L., Zheng, Q., Wei, M., Shi, Y., Wang, Z., Ma, J., Wang, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.10.011 · Cited by 35
“620 NTD harbored amino-acid 7 deletions of Δ69-70, Δ145, and Δ242-244, correspond to changed epitopes on 8 the N2, N3, and N5 loops (31).”
Torales, J. C., Cuenca-Torres, O., Barrios, L., Armoa, L., Estigarribia, G., Sanabria, G., Lin, M., Estrada, J. A. G., Estephan, L., Cheng, H., et al. (2022) · Vaccine · doi:10.1016/j.vaccine.2022.10.030 · Cited by 36
“[2] P-value: Pearson’s Chi-square test.”
BackgroundMethodInfluentialSievering, A. W., Wohlmuth, P., Geßler, N., Gunawardene, M., Herrlinger, K. R., Bein, B., Arnold, D., Bergmann, M., Nowak, L., Gloeckner, C., et al. (2022) · BMC Medical Informatics and Decision Making · doi:10.1186/s12911-022-02057-4 · Cited by 37
“This particularly limits generalizability to the actual pandemic period under new influences from virus mutants, [46] vaccination, [47] improved testing, [48] and evolving drug treatments, such as anticoagulation [49] or dexamethasone [50].”
BackgroundAdaptive Evolution of the Spike Protein in Coronaviruses
Tang, X., Qian, Z., Lu, X., & Lü, J. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad089 · Cited by 36
“However, changes in the S gene have drawn the most attention since the sequence of the S protein influences the virus’s ability to infect cells and evade host immune responses (Harvey et al. 2021).”
BackgroundInfluentialFully synthetic platform to rapidly generate tetravalent bispecific nanobody–based immunoglobulins
Misson, L., Liu, H., Ozorowski, G., Tran, Q., Woehl, J. L., Khalek, I. S., Smith, J., Barman, S., Zhao, F., Keating, C., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2216612120 · Cited by 36
“This was exemplified by the evolution of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) variants of concern (VOCs) during the COVID-19 pandemic that were partially or fully resistant to the therapeutic antibody countermeasures (1).”
Zeng, L., Li, J., Lv, M., Li, Z., Yao, L., Gao, J., Wu, Q., Wang, Z., Yang, X., Tang, G., et al. (2023) · Environment & Health · doi:10.1021/envhealth.3c00005 · Cited by 35
Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1)
Hedskog, C., Rodriguez, L., Roychoudhury, P., Huang, M.-L. W., Jerome, K. R., Hao, L., Ireton, R. C., Li, J., Perry, J. K., Han, D., et al. (2023) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiad270 · Cited by 36
“…(the parent nucleoside of remdesivir [21]). shows that therapeutic monoclonal antibodies lose efficacy against Omicron variants, such that there are no US Food and Drug Administration–authorized therapeutic monoclonal antibodies for treatment of COVID-19 at the time of writing [33, 47–49].”
BackgroundSARS-CoV-2 evolution during prolonged infection in immunocompromised patients
Marques, A. D., Graham-Wooten, J., Fitzgerald, A. S., Leonard, A. S., Cook, E. J., Everett, J. K., Rodino, K. G., Moncla, L. H., Kelly, B. J., Collman, R. G., et al. (2024) · mBio · doi:10.1128/mbio.00110-24 · Cited by 35
“Thus, in immunocompromised hosts, we observe preferential accumulation of substitutions in spike relative to the rest of the genome, as has been observed in the general population (44).”
BackgroundTuttle, J. B., Allais, C., Allerton, C. M. N., Anderson, A. S., Arcari, J. T., Aschenbrenner, L. M., Avery, M., Bellenger, J., Berritt, S., Boras, B. W., et al. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c02561 · Cited by 36
Savvateeva, E. N., Filippova, M. A., Треворович, В.-Э. В., Nuralieva, N. F., Yukina, M., Troshina, E. A., Baklaushev, V. P., Ivanov, A. V., & Gryadunov, D. A. (2021) · Viruses · doi:10.3390/v13122553 · Cited by 41
“Third, the sensitivity of detection of antibodies against spike RBD differs for multiple SARS-CoV-2 variants due to changing antigenicity of the SARSCoV-2 spike protein [36].”
Backgroundda Silva, S. J. R., de Lima, S. C., da Silva, R. C., Kohl, A., & Pena, L. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2021.836826 · Cited by 35
“Beneficial mutations tend to occur in the minority of cases, when compared to negative effect or no effect “neutral” mutations (21).”
BackgroundInterferon antagonists encoded by SARS-CoV-2 at a glance
Lee, J., Koepke, L., Kirchhoff, F., & Sparrer, K. M. J. (2022) · Medical Microbiology and Immunology · doi:10.1007/s00430-022-00734-9 · Cited by 39
“SARS-CoV-2 continues to adapt for an efficient spread in the human population resulting in the emergence of variants [52, 53].”
BackgroundSARS-CoV-2 Variants of Concern Hijack IFITM2 for Efficient Replication in Human Lung Cells
Nchioua, R., Schundner, A., Kmieć, D., Bozzo, C. P., Zech, F., Koepke, L., Graf, A., Krebs, S., Blum, H., Frick, M., et al. (2022) · Journal of Virology · doi:10.1128/jvi.00594-22 · Cited by 38
Kim, Y., Gaudreault, N. N., Meekins, D. A., Perera, K. D., Bold, D., Trujillo, J. D., Morozov, I., McDowell, C. D., Chang, K., & Richt, J. A. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01789-21 · Cited by 35
“Mutations affecting the S protein, including the RBD, are of particular concern because they may enhance virus transmissibility and reduce antibody binding and immune protection, thus compromising vaccine efficacy [30].”
Mutations in SARS-CoV-2 are on the increase against the acquired immunity
Konishi, T. (2022) · PLoS ONE · doi:10.1371/journal.pone.0271305 · Cited by 35
“The mutations mainly occur in S and N, which are the surface and nucleocapsid proteins of the virus, respectively; therefore, there must be a strong selection pressure to overcome immunity [41].”
BackgroundVellas, C., Bello, A. D., Debard, A., Steinmeyer, Z., Tribaudeau, L., Ranger, N., Jeanne, N., Martin‐Blondel, G., Delobel, P., Kamar, N., et al. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.09.008 · Cited by 34
“New SARS-CoV-2 variants containing key changes in the receptor-binding domain have recently appeared that can be more transmissible, more pathogenic, and resistant to endogenous or exogenous antibodies than the original virus [4,5].”
Wang, M., Zhang, L., Li, Q., Wang, B., Liang, Z., Sun, Y., Nie, J., Wu, J., Su, X., Qu, X., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.2008775 · Cited by 33
Drug-Repurposing Screening Identified Tropifexor as a SARS-CoV-2 Papain-like Protease Inhibitor
Ma, C., Hu, Y., Wang, Y., Choza, J. I., & Wang, J. (2022) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.1c00629 · Cited by 34
Cold atmospheric plasma for preventing infection of viruses that use ACE2 for entry
Wang, P., Zhou, R., Zhou, R., Li, W., Weerasinghe, J., Chen, S., Rehm, B. H. A., Zhao, L., Frentiu, F. D., Zhang, Z., et al. (2022) · Theranostics · doi:10.7150/thno.70098 · Cited by 35
“, T95I, K417N, T478K, N501Y, N655Y, N679K, P681H) ([18]), which lead to enhanced transmissibility and extreme escape from immunological control([19-23]).”
BackgroundZheng, B., Xiao, Y., Tong, B., Mao, Y., Ge, R., Tian, F., Dong, X., & Zheng, P. (2023) · JACS Au · doi:10.1021/jacsau.3c00142 · Cited by 30
Recent Advances in Field‐Effect Transistor‐Based Biosensors for Label‐Free Detection of SARS‐CoV‐2
Yu, H., Zhang, H., Liu, J. Z., Feng, L., Su, Y., Li, J., Tang, W., & Yan, F. (2023) · Small Science · doi:10.1002/smsc.202300058 · Cited by 35
Aram, C., Alijanizadeh, P., Saleki, K., & Karami, L. (2024) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2024.101745 · Cited by 34
“However, the S protein in SARS-CoV-2 has a somewhat variable sequence which makes different pandemics and variants of concern such as Alpha, Beta, Gamma, Delta, and especially Omicron that spike aimed at viruses to avoid the immunological mechanisms [16].”
BackgroundWekalao, J., Baz, A., & Patel, S. K. (2024) · Diamond and Related Materials · doi:10.1016/j.diamond.2024.111601 · Cited by 34
Vaquero, S. T., de Campos‐Mata, L., Ramada, J. M., Díaz, P., Navarro‐Barriuso, J., Ribas‐Llauradó, C., Melero, N. R., Carolis, C., Cerutti, A., Gimeno, R., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.737083 · Cited by 34
Trapping and Detection of Single Viruses in an Optofluidic Chip
Shi, Y., Nguyen, K. T., Chin, L. K., Li, Z., Xiao, L., Cai, H. N., Yu, R., Huang, W., Feng, S., Yap, P. H., et al. (2021) · ACS Sensors · doi:10.1021/acssensors.1c01350 · Cited by 33
Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant
Kant, R., Kareinen, L., Smura, T., Freitag, T. L., Jha, S. K., Alitalo, K. K., Meri, S., Sironen, T. A., Saksela, K., Strandin, T. M., et al. (2021) · Viruses · doi:10.3390/v13112263 · Cited by 36
“The wt SARS-CoV-2 is unable to infect mice due to a receptor mismatch, but accumulating evidence suggests that naturally occurring VOCs might be able to acquire this capability [4,16].”
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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