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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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Citations
Cites
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2180-5 · Cited by 5,983
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
Letko, M., Marzi, A., & Munster, V. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0688-y · Cited by 3,109
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0770-5 · Cited by 2,543
Self-citationTegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Starr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956
Hoffmann, M., Kleine-Weber, H., & Pöhlmann, S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.022 · Cited by 1,852
Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., et al. (2021) · doi:10.1101/2020.12.30.20249034 · Cited by 1,611
Self-citation
Cited by
Sorted by citations
Items 601–700 of 1,002
Kim, S. J., Yao, Z., Marsh, M., Eckert, D. M., Kay, M. S., Lyakisheva, A., Pasic, M. D., Bansal, A., Birnboim, C., Jha, P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31300-9 · Cited by 28
Britto, C., & Alter, G. (2022) · Current Opinion in Immunology · doi:10.1016/j.coi.2022.102234 · Cited by 32
Chen, C., Chang, C.-N., Hu, C.-F., Jian, M., Chung, H., Chang, C.-K., Perng, C., Hung, K., Chang, F., Wang, C., et al. (2022) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2022.09.001 · Cited by 28
Tsilioni, I., & Theoharides, T. C. (2023) · Molecular Neurobiology · doi:10.1007/s12035-023-03493-7 · Cited by 29
“As such, long-COVID could be considered a state of “brain autoimmunity” [73].”
BackgroundAn IgM-like inhalable ACE2 fusion protein broadly neutralizes SARS-CoV-2 variants
Liu, J., Mao, F., Chen, J., Lu, S., Qi, Y., Sun, Y., Fang, L., Yeung, M. L., Liu, C., Yu, G., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40933-3 · Cited by 29
Yeh, T., & Contreras, G. P. (2021) · medRxiv · doi:10.1101/2021.08.08.21261768 · Cited by 28
The adaptation of SARS-CoV-2 to humans
Tosta, E. (2021) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760210127 · Cited by 27
COVID-19 diverse outcomes: Aggravated reinfection, type I interferons and antibodies
Silva, R. C. M. C., Bandeira‐Melo, C., Neto, H. A. P., Vale, A. M., & Travassos, L. H. (2022) · Medical Hypotheses · doi:10.1016/j.mehy.2022.110943 · Cited by 36
Nirmatrelvir combined with ritonavir for preventing and treating COVID-19
Reis, S., Metzendorf, M., Kuehn, R., Popp, M., Gágyor, I., Kranke, P., Meybohm, P., Skoetz, N., & Weibel, S. (2023) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd015395.pub3 · Cited by 31
Analysis of SARS-CoV-2 genome evolutionary patterns
Gupta, S., Gupta, D., & Bhatnagar, S. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.02654-23 · Cited by 29
“The ratio of d N /d S > 1 indicates positive selection and has been reported in the S glycoprotein (22, 23).”
BackgroundBeyond schistosomiasis: unraveling co-infections and altered immunity
Perera, D. J., Koger-Pease, C., Paulini, K., Daoudi, M., & Ndao, M. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00098-23 · Cited by 27
“Moreover, this virus appears to be becoming endemic, with mutations in the N-terminus and receptor-binding region, including p.Glu484Lys which can be found in the most dangerous variants (293).”
BackgroundImmune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development
Magazine, N., Zhang, T., Bungwon, A. D., McGee, M. C., Wu, Y., Veggiani, G., & Huang, W. (2024) · ImmunoHorizons · doi:10.4049/immunohorizons.2400003 · Cited by 32
“Hostvirus interactions mediated by Spike protein appear to be the primary driver of SARS-CoV-2 evolution (23, 24).”
BackgroundResultAnti-SARS-CoV-1 and −2 nanobody engineering towards avidity-inspired therapeutics
Obeng, E. M., Dzuvor, C. K. O., & Danquah, M. K. (2021) · Nano Today · doi:10.1016/j.nantod.2021.101350 · Cited by 27
Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants
Yang, Q., Jian, X., Syed, A. A. S., Fahira, A., Zheng, C., Zhu, Z., Wang, K., Zhang, J., Wen, Y., Li, Z., et al. (2022) · Research · doi:10.34133/2022/9781758 · Cited by 30
Luedemann, M., Stadler, D., Cheng, C., Protzer, U., Knolle, P. A., & Donakonda, S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.01.024 · Cited by 27
“This suggested continuous strong binding of montelukast to the S1-RBD of variant SARS-CoV-2, which was not surprising as the mutations in the RBD of the alpha SARSCoV-2 variant were outside of the montelukast binding site [13].”
InfluentialMatos, A. D. R., Caetano, B. C., Filho, J. L. D. A., Martins, J., de Oliveira, M. G. P., Sousa, T. D. C., Horta, M. A. P., Siqueira, M. M., & Fernández, J. H. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.828984 · Cited by 27
Caduff, L., Dreifuss, D., Schindler, T., Devaux, A. J., Ganesanandamoorthy, P., Kull, A., Stachler, E., Fernandez-Cassi, X., Beerenwinkel, N., Kohn, T., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.10.2100806 · Cited by 27
“Examples include mutations that may influence not only transmissibility but also virulence and/or vaccine-induced antibody escape [13].”
BackgroundAileni, M., Rohela, G. K., Jogam, P., Soujanya, S., & Zhang, B. (2022) · Cells · doi:10.3390/cells11071182 · Cited by 30
“, the spike protein of SARS-CoV-2) [51].”
Rajpal, V. R., Sharma, S., Kumar, A., Chand, S., Joshi, L., Chandra, A., Babbar, S., Goel, S., Raina, S. N., & Shiran, B. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27749 · Cited by 26
“N439K has been observed to enhance the binding affinity with ACE2 receptor and to neutralize the activity of monoclonal and polyclonal antibodies in people who recovered from infection.(23,28) Omicron Spike protein (all three lineages) carries ten deletion mutations (L24del, P25del, P26del, H69del, V70del, V143del, Y1…”
BackgroundResearch progress on vaccine efficacy against SARS-CoV-2 variants of concern
Bian, L., Liu, J., Gao, F., Gao, Q., He, Q., Mao, Q., Wu, X., Xu, M., & Liang, Z. (2022) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2022.2057161 · Cited by 30
Yang, Y., Zhou, D., Zhang, X., Shi, Y., Han, J., Zhou, L., Wu, L., Ma, M., Li, J., Peng, S., et al. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac147 · Cited by 27
“Although the vaccines against COVID-19 have shown great success, immune escape is becoming a real threat as new variants of the virus are emerging from time to time [5, 6].”
Khan, K., Khan, S., Jalal, K., Ul-haq, Z., & Uddin, R. (2022) · Virology · doi:10.1016/j.virol.2022.05.001 · Cited by 25
Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance
Xu, X., Deng, Y., Ding, J., Zheng, X., Li, S., Liu, L., Chui, H.-K., Poon, L. L. M., & Zhang, T. (2022) · Water Research · doi:10.1016/j.watres.2022.118686 · Cited by 26
Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection
Pandey, S. K., Mohanta, G. C., Kumar, V., & Gupta, K. (2022) · Vaccines · doi:10.3390/vaccines10081200 · Cited by 28
“All viruses continually mutate and evolve toward better adaptation to the host cells, either through host-cell-receptor binding with higher affinity or escaping the host’s immunity, or both [20].”
BackgroundZahmatkesh, S., Sillanpää, M. E. T., Rezakhani, Y., & Wang, C. (2022) · Journal of Hazardous Materials Advances · doi:10.1016/j.hazadv.2022.100140 · Cited by 28
Ouyang, W. O., Tan, T. J. C., Lei, R., Song, G., Kieffer, C., Andrabi, R., Matreyek, K. A., & Wu, N. C. (2022) · Science Advances · doi:10.1126/sciadv.add7221 · Cited by 27
Scharf, L., Axelsson, H., Emmanouilidi, A., Mathew, N. R., Sheward, D. J., Leach, S., Isakson, P., Smirnov, I. V., Marklund, E., Miron, N., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.165299 · Cited by 29
RNA recording in single bacterial cells using reprogrammed tracrRNAs
Jiao, C., Reckstadt, C., König, F., Homberger, C., Yu, J., Vogel, J., Westermann, A. J., Sharma, C. M., & Beisel, C. L. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01604-8 · Cited by 28
Genetic variety of ORF3a shapes SARS‐CoV‐2 fitness through modulation of lipid droplet
Wang, W., Qu, Y., Wang, X., Xiao, M. Z. X., Fu, J., Chen, L., Zheng, Y., & Liang, Q. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28630 · Cited by 27
Liu, G., & Gack, M. U. (2023) · Virology Journal · doi:10.1186/s12985-023-02025-y · Cited by 26
Emergence of COVID-19 Variants: An Update
Gupta, P., Gupta, V., Singh, C. M., & Singhal, L. (2023) · Cureus · doi:10.7759/cureus.41295 · Cited by 34
“However, the deep mutational scanning study didn’t have the same findings, and the discordance has been attributed to the mechanism of immune escape exhibited by this mutation [51].”
BackgroundInfluentialPreclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants
Tan, S., Zhao, J., Hu, X., Li, Y., Wu, Z., Lu, G., Yu, Z., Du, B., Liu, Y., Li, L., et al. (2023) · 中国科学通报:英文版 · doi:10.1016/j.scib.2023.11.024 · Cited by 25
S glycoprotein diversity of the Omicron variantPreprint
Sarkar, R., Lo, M., Saha, R., Dutta, S., & Chawla‐Sarkar, M. (2021) · medRxiv · doi:10.1101/2021.12.04.21267284 · Cited by 26
“All these mutations have previously been linked with high transmissibility, increased viral binding affinity, and immune evasion [15, 20-22].”
BackgroundImmunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein
Umitaibatin, R., Harisna, A. H., Jauhar, M. M., Syaifie, P. H., Arda, A. G., Nugroho, D., Ramadhan, D., Mardliyati, E., Shalannanda, W., & Anshori, I. (2023) · Vaccines · doi:10.3390/vaccines11020399 · Cited by 26
“Several studies reported that these mutations can evade monoclonal antibodies [56,61] and influence polyclonal antibody recognition [62,63].”
BackgroundTeimouri, H., Taheri, S., Saidabad, F. E., Nakazato, G., Maghsoud, Y., & Babaei, A. (2025) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2025.117844 · Cited by 26
Koike, T., Sugimoto, A., Kosono, S., Komaba, S., Kanno, Y., Kitamura, T., Anzai, I., Watanabe, T., Takahashi, D., & Toshima, K. (2021) · RSC Medicinal Chemistry · doi:10.1039/d1md00264c · Cited by 26
SARS-CoV2 Infection Alters Tryptophan Catabolism and Phospholipid Metabolism
Kaur, G., Ji, X., & Rahman, I. (2021) · Metabolites · doi:10.3390/metabo11100659 · Cited by 26
“Emergence of newer variants with higher transmissibility adds to the challenge of infection containment [4,5].”
BackgroundStructural Biology of Nanobodies against the Spike Protein of SARS-CoV-2
Tang, Q., Owens, R. J., & Naismith, J. H. (2021) · Viruses · doi:10.3390/v13112214 · Cited by 24
“This change has led to concerns about immune evasion as this mutation leads to a notable deterioration in the human antibody response (whether by vaccine or by previous infection) [59].”
BackgroundModeling serological testing to inform relaxation of social distancing for COVID-19 control
Kraay, A. N. M., Nelson, K., Zhao, C., Demory, D., Weitz, J. S., & Lopman, B. A. (2021) · Nature Communications · doi:10.1038/s41467-021-26774-y · Cited by 27
Shenoy, P. D., Ahmed, S., Paul, A., Cherian, S., Umesh, R., Shenoy, V., Vijayan, A., Babu, S., Nivin, S., & Thambi, A. (2021) · The Lancet Rheumatology · doi:10.1016/s2665-9913(21)00356-8 · Cited by 26
Nag, A., Arora, S., Sinha, V., Meena, E., Sutaria, D., Gupta, A. B., & Medicherla, K. M. (2022) · Water · doi:10.3390/w14030297 · Cited by 26
“Some alterations or combinations of mutations—such as greater transmissibility via increased receptor binding or the ability to avoid the host immune response by changing surface features recognized by antibodies [3,4]—may do so.”
BackgroundAnderson, E. R., Patterson, E. I., Richards, S., Pitol, A. K., Edwards, T., Wooding, D., Buist, K., Green, A., Mukherjee, S., Hoptroff, M., et al. (2022) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001508 · Cited by 26
“Over the course of the global pandemic, several SARS- CoV2 variants have emerged with mutations changing the amino acid sequence of the receptor- binding domain of the spike protein [36].”
BackgroundBaindara, P., Dinata, R., Mandal, S. M., & Schrum, A. G. (2022) · Infectious Disease Reports · doi:10.3390/idr14020029 · Cited by 26
“Largely, much of the analysis of major sequence alterations between different variants has emphasized SARS-CoV-2 spike glycoprotein [11], where the receptor binding domain (RBD) and amino (N)-terminal domain (NTD) are particularly relevant to infectivity [7].”
BackgroundHotop, S., Reimering, S., Shekhar, A., Asgari, E., Beutling, U., Dahlke, C., Fathi, A., Khan, F., Lütgehetmann, M., Ballmann, R., et al. (2022) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2057874 · Cited by 26
“are located adjacent to the S286–S290 region (aa 853–879) [32].”
BackgroundSARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets
Shivshankar, P., Karmouty‐Quintana, H., Mills, T., Doursout, M., Wang, Y., Czopik, A. K., Evans, S. E., Eltzschig, H. K., & Yuan, X. (2022) · Inflammation · doi:10.1007/s10753-022-01656-7 · Cited by 28
Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)
Mandal, N., Padhi, A. K., & Rath, S. L. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2022.108194 · Cited by 28
“Mutation is also one of the primary generators of diversity among the genomes, including the viral genomes.(6,7) Thus, we are observing an emergence of variants of SARSCoV-2 since the first incidence of the Coronavirus disease 2019 (COVID-19).”
BackgroundSullivan, E., Sung, P.-Y., Wu, W., Berry, N. J., Kempster, S. L., Ferguson, D., Almond, N. M., Jones, I. M., & Roy, P. (2022) · Viruses · doi:10.3390/v14050914 · Cited by 27
“7 S variant that carries the N501Y residue change [62], which has been reported to improve ACE-2 binding and partly evade the neutralizing antibody response [63,64].”
BackgroundInfection fatality rate and infection attack rate of COVID-19 in South American countries
Musa, S. S., Tariq, A., Liu, Y., Wei, H., & He, D. (2022) · Infectious Diseases of Poverty · doi:10.1186/s40249-022-00961-5 · Cited by 29
Pandemic responsiveness: Evidence from social distancing and lockdown policy during COVID-19
Besley, T. J., & Dray, S. (2022) · PLoS ONE · doi:10.1371/journal.pone.0267611 · Cited by 23
Development of an LNP-Encapsulated mRNA-RBD Vaccine against SARS-CoV-2 and Its Variants
Liu, C., Rcheulishvili, N., Shen, Z., Papukashvili, D., Xie, F., Wang, Z., Wang, X., He, Y., & Wang, P. G. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14051101 · Cited by 27
“The variants have the capacity to escape neutralization by serum from convalescent humans and monoclonal antibodies [43,44].”
BackgroundSuntronwong, N., Kanokudom, S., Auphimai, C., Assawakosri, S., Thongmee, T., Vichaiwattana, P., Duangchinda, T., Chantima, W., Pakchotanon, P., Chansaenroj, J., et al. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28044 · Cited by 25
“Among these, 15 mutations located on the receptor‐ binding domain (RBD), which are responsible for interactions with the angiotensin‐converting enzyme 2 (ACE2) receptor, and 8 amino acid changes are found at the N‐terminal domain (NTD).(6) In a study of mutated RBD profiles, various omicron mutations capable of escapi…”
BackgroundInteractions between heparin and SARS-CoV-2 spike glycoprotein RBD from omicron and other variants
Gelbach, A. L., Zhang, F., Kwon, S., Bates, J. T., Farmer, A. P., Dordick, J. S., Wang, C., & Linhardt, R. J. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.912887 · Cited by 26
“With the prevalence of new SARSCoV-2 variants, SGP mutations have been observed, which greatly change SARS-CoV-2 infectivity, disease severity and the effectiveness of vaccines (Harvey et al., 2021).”
BackgroundCampos, D. M. D. O., da Silva, M. K., Barbosa, E. D., Leow, C. Y., Fulco, U. L., & Oliveira, J. I. N. (2022) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2022.107754 · Cited by 26
“Thus, affinities for MHC molecules can be predicted, with classification into binders and nonbinders Jensen et al. (2018). The NetMHCIIpan (http://www.cbs.dtu. DK/services/NetMHCIIpan/) has also been used as a guide for T cell peptide identification. It is based on a comprehensive dataset of > 100, 000 quantitative pe…”
Parihar, A., Ahmed, S. S., Sharma, P., Choudhary, N. K., Akter, F., Ali, M., Sonia, Z. F., & Khan, R. (2022) · Molecular Simulation · doi:10.1080/08927022.2022.2113811 · Cited by 26
“Δ69–70 mutation has been linked to enhanced infectivity and is projected to change the structure of NTD loop of virus [4].”
BackgroundEarly Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater
Wilhelm, A., Agrawal, S., Schoth, J., Meinert‐Berning, C., Bastian, D., Orschler, L., Ciesek, S., Teichgräber, B., Wintgens, T., Lackner, S., et al. (2022) · Viruses · doi:10.3390/v14091876 · Cited by 25
“During the evolutionary process, nucleotide polymorphisms might arise in the SARS-CoV-2 genome, potentially affecting the viral transmissibility and the susceptibility to monoclonal antibodies (mAb) and antibodies from convalescent as well as vaccine-elicited sera [3].”
BackgroundLiu, H., Yin, X., Tian, H., Qiu, Y., Wang, Z., Chen, J., Ma, D., Zhao, B., Du, Q., Tong, D., et al. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14740 · Cited by 26
Subclass-switched anti-spike IgG3 oligoclonal cocktails strongly enhance Fc-mediated opsonization
Izadi, A., Hailu, A., Godzwon, M., Wrighton, S., Olofsson, B., Schmidt, T., Söderlund‐Strand, A., Elder, E., Appelberg, S., Valsjö, M., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2217590120 · Cited by 28
“Due to the rise of extensive mutations found in the RBD of the emerging variants of concern (VOC), most of the therapeutic antibodies isolated early during the pandemic lost binding, leading to loss of function and treatment failure (23, 24).”
Vaccines Alone Cannot Slow the Evolution of SARS-CoV-2
Egeren, D. V., Stoddard, M., White, L. F., Hochberg, N. S., Rogers, M. S., Zetter, B. R., Joseph‐McCarthy, D., & Chakravarty, A. (2023) · Vaccines · doi:10.3390/vaccines11040853 · Cited by 28
“Since many previous major SARS-CoV-2 lineages have arisen through the accumulation of point mutations [57,58], we did not include other mechanisms of genetic variation in our model, including recombination.”
BackgroundZhang, Y., Chen, B., Chen, D., Wang, Y., Lu, Q., Tan, J., Chen, L., Zhou, L., Tan, W., Yang, Y., et al. (2023) · ACS Sensors · doi:10.1021/acssensors.3c00453 · Cited by 26
Sharifi, E., Yousefiasl, S., Trovato, M., Sartorius, R., Esmaeili, Y., Goodarzi, H., Ghomi, M., Bigham, A., Moghaddam, F. D., Heidarifard, M., et al. (2023) · Journal of Nanobiotechnology · doi:10.1186/s12951-023-01938-8 · Cited by 29
“Although the COVID-19 vaccines currently in use are effective in mitigating the severe symptoms of SARSCoV-2 infection, the emergence of VOCs and the occurrence of breakthrough infections indicate an urgent need for new diagnostic and therapeutic tools for the prevention and treatment of the disease.”
BackgroundInfluentialWang, X., Sun, L., Liu, Z., Xing, L., Zhu, Y., Xu, W., Xia, S., Lu, L., & Jiang, S. (2023) · Emerging Microbes & Infections · doi:10.1080/22221751.2023.2244084 · Cited by 26
Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group
Ren, P., Li, H., Nie, T., Jian, X., Yu, C., Li, J., Su, H., Zhang, X., Li, S., Yang, X., et al. (2023) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.3c00818 · Cited by 25
Cool, K. R., Gaudreault, N. N., Morozov, I., Trujillo, J. D., Meekins, D. A., McDowell, C. D., Carossino, M., Bold, D., Kwon, T., Balaraman, V., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.15.456341 · Cited by 26
Moore, K. A., Leighton, T., Ostrowsky, J. T., Anderson, C. J., Danila, R. N., Ulrich, A. K., Lackritz, E. M., Mehr, A. J., Baric, R. S., Baylor, N. W., et al. (2023) · Vaccine · doi:10.1016/j.vaccine.2023.02.032 · Cited by 25
Shawky, A. M., Almalki, F. A., Alzahrani, H. A., Abdalla, A. N., Youssif, B. G. M., Ibrahim, N. A., Gamal, M., El-Sherief, H. A. M., Abdel‐Fattah, M. M., Hefny, A. A., et al. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116704 · Cited by 26
Xu, K., An, Y., Li, Q., Huang, W., Han, Y., Zheng, T., Fang, F., Liu, H., Liu, C., Gao, P., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1959270 · Cited by 25
Murugan, C., Ramamoorthy, S., Kuppuswamy, G. P., Murugan, R. K., Sivalingam, Y., & Sundaramurthy, A. (2021) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2021.10.144 · Cited by 28
Counting on COVID-19 Vaccine: Insights into the Current Strategies, Progress and Future Challenges
Kandimalla, R. J. L., Chakraborty, P., Vallamkondu, J., Chaudhary, A., Samanta, S., Reddy, P. H., Feo, V. D., & Dewanjee, S. (2021) · Biomedicines · doi:10.3390/biomedicines9111740 · Cited by 25
“The viral genome is prone to mutations by antigenic shift and antigenic drift while spreading through different populations in different environmental conditions [271].”
BackgroundRahman, M., Irmler, M., Keshavan, S., Introna, M., Beckers, J., Palmberg, L., Johanson, G., Ganguly, K., & Upadhyay, S. (2021) · Viruses · doi:10.3390/v13122537 · Cited by 24
Human Milk Oligosaccharides: Potential Applications in COVID-19
Chutipongtanate, S., Morrow, A. L., & Newburg, D. S. (2022) · Biomedicines · doi:10.3390/biomedicines10020346 · Cited by 25
“SARS-CoV-2 mutations can have substantial effects on viral transmissibility and immune escape [2,3].”
BackgroundRosenthal, S. H., Gerasimova, A., Ruiz-Vega, R., Livingston, K., Kagan, R., Liu, Y., Anderson, B., Owen, R., Bernstein, L., Smolgovsky, A., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-06091-0 · Cited by 20
Aptamers as promising nanotheranostic tools in the COVID ‐19 pandemic era
Dzuvor, C. K. O., Tettey, E. L., & Danquah, M. K. (2022) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1785 · Cited by 24
“Despite the tremendous efforts and countermeasures in development against the SARS-COV-2, there still prevail frequent circulating mutations and viral variants across the globe leading to immune escape (Harvey et al., 2021).”
BackgroundAntigenic Cross-Reactivity Between SARS-CoV-2 S1-RBD and Its Receptor ACE2
Lai, Y., Cheng, Y., Chao, C.-H., Chang, Y., Chen, C.-D., Tsai, W., Wang, S., Lin, Y., Chang, C., Chuang, W., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.868724 · Cited by 26
“Since the emergence of SARS-CoV-2 in late 2019, many mutations have emerged in different variants of concern (VOCs) to escape neutralization by antibodies (43, 44).”
BackgroundMechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics
Desikan, R., Padmanabhan, P., Kierzek, A. M., & van der Graaf, P. H. (2022) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2022.106606 · Cited by 24
“6 [7] Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al.”
Pavan, M., Bassani, D., Sturlese, M., & Moro, S. (2022) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2022.2081847 · Cited by 24
Antibody-mediated immunity to SARS-CoV-2 spike
Errico, J. M., Adams, L. J., & Fremont, D. H. (2022) · Advances in immunology · doi:10.1016/bs.ai.2022.07.001 · Cited by 22
“…2021; Liu, VanBlargan, et al., 2021; Weisblum et al., 2020), disrupts neutralization by both class 1 and class 2 RBM antibodies (Barnes, Jette, et al., 2020; Greaney, Starr, Barnes, et al., 2021; Harvey et al., 2021; Planas, Bruel, et al., 2021; Wang, Nair, et al., 2021; Wang, Zhang, et al., 2021).”
Schiavina, M., Pontoriero, L., Tagliaferro, G., Pierattelli, R., & Felli, I. C. (2022) · Biomolecules · doi:10.3390/biom12091302 · Cited by 25
“It is strongly affected by mutations [5,6], some of which are of concern since they affect the transmissibility and antigenicity of the disease.”
BackgroundThe diverse role of heparan sulfate and other GAGs in SARS-CoV-2 infections and therapeutics
Eilts, F., Bauer, S., Fraser, K., Dordick, J. S., Wolff, M. W., Linhardt, R. J., & Zhang, F. (2022) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2022.120167 · Cited by 24
Discovery of novel SARS-CoV-2 3CL protease covalent inhibitors using deep learning-based screen
Wang, L., Yu, Z., Wang, S., Guo, Z., Sun, Q., & Lai, L. (2022) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2022.114803 · Cited by 25
“On the one hand, the continuous emergence of virus variants compromises the efficacy of available vaccines [2], while the durability and long-term side effects of vaccines are unknown currently [3].”
de Sousa, I. P., Wallace, Z. S., Cavalcante, S. C., Ribeiro, M. P. F., Silva, J. A. B. M., Cavalcante, R. C. M., Scheuermann, R. H., & Palatnik, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-21207-2 · Cited by 29
Chakraborty, C., Bhattacharya, M., Sharma, A. R., Dhama, K., & Lee, S. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2022.10.004 · Cited by 25
Salod, Z., & Mahomed, O. H. (2022) · Vaccines · doi:10.3390/vaccines10111785 · Cited by 24
The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus
García‐Machorro, J., Ramírez-Salinas, G. L., Martínez‐Archundia, M., & Correa‐Basurto, J. (2022) · Vaccines · doi:10.3390/vaccines10111844 · Cited by 24
“The emergence of variants is not simply the addition of single amino-acid changes [84], but several other correlated mutations also need to occur to maintain the structural integrity of the virus [85].”
BackgroundMemory B‐cell diversity: From early generation to tissue residency and reactivation
Reusch, L., & Angeletti, D. (2023) · European Journal of Immunology · doi:10.1002/eji.202250085 · Cited by 27
Rabaan, A. A., Al-Ahmed, S. H., Albayat, H., Alwarthan, S. M., Alhajri, M. M., Najim, M. A., Alshehail, B. M., Al-Adsani, W., Alghadeer, A., Abduljabbar, W. A., et al. (2023) · Medicina · doi:10.3390/medicina59030507 · Cited by 26
“Such alterations may also be linked to elevated affinities of the S Protein for the ACE2 receptor [26].”
BackgroundSARS-CoV-2 before and after Omicron: two different viruses and two different diseases?
Gili, R., & Burioni, R. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04095-6 · Cited by 25
“Indeed, thanks to the molecular tools at our disposal today, viral sequences have been analysed and shared at an unprecedented pace, allowing almost real-time surveillance of the emergence of new mutations potentially linked to changes in viral properties [3, 4], that are the results of a process aimed at optimizing t…”
BackgroundWithin-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection
Farjo, M., Koelle, K., Martin, M. A., Gibson, L. L., Walden, K. K. O., Rendon, G., Fields, C. J., Alnaji, F. G., Gallagher, N., Luo, C. H., et al. (2024) · Journal of Virology · doi:10.1128/jvi.01618-23 · Cited by 27
Kalkeri, R., Cai, Z., Lin, S., Farmer, J., Kuzmichev, Y. V., & Koide, F. (2021) · Microorganisms · doi:10.3390/microorganisms9081744 · Cited by 25
“While the development of novel prophylactic and therapeutic measures, such as vaccines, monoclonal antibodies, and antiviral medications, has been instrumental in slowing down the pace of the pandemic, the emergence of several variants of concern (VOCs) has raised issues about potential immune escape [2].”
BackgroundTorres, C., Mojsiejczuk, L. N., Acuña, D., Alexay, S., Amadío, A., Aulicino, P. C., Debat, H., Fay, F. F., Fernández, F. D., Giri, A. A., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.755463 · Cited by 25
“Importantly, some of these variants share mutations in the Spike protein—several of them in the receptor-binding domain region—that potentially affect transmissibility, pathogenesis, and/or response to vaccination and immune-based therapies (7, 8).”
BackgroundSathi, S. N., Umasankar, P. K., Sreekumar, E., Nair, R. R., Joseph, I., Nori, S. R. C., Philip, J. S., Prasad, R., Navyasree, K. V., Ramesh, S. T., et al. (2022) · BMC Molecular and Cell Biology · doi:10.1186/s12860-021-00403-4 · Cited by 26
“RBD have been shown to escape from highly neutralizing COVID-19 convalescent plasma [2, 40, 41].”
BackgroundLRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein
(2023) · doi:10.1371/journal.pbio.3001959 · Cited by 28
“Interactions involving the viral spike protein are particularly important to characterize, not only because the spike protein enables cell entry by binding to angiotensin-converting enzyme 2 (ACE2) [4] but also because the spike protein is the central component of many of the current vaccines and therapeutics under de…”
Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses
Liu, C., Xu, S., Zheng, Y., Xie, Y., Xu, K., Chai, Y., Luo, T., Dai, L., & Gao, G. F. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114235 · Cited by 24
Vaccine Strategies Against RNA Viruses: Current Advances and Future Directions
Hsiung, K. C., Chiang, H.-J., Reinig, S., & Shih, S. (2024) · Vaccines · doi:10.3390/vaccines12121345 · Cited by 25
“…RNA viruses or even different viruses [150], which is an essential facet for combatting rapidly mutating RNA viruses such as SARS-CoV-2, influenza viruses, or mpox viruses, among which, there is a high likelihood of the emergence of novel variants that might evade pre-existing immunity [151–153].”
Has SARS-CoV-2 reached peak fitness?
Burioni, R., & Topol, E. J. (2021) · Nature Medicine · doi:10.1038/s41591-021-01421-7 · Cited by 23
Imai, N., Hogan, A. B., Williams, L. R., Cori, A., Mangal, T. D., Winskill, P., Whittles, L. K., Watson, O. J., Knock, E., Baguelin, M., et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16992.1 · Cited by 21
Contamination of Hospital Surfaces with Bacterial Pathogens under the Current COVID-19 Outbreak
Pochtovyi, A. A., Vasina, D. V., Kustova, D. D., Divisenko, E. V., Kuznetsova, N. A., Burgasova, O., Kolobukhina, L. V., Петрович, Т. А., Gushchin, V. А., & Al, G. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph18179042 · Cited by 22
COVID-19 and oral diseases: Assessing manifestations of a new pathogen in oral infections
Naqvi, A. R., Schwartz, J., Brandini, D. A., Schaller, S. J., Hussein, H., Valverde, A. M., Naqvi, R. A., & Shukla, D. (2021) · International Reviews of Immunology · doi:10.1080/08830185.2021.1967949 · Cited by 24
“Variants that change residues can change fusion peptide (FP) conformational sites affinity by enhancing S2 exposure and charge display [78].”
BackgroundCOVID-19 Vaccines: Current Conditions and Future Prospects
Zieneldien, T., Kim, J., Cao, J. A., & Cao, C. (2021) · Biology · doi:10.3390/biology10100960 · Cited by 24
“The viral mutations and variants have specific attributes resulting in increases of infections to a specific variant, changes in transmission, diagnosis and therapeutic treatment, and changes in the elicited immune cell populations [167].”
BackgroundMonoclonal Antibodies against Nucleocapsid Protein of SARS-CoV-2 Variants for Detection of COVID-19
Lu, R., Ko, S.-H., Wy, C., Chang, Y., Lin, H.-T., & Wu, H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212412 · Cited by 25
“Mutations in the S protein, especially those in the viral variants of concern (VoCs), have attracted much recent attention, because immune escape by mutants could compromise the neutralizing functions of therapeutic antibodies and antibodies present in vaccinated individuals [21].”
BackgroundDenaturation of the SARS-CoV-2 spike protein under non-thermal microwave radiation
Afaghi, P., Lapolla, M. A., & Ghandi, K. (2021) · Scientific Reports · doi:10.1038/s41598-021-02753-7 · Cited by 23
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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