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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 201–300 of 1,002
Tré‐Hardy, M., Cupaiolo, R., Wilmet, A., Antoine-Moussiaux, T., Vecchia, A. D., Horeanga, A., Papleux, E., Vekemans, M., Beukinga, I., & Blairon, L. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.08.031 · Cited by 70
Chakraborty, C., Bhattacharya, M., Sharma, A. R., & Mallik, B. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.07.254 · Cited by 74
COVID-19 vaccine and booster hesitation around the world: A literature review
Shah, A., & Coiado, O. C. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2022.1054557 · Cited by 78
“This decrease in vaccination effectiveness can be attributed to natural decreases in antibody titers after vaccination and the gradual accumulation of mutations in SARS-CoV-2 spike proteins per variant (17, 18).”
BackgroundRole of Senescence and Aging in SARS-CoV-2 Infection and COVID-19 Disease
Lynch, S. M., Guo, G., Gibson, D. S., Bjourson, A. J., & Singh, T. (2021) · Cells · doi:10.3390/cells10123367 · Cited by 70
Goethem, N. V., Chung, P. Y. J., Meurisse, M., Vandromme, M., Mot, L. D., Brondeel, R., Stouten, V., Klamer, S., Cuypers, L., Braeye, T., et al. (2022) · Viruses · doi:10.3390/v14061297 · Cited by 69
Seephetdee, C., Bhukhai, K., Buasri, N., Leelukkanaveera, P., Lerdwattanasombat, P., Manopwisedjaroen, S., Phueakphud, N., Kuhaudomlarp, S., Olmedillas, E., Saphire, E. O., et al. (2022) · Antiviral Research · doi:10.1016/j.antiviral.2022.105370 · Cited by 73
Daniell, H., Nair, S. K., Esmaeili, N., Wakade, G., Shahid, N., Ganesan, P. K., Islam, M. R., Shepley‐McTaggart, A., Feng, S., Gary, E. N., et al. (2021) · Molecular Therapy · doi:10.1016/j.ymthe.2021.11.008 · Cited by 72
SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review
Mendiola-Pastrana, I. R., López‐Ortiz, E., de la Loza-Zamora, J. G. R., González, J., Gómez‐García, A., & López-Ortiz, G. (2022) · Life · doi:10.3390/life12020170 · Cited by 69
“One of the first variants to be recognized was D614G in the spike protein [6,8], and as genome sequencing subsequently progressed in different countries, it was reported that different mutations influence the adaptation of the virus to environmental and population contexts, in addition to conferring various phenotypes…”
BackgroundStructural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1
Geng, Q., Shi, K., Ye, G., Zhang, W., Aihara, H., & Li, F. (2022) · Journal of Virology · doi:10.1128/jvi.00249-22 · Cited by 69
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
Dokainish, H. M., Re, S., Mori, T., Kobayashi, C., Jung, J., & Sugita, Y. (2022) · eLife · doi:10.7554/elife.75720 · Cited by 70
Pang, Y. T., Acharya, A., Lynch, D. L., Pavlova, À., & Gumbart, J. C. (2022) · Communications Biology · doi:10.1038/s42003-022-04138-6 · Cited by 66
Oral Antiviral Treatment for COVID-19: A Comprehensive Review on Nirmatrelvir/Ritonavir
Akinosoglou, K., Schinas, G., & Gogos, C. A. (2022) · Viruses · doi:10.3390/v14112540 · Cited by 71
CRISPR-based nucleic acid diagnostics for pathogens
Yang, H., Zhang, Y., Teng, X., Hou, H., Deng, R., & Li, J. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.116980 · Cited by 69
Islam, M. M., & Koirala, D. (2021) · Analytica Chimica Acta · doi:10.1016/j.aca.2021.339338 · Cited by 68
“These mutations in the RBD likely allow variants more effective in binding and infecting host cells and contribute toward high transmission and rapid spread in many countries [345,346].”
SARS-CoV-2 variants, immune escape, and countermeasures
Zhang, Y., Zhang, H. C., & Zhang, W. (2022) · Frontiers of Medicine · doi:10.1007/s11684-021-0906-x · Cited by 72
“Furthermore, SARS-CoV-2 is highly glycosylated especially in its spike and N proteins [7].”
BackgroundInfluentialMoitra, P., Chaichi, A., Hasan, S. M. A., Dighe, K., Alafeef, M., Prasad, A., Gartia, M. R., & Pan, D. (2022) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2022.114200 · Cited by 67
“However, the characterization of different SARS-CoV-2 N-gene mutated forms will continue to evolve and provide extremely useful information on specific mutations or their combinations those may not have been identified yet in circulating viruses (Harvey et al., 2021).”
Zhang, B., Shuai, H., Gong, H., Hu, J., Yan, B., Yuen, T. T., Hu, Y., Yoon, C., Wang, X., Hou, Y., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.157393 · Cited by 67
“The emergence of SARS-CoV-2 variants with potential escape mutations is a major concern (7).”
Jawad, B., Adhikari, P., Podgornik, R., & Ching, W. Y. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c00423 · Cited by 66
Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults
Kared, H., Wolf, A., Alirezaylavasani, A., Ravussin, A., Solum, G., Tran, T. T., Lund‐Johansen, F., Vaage, J. T., Nissen‐Meyer, L. S. H., Nygaard, U. C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31888-y · Cited by 65
SARS‐CoV‐2 Papain‐Like Protease: Structure, Function and Inhibition
Ullrich, S., & Nitsche, C. (2022) · ChemBioChem · doi:10.1002/cbic.202200327 · Cited by 71
Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection
Heyer, A., Günther, T., Robitaille, A., Lütgehetmann, M., Addo, M. M., Jarczak, D., Kluge, S., Aepfelbacher, M., Wiesch, J. S. Z., Fischer, N., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100735 · Cited by 65
“6, 8, 11, 22, 23 Our study extends these reports Interestingly, Lythgoe and colleagues examined intra-host diversity in temporal samples of infected individuals in households in a 20-day time window and observed little consistency in the frequency of minor variants between time points within…”
Mannar, D., Saville, J. W., Sun, Z., Zhu, X. Q., Martí, M. M., Srivastava, S. S., Berezuk, A., Zhou, S., Tuttle, K. S., Sobolewski, M. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32262-8 · Cited by 65
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. (2022) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd015395.pub2 · Cited by 66
“Viral variants mainly present mutational changes in the spike glycoprotein (Harvey 2021).”
BackgroundPossible cancer-causing capacity of COVID-19: Is SARS-CoV-2 an oncogenic agent?
Jahankhani, K., Ahangari, F., Adcock, I. M., & Mortaz, E. (2023) · Biochimie · doi:10.1016/j.biochi.2023.05.014 · Cited by 67
“Mutations in the S protein impair the ability of circulating antibodies to bind to and protect against viral infection which undermines the protection against recurrent infection with this virus [6].”
Wurtzer, S., Waldman, P., Levert, M., Cluzel, N., Almayrac, J.-L., Charpentier, C., Masnada, S., Gillon-Ritz, M., Mouchel, J., Maday, Y., et al. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.152213 · Cited by 65
“Several studies showed that multiplesmutations give the variant new characteristics, such as increasing of infectivity and transmissibility or escaping from neutralizing antibodies induced by natural infection or vaccination (Harvey et al., 2021).”
COVID-19 Pathogenesis and Clinical Manifestations
Acosta, R. A. H., Garrigos, Z. E., Marcelin, J. R., & Vijayvargiya, P. (2022) · Infectious Disease Clinics of North America · doi:10.1016/j.idc.2022.01.003 · Cited by 71
B.1.617.2 (Delta) Variant of SARS-CoV-2: features, transmission and potential strategies
Zhan, Y., Yin, H. Y., & Yin, J. (2022) · International Journal of Biological Sciences · doi:10.7150/ijbs.66881 · Cited by 68
SARS-CoV-2 infects adipose tissue in a fat depot- and viral lineage-dependent manner
Saccon, T. D., Mousovich‐Neto, F., Ludwig, R. G., Carregari, V. C., Souza, A. B. D. A., dos Passos, A. S. C., Martini, M. C., Barbosa, P. P., de Souza, G. F., Muraro, S. P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33218-8 · Cited by 70
SARS-CoV-2 down-regulates ACE2 through lysosomal degradation
Lu, Y., Zhu, Q., Fox, D., Gao, C., Stanley, S. A., & Luo, K. (2022) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-02-0045 · Cited by 66
“These mutations include D614G, N501Y/D614G, N501Y/ D614G/∆69-70/P681H (Alpha), and N501Y/D614G/K417N/E484K (Beta) variants (Garcia-Beltran et al., 2021; Harvey et al., 2021; Li et al., 2021; Martin et al., 2021; Washington et al., 2021; Zhou et al., 2021).”
An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines
Bayani, F., Hashkavaei, N. S., Arjmand, S., Rezaei, S., Uskoković, V., Alijanianzadeh, M., Uversky, V. N., Siadat, S. O. R., Mozaffari‐Jovin, S., & Sefidbakht, Y. (2023) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2023.02.004 · Cited by 67
Carreño, J. M., Alshammary, H., Singh, G., Raskin, A. J., Amanat, F., Amoako, A. A., Gonzalez-Reiche, A. S., van de Guchte, A., PARIS study group, Awawda, M. H., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103626 · Cited by 61
“Since the detection of these first variants, several other Variants of Interest (VoIs) and Variants of Concern (VoCs) have spread locally as well as globally [9].”
Souza, P. F. N., Mesquita, F. P., Amaral, J. L., Landim, P. G. C., Lima, K. R. P., Costa, M. B., Farias, I. R., Belém, M. O., Pinto, Y. O., Moreira, H. H. T., et al. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.03.058 · Cited by 67
Vo, V., Tillett, R. L., Papp, K., Shen, S., Gu, R., Gorzalski, A. J., Siao, D. D., Markland, R., Chang, C.-L., Baker, H., et al. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.155410 · Cited by 60
“…(e.g., capacity limits and mask mandates) (Anderson et al., 2020; Hatef et al., 2021), known and emerging SARS-CoV-2 variants of concern (VOCs) and interest (VOIs) have the potential to trigger newwaves of infection (Abdelnabi et al., 2021; Abdool Karim and de Oliveira, 2021; Harvey et al., 2021).”
SARS-CoV-2’s Variants of Concern: A Brief Characterization
Scovino, A. M., Dahab, E. C., Vieira, G. F., Freire‐de‐Lima, L., Freire-de-Lima, C. G., & Morrot, A. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.834098 · Cited by 69
Dinda, B., Dinda, M., Dinda, S., & De, U. C. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115629 · Cited by 62
Li, H., Gong, H., Wong, T. H., Zhou, J., Wang, Y., Lin, L., Dou, Y., Jia, H., Huang, X., Gao, Z., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43189-z · Cited by 67
Yin, J., Li, C., Ye, C., Ruan, Z., Liang, Y., Li, Y., Wu, J., & Luo, Z. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.01.026 · Cited by 66
“It will increase the affinity of the spike protein to ACE2 and is kind of destructive to NAb binding [177] and make the virus evade the monoclonal antibody LY-CoV555 [178].”
Fast-track development of vaccines for SARS-CoV-2: The shots that saved the world
Chavda, V. P., Yao, Q., Vora, L. K., Apostolopoulos, V., Patel, C. A., Bezbaruah, R., Patel, A., & Chen, Z. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.961198 · Cited by 63
“A possible solution to this is by updating the vaccine sequences considering major mutations of the emerging variants and their interrelationships (24).”
BackgroundWu, Y., Dang, H., Park, S., Chen, L., & Choo, J. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113736 · Cited by 63
Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform
He, C., Lin, C., Mo, G., Xi, B., Li, A., Huang, D., Wan, Y., Chen, F., Liang, Y., Zuo, Q., et al. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113857 · Cited by 61
Ortega, J. T., Jastrzębska, B., & Rangel, H. R. (2021) · Pathogens · doi:10.3390/pathogens11010045 · Cited by 60
“However, a change in neutralization efficiency was observed for variants carrying the E484K mutation [33].”
BackgroundBhattacharya, M., Sharma, A. R., Dhama, K., Agoramoorthy, G., & Chakraborty, C. (2022) · GeroScience · doi:10.1007/s11357-022-00532-4 · Cited by 63
Structures of Omicron spike complexes and implications for neutralizing antibody development
Guo, H., Gao, Y., Li, T., Li, T., Lu, Y., Zheng, L., Liu, Y., Yang, T., Luo, F., Song, S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110770 · Cited by 61
SARS-CoV-2 variants – Evolution, spike protein, and vaccines
Chen, K.-W. K., Huang, D. T., & Huang, L. (2022) · Biomedical Journal · doi:10.1016/j.bj.2022.04.006 · Cited by 63
“[19] Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al.”
Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals
Brizzi, A., Whittaker, C., Servo, L. M. S., Hawryluk, I., Junior, C. A. P., de Souza, W. M., Aguiar, R. S., de Araújo, L. J. T., Bastos, L. S., Blenkinsop, A., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01807-1 · Cited by 74
He, W., Musharrafieh, R. G., Song, G., Dueker, K., Tse, L. V., Martinez, D. R., Schäfer, A., Callaghan, S., Yong, P., Beutler, N., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01222-1 · Cited by 58
Choosing a cellular model to study SARS-CoV-2
de Souza, G. A. P., Bideau, M. L., Boschi, C., Wurtz, N., Colson, P., Aherfi, S., Devaux, C. A., & Scola, B. L. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.1003608 · Cited by 63
“However, with the emergence of many variants of SARSCoV-2, several of them being classified as variants of concern by the WHO, it is unclear whether mutations acquired by the virus within the population can impact viral fitness (Harvey et al., 2021).”
BackgroundDiscovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers
Vanshylla, K., Fan, C., Wunsch, M., Poopalasingam, N., Meijers, M., Kreer, C., Kleipass, F., Ruchnewitz, D., Ercanoglu, M. S., Gruell, H., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.010 · Cited by 58
Colson, P., Fournier, P., Chaudet, H., Delerce, J., Giraud‐Gatineau, A., Houhamdi, L., Andrieu, C., Bréchard, L., Bedotto, M., Prudent, E., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.786233 · Cited by 64
Focosi, D., Maggi, F., Franchini, M., McConnell, S. A., & Casadevall, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010029 · Cited by 61
“Hence, evidence exclusively stems from case series and case reports [53] and is further complicated by exposure to multiple CCP units from different donors, each one having a polyclonal response at differing titers and affinity.”
BackgroundSrinivasan, V., Brognaro, H., Prince, P. R., de Souza, E. E., Günther, S., Reinke, P. Y. A., Lane, T. J., Ginn, H. M., Han, H., Ewert, W., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03737-7 · Cited by 60
ACTIV-3/TICO Study Group, Rogers, A. J., Wentworth, D. N., Phillips, A. N., Shaw‐Saliba, K., Dewar, R. L., Aggarwal, N. R., Babiker, A. G., Chang, W., Dharan, N. J., et al. (2022) · Annals of Internal Medicine · doi:10.7326/m22-0924 · Cited by 60
“A core aspect of this response includes the production of neutralizing antibodies, most of which are aimed at epitopes in the receptor-binding domain of the viral spike protein (20).”
BackgroundClinical grade ACE2 as a universal agent to block SARS‐CoV‐2 variants
Monteil, V., Eaton, B., Postnikova, E. N., Murphy, M. J., Braunsfeld, B., Crozier, I., Kricek, F., Niederhöfer, J., Schwarzböck, A., Breid, H., et al. (2022) · EMBO Molecular Medicine · doi:10.15252/emmm.202115230 · Cited by 54
“…infectivity and transmissibility of SARS-CoV-2, but also reduce the potency of vaccines, convalescent sera, and monoclonal antibody therapeutics (Harvey et al, 2021; Planas et al, 2021; Garcia-Beltran et al, 2021; Cele et al, 2021; Greaney et al, 2021; Lopez Bernal et al, 2021; Jangra et al,…”
BackgroundInfluentialSARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
Stanevich, O. V., Alekseeva, E. I., Sergeeva, M. V., Fadeev, A. V., Komissarova, K., Ivanova, A. A., Simakova, T., Vasilyev, K., Shurygina, A.-P. S., Stukova, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-34033-x · Cited by 60
“sampling dates regression line for the three separate datasets: (1) patient S samples, (2) B.”
BackgroundMethodColson, P., Delerce, J., Burel, E., Dahan, J., Jouffret, A., Fenollar, F., Yahi, N., Fantini, J., Scola, B. L., & Raoult, D. (2022) · Archives of Virology · doi:10.1007/s00705-022-05385-y · Cited by 21
Nikolaidis, M., Papakyriakou, A., Chlichlia, K., Markoulatos, P., Oliver, S. G., & Amoutzias, G. D. (2022) · Viruses · doi:10.3390/v14040707 · Cited by 57
“A relatively small number of mutations is sufficient to change important properties and characteristics of a Coronavirus (CoV), such as transmissibility, replication, and even immune escape [15,23,25].”
BackgroundMohamed, F. F., Anhlan, D., Schöfbänker, M., Schreiber, A., Classen, N., Hensel, A., Hempel, G., Scholz, W., Kühn, J., Hrincius, E. R., et al. (2022) · Pharmaceuticals · doi:10.3390/ph15050530 · Cited by 60
“Shortly after the beginning of the pandemic, distinct genetic lineages (variants) of the virus emerged and continued circulating across the world [13,14].”
BackgroundSARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA
Hoffman, S. A., Costales, C., Sahoo, M. K., Palanisamy, S., Yamamoto, F. F., Huang, C., Verghese, M., Solis, D., Sibai, M., Subramanian, A. K., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2710.211461 · Cited by 55
“Deletions and insertions in the NTD are also involved in immune escape, including the common del141_144 mutation and insertions at position Y248 (5).”
BackgroundRecent insights into SARS‐CoV‐2 omicron variant
da Silva, S. J. R., Kohl, A., Pena, L., & Pardee, K. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2373 · Cited by 56
“modulated virulence, and escape from host immune response induced by vaccination or previous infection.(6) Approximately 23 months since the first reported case of COVID‐ 19, the omicron variant (B.”
BackgroundChest CT Findings in Hospitalized Patients with SARS-CoV-2: Delta versus Omicron Variants
Yoon, S. H., Lee, J. H., & Kim, B.-N. (2022) · Radiology · doi:10.1148/radiol.220676 · Cited by 59
“Several variants of SARS-CoV-2 have been reported worldwide throughout the pandemic, and some variants are classified as variants of concern due to increased transmissibility, disease severity, or evasiveness of treatments and vaccines (3).”
COVID-19 and pregnancy: clinical outcomes; mechanisms, and vaccine efficacy
Kumar, D., Verma, S., & Mysorekar, I. U. (2022) · Translational research · doi:10.1016/j.trsl.2022.08.007 · Cited by 59
Shim, J.-E., Kim, Y. J., Choe, J., Lee, T. G., & You, E. (2022) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.2c07497 · Cited by 57
Toll-like receptor (TLRs) agonists and antagonists for COVID-19 treatments
Liu, Z., Yang, M., Yu, K., Lian, Z., & Deng, S. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.989664 · Cited by 58
“Furthermore, there are other new variants virus, which may lead to available vaccines failure (Harvey et al., 2021).”
BackgroundSARS-CoV-2 Omicron variant emerged under immune selection
Tan, C. W., Chia, W. N., Zhu, F., Young, B. E., Chantasrisawad, N., Hwa, S.-H., Yeoh, A. Y.-Y., Lim, B. L., Yap, W. C., Pada, S., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01246-1 · Cited by 55
Chen, S. A., Arutyunova, E. I., Lu, J., Khan, M. B., Rut, W., Żmudziński, M., Shahbaz, S., Iyyathurai, J., Moussa, E. W., Turner, Z., et al. (2023) · ACS Central Science · doi:10.1021/acscentsci.3c00054 · Cited by 56
SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx
Kim, S. H., Kearns, F. L., Rosenfeld, M. A., Votapka, L. W., Casalino, L., Papanikolas, M., Amaro, R. E., & Freeman, R. (2023) · Cell Reports Physical Science · doi:10.1016/j.xcrp.2023.101346 · Cited by 56
CRISPR‐Mediated Profiling of Viral RNA at Single‐Nucleotide Resolution
Chen, D., Huang, W., Zhang, Y., Chen, B., Tan, J., Yuan, Q., & Yang, Y. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202304298 · Cited by 59
Kayesh, M. E. H., Kohara, M., & Tsukiyama–Kohara, K. (2021) · Viruses · doi:10.3390/v13112302 · Cited by 59
“In addition, several new variants of the virus have also evolved, which may threaten the success of the currently available SARS-CoV-2 vaccines [14].”
BackgroundTransmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
Siddle, K. J., Krasilnikova, L. A., Moreno, G. K., Schaffner, S. F., Vostok, J., Fitzgerald, N. A., Lemieux, J. E., Barkas, N., Loreth, C., Specht, I., et al. (2021) · Cell · doi:10.1016/j.cell.2021.12.027 · Cited by 53
“…a maximum-likelihood (ML) phylogenetic tree (Sagulenko et al., 2018) with associated visualizations using a SARSCoV-2-tailored Augur pipeline (Huddleston et al., 2021) (sarscov2_nextstrain_aligned_input), part of the Nextstrain project (Hadfield et al., 2018), adapted from…”
MethodKrueger, T., Gogolewski, K., Bodych, M., Gambin, A., Giordano, G., Cuschieri, S., Czypionka, T., Perc, M., Petelos, E., Rosińska, M., et al. (2022) · Communications Medicine · doi:10.1038/s43856-022-00084-w · Cited by 56
Rénia, L., Goh, Y. S., Rouers, A., Bert, N. L., Chia, W. N., Chavatte, J., Fong, S., Chang, Z. W., Zhuo, N. Z., Tay, M. Z., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32312-1 · Cited by 62
Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis
Kumar, R., Srivastava, Y., Muthuramalingam, P., Singh, S. K., Verma, G., Tiwari, S., Tandel, N., Beura, S. K., Panigrahi, A. R., Maji, S., et al. (2023) · Viruses · doi:10.3390/v15040856 · Cited by 57
“The Omicron variant (B.1.1.529) is considered the most recent VoCs (considering 35 mutations) with increased risk of reinfection [89].”
BackgroundInfluentialA scalable and highly immunogenic virus‐like particle‐based vaccine against SARS‐CoV‐2
Mohsen, M. O., Baļķe, I., Zinkhan, S., Zeltina, V., Liu, X., Chang, X., Krenger, P. S., Plattner, K., Gharailoo, Z., Vogt, A. S., et al. (2021) · Allergy · doi:10.1111/all.15080 · Cited by 54
Haslwanter, D., Dieterle, M. E., Wec, A. Z., O’Brien, C. M., Sakharkar, M., Florez, C., Tong, K., Rappazzo, C. G., Lasso, G., Vergnolle, O., et al. (2021) · mBio · doi:10.1128/mbio.02473-21 · Cited by 55
Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants
Gupta, D., Sharma, P., Singh, M., Kumar, M., Ethayathulla, A. S., & Kaur, P. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04008-0 · Cited by 56
“Based on the protein’s conformational epitope, the key antigenic site where the antibodies interact with the S2 domain have been hypothesized in several loop regions of the S2 domain (793–794, 808–812, 850–854, 978–984, 1,099–1,100, and 1,139–1,146) [34].”
BackgroundInfluentialBate, N., Savva, C. G., Moody, P. C. E., Brown, E. A., Evans, S. E., Ball, J. K., Schwabe, J. W. R., Sale, J. E., & Brindle, N. P. J. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010733 · Cited by 52
“This is leading to the emergence of viral variants with increased transmissibility as well as the ability to evade therapeutics and antibodies induced by infection or vaccination [3].”
BackgroundInfluentialJaewjaroenwattana, J., Phoolcharoen, W., Pasomsub, E., Teengam, P., & Chailapakul, O. (2022) · Talanta · doi:10.1016/j.talanta.2022.123783 · Cited by 55
A highly efficient needle-free-injection delivery system for mRNA-LNP vaccination against SARS-CoV-2
Mao, S., Li, S., Zhang, Y., Long, L., Peng, J., Cao, Y., Mao, J. Z., Qi, X., Qi, X., San, G., et al. (2022) · Nano Today · doi:10.1016/j.nantod.2022.101730 · Cited by 55
Blood group A enhances SARS-CoV-2 infection
Wu, S., Arthur, C. M., Jan, H.-M., García-Beltrán, W. F., Patel, K., Rathgeber, M. F., Verkerke, H., Cheedarla, N., Jajosky, R. P., Paul, A., et al. (2023) · Blood · doi:10.1182/blood.2022018903 · Cited by 58
Zhang, L., Jiang, Y., He, J., Chen, J., Qi, R., Yuan, L., Shao, T., Zhao, H. J., Chen, C., Chen, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39560-9 · Cited by 62
Liu, Y., Yang, Y., Wang, G., Wang, D., Shao, P., Tang, J., He, T., Zheng, J., Hu, R., Liu, Y., et al. (2023) · Nature Biomedical Engineering · doi:10.1038/s41551-023-01092-4 · Cited by 55
“The global infectious-disease-surveillance system has been challenged by the rapid spread of the virus and the continuous emergence of SARS-CoV-2 variants and subvariants induced by frequent mutations altering viral pathogenicity, infectivity, transmissibility and antigenicity 1–6 .”
Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape
Lou, F., Li, M., Pang, Z., Jiang, L., Guan, L., Tian, L., Hu, J., Fan, J., & Fan, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.744242 · Cited by 54
Emerging SARS-CoV-2 Variants Can Potentially Break Set Epidemiological Barriers in COVID-19
Kumar, A., Parashar, R., Kumar, S., Faiq, M. A., Kumari, C., Kulandhasamy, M., Narayan, R. K., Jha, R. K., Singh, H. N., Prasoon, P., et al. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27467 · Cited by 53
“It has also a greater number of spike mutations at or in vicinity of the RBM (L452R, E484K, and T478K) of spike protein, which suggests it may have a greater advantage in binding to host ACE2.”
BackgroundInfluentialA Comprehensive Review of Drug Repurposing Strategies against Known Drug Targets of COVID-19
Khataniar, A., Pathak, U., Rajkhowa, S., & Jha, A. N. (2022) · COVID · doi:10.3390/covid2020011 · Cited by 56
Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro
Zeng, L., Liu, Y., Wrynla, X. H., Abbott, T. R., Han, M., Zhu, Y., Chemparathy, A., Lin, X., Chen, X., Wang, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30546-7 · Cited by 53
COVID‐19 immunopathology: From acute diseases to chronic sequelae
Arish, M., Qian, W. G., Narasimhan, H., & Sun, J. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28122 · Cited by 55
“The emergence of new variants of concern as a result of the mutation in the structural and nonstructural proteins (NSP) of SARS‐CoV‐2 is making the vaccine less efficient, creating inevitable hurdles in the vaccination programs.(2) The pathophysiology of COVID‐19 is mainly attributed due to the dysfunction of innate a…”
Nasal vaccines: solutions for respiratory infectious diseases
Nakahashi-Ouchida, R., Fujihashi, K., Kurashima, Y., Yuki, Y., & Kiyono, H. (2022) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2022.10.009 · Cited by 54
Scanning the RBD-ACE2 molecular interactions in Omicron variant
Rath, S. L., Padhi, A. K., & Mandal, N. (2021) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2022.01.006 · Cited by 55
Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City
Duerr, R., Dimartino, D., Marier, C., Zappile, P., Wang, G., Lighter, J., Elbel, B. D., Troxel, A. B., & Heguy, A. (2021) · Journal of Clinical Investigation · doi:10.1172/jci152702 · Cited by 53
SARS-CoV-2 subunit vaccine adjuvants and their signaling pathways
Mekonnen, D. S., Mengist, H. M., & Jin, T. (2021) · Expert Review of Vaccines · doi:10.1080/14760584.2021.1991794 · Cited by 55
Yaniv, K., Ozer, E., Lewis, Y. E., & Kushmaro, A. (2021) · Water Research · doi:10.1016/j.watres.2021.117808 · Cited by 50
Rapid detection and tracking of Omicron variant of SARS-CoV-2 using CRISPR-Cas12a-based assay
Liang, Y., Lin, H., Zou, L., Deng, X., & Tang, S. (2022) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2022.114098 · Cited by 52
Islam, F., Dhawan, M. K., Nafady, M. H., Emran, T. B., Mitra, S., Choudhary, O. P., & Akter, A. (2022) · Annals of Medicine and Surgery · doi:10.1016/j.amsu.2022.103737 · Cited by 55
“These variants have been related to a significant increase in fatality rates in several countries [1,2].”
Bruno, P. M., Timms, R. T., Abdelfattah, N. S., Leng, Y., Lelis, F., Wesemann, D. R., Yu, X. G., & Elledge, S. J. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01566-x · Cited by 50
Hulme, K. D., Noye, E. C., Short, K. R., & Labzin, L. I. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.770066 · Cited by 52
Valanparambil, R. M., Carlisle, J. W., Linderman, S. L., Akhtar, A., Millett, R. L., Lai, L., Chang, A., McCook‐Veal, A. A., Switchenko, J. M., Nasti, T. H., et al. (2022) · Journal of Clinical Oncology · doi:10.1200/jco.21.02986 · Cited by 48
D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity
Bhattacharya, M., Chatterjee, S., Sharma, A. R., Agoramoorthy, G., & Chakraborty, C. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11676-2 · Cited by 55
“D614G in the spike protein outside the RBD is also present (Harvey et al. 2021; Wang et al. 2021a).”
BackgroundLou, E. G., Sapoval, N., McCall, C., Bauhs, L., Carlson‐Stadler, R., Kalvapalle, P. B., Lai, Y., Palmer, K., Penn, R., Rich, W., et al. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.155059 · Cited by 48
Wang, C., Hesketh, E. L., Shamorkina, T. M., Li, W., Franken, P. J., Drabek, D., van Haperen, R., Townend, S., van Kuppeveld, F. J. M., Grosveld, F. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30658-0 · Cited by 52
OMICRON: Virology, immunopathogenesis, and laboratory diagnosis
Bazargan, M., Elahi, R., & Esmaeilzadeh, A. (2022) · The Journal of Gene Medicine · doi:10.1002/jgm.3435 · Cited by 53
“This is most likely due to spike protein variations, which are critical for viral propagation and host cell entrance.(92)”
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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