Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies

References

• Abdelnabi, R., Foo, C. S., Zhang, X., Lemmens, V., Maes, P., Slechten, B., Raymenants, J., André, E., Weynand, B., Dallmeier, K., & Neyts, J. (2022). The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Antiviral Research, 198, 105253. https://doi.org/10.1016/j.antiviral.2022.105253
   PubMed Web of Science ®Google Scholar
• Abdool Karim, S. S., & de Oliveira, T. (2021). New SARS-CoV-2 variants: Clinical, public health, and vaccine implications. The New England Journal of Medicine, 384(19), 1866–1868. https://doi.org/10.1056/NEJMc2100362
   PubMed Web of Science ®Google Scholar
• Allen, M. P., & Tildesley, D. J. (1989). Computer simulation of liquids. Clarendon Press.
   Google Scholar
• Andreano, E., Nicastri, E., Paciello, I., Pileri, P., Manganaro, N., Piccini, G., Manenti, A., Pantano, E., Kabanova, A., Troisi, M., Vacca, F., Cardamone, D., De Santi, C., Torres, J. L., Ozorowski, G., Benincasa, L., Jang, H., Di Genova, C., Depau, L., … Rappuoli, R. (2021). Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Cell, 184(7), 1821–1835.e16. https://doi.org/10.1016/j.cell.2021.02.035
   PubMed Web of Science ®Google Scholar
• Bai, C., & Warshel, A. (2020). Critical differences between the binding features of the spike proteins of SARS-CoV-2 and SARS-CoV. The Journal of Physical Chemistry. B, 124(28), 5907–5912. https://doi.org/10.1021/acs.jpcb.0c04317
   PubMed Web of Science ®Google Scholar
• Bakhshandeh, B., Sorboni, S. G., Javanmard, A.-R., Mottaghi, S. S., Mehrabi, M., Sorouri, F., Abbasi, A., & Jahanafrooz, Z. (2021). Variants in ACE2; potential influences on virus infection and COVID-19 severity. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 90, 104773. https://doi.org/10.1016/j.meegid.2021.104773
   PubMed Web of Science ®Google Scholar
• Barroso da Silva, F. L., Carloni, P., Cheung, D., Cottone, G., Donnini, S., Foegeding, E. A., Gulzar, M., Jacquier, J. C., Lobaskin, V., MacKernan, D., Mohammad Hosseini Naveh, Z., Radhakrishnan, R., & Santiso, E. E. (2020). Understanding and controlling food protein structure and function in foods: perspectives from experiments and computer simulations. Annual Review of Food Science and Technology, 11(1), 365–387. https://doi.org/10.1146/annurev-food-032519-051640
   PubMedGoogle Scholar
• Barroso da Silva, F. L., Derreumaux, P., & Pasquali, S. (2018). Protein-RNA complexation driven by the charge regulation mechanism. Biochemical and Biophysical Research Communications, 498(2), 264–273. https://doi.org/10.1016/j.bbrc.2017.07.027
   PubMed Web of Science ®Google Scholar
• Barroso da Silva, F. L., & Dias, L. G. (2017). Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophysical Reviews, 9(5), 699–728. https://doi.org/10.1007/s12551-017-0311-5
   PubMedGoogle Scholar
• Barroso da Silva, F. L., Giron, C. C., & Laaksonen, A. (2022). Electrostatic features for the Receptor binding domain of SARS-COV-2 wildtype and its variants. Compass to the severity of the future variants with the charge-rule. BioRxiv. https://doi.org/10.1101/2022.06.16.496458
   Google Scholar
• Barroso da Silva, F. L., & MacKernan, D. (2017). Benchmarking a fast proton titration scheme in implicit solvent for biomolecular simulations. Journal of Chemical Theory and Computation, 13(6), 2915–2929. https://doi.org/10.1021/acs.jctc.6b01114
   PubMed Web of Science ®Google Scholar
• Barroso da Silva, F. L., Pasquali, S., Derreumaux, P., & Dias, L. G. (2016). Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin. Soft Matter, 12(25), 5600–5612. https://doi.org/10.1039/c6sm00860g
   PubMed Web of Science ®Google Scholar
• Barton, M. I., MacGowan, S. A., Kutuzov, M. A., Dushek, O., Barton, G. J., & van der Merwe, P. A. (2021). Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. eLife, 10, e70658. https://doi.org/10.7554/eLife.70658
   PubMed Web of Science ®Google Scholar
• Bate, N., Savva, C. G., Moody, P. C., Brown, E. A., Ball, J. K., Schwabe, J. W., Sale, J. E., & Brindle, N. P. (2021). In vitro evolution predicts emerging CoV-2 mutations with high affinity for ACE2 and cross-species binding. https://doi.org/10.1101/2021.12.23.473975
   Google Scholar
• Batra, R., Chan, H., Kamath, G., Ramprasad, R., Cherukara, M. J., & Sankaranarayanan, S. (2020). Screening of therapeutic agents for COVID-19 using machine learning and ensemble docking studies. The Journal of Physical Chemistry Letters, 11(17), 7058–7065. https://doi.org/10.1021/acs.jpclett.0c02278
   PubMed Web of Science ®Google Scholar
• Baum, A., Ajithdoss, D., Copin, R., Zhou, A., Lanza, K., Negron, N., Ni, M., Wei, Y., Mohammadi, K., Musser, B., Atwal, G. S., Oyejide, A., Goez-Gazi, Y., Dutton, J., Clemmons, E., Staples, H. M., Bartley, C., Klaffke, B., Alfson, K., … Kyratsous, C. A. (2020). REGN-COV2 antibodies prevent and treat SARS-CoV-2 infection in rhesus macaques and hamsters. Science (New York, N.Y.), 370(6520), 1110–1115. https://doi.org/10.1126/science.abe2402
   PubMed Web of Science ®Google Scholar
• Bayarri-Olmos, R., Rosbjerg, A., Johnsen, L. B., Helgstrand, C., Bak-Thomsen, T., Garred, P., & Skjoedt, M.-O. (2021). The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The Journal of Biological Chemistry, 296, 100536. https://doi.org/10.1016/j.jbc.2021.100536
   PubMed Web of Science ®Google Scholar
• Bentley, E. G., Kirby, A., Sharma, P., Kipar, A., Mega, D. F., Bramwell, C., Penrice-Randal, R., Prince, T., Brown, J. C., Zhou, J., Screaton, G. R., Barclay, W. S., Owen, A., Hiscox, J. A., & Stewart, J. P. (2021). SARS-CoV-2 Omicron-B.1.1.529 variant leads to less severe disease than Pango B and delta variants strains in a mouse model of severe COVID-19. https://doi.org/10.1101/2021.12.26.474085
   Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bertoglio, F., Fühner, V., Ruschig, M., Heine, P. A., Abassi, L., Klünemann, T., Rand, U., Meier, D., Langreder, N., Steinke, S., Ballmann, R., Schneider, K.-T., Roth, K. D. R., Kuhn, P., Riese, P., Schäckermann, D., Korn, J., Koch, A., Chaudhry, M. Z., … Hust, M. (2021). A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients binds to the ACE2-RBD interface and is tolerant to most known RBD mutations. Cell Reports, 36(4), 109433. https://doi.org/10.1016/j.celrep.2021.109433
   PubMed Web of Science ®Google Scholar
• Bozek, K., Nakayama, E. E., Kono, K., & Shioda, T. (2012). Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins. Frontiers in Microbiology, 3, 206. https://doi.org/10.3389/fmicb.2012.00206
   PubMed Web of Science ®Google Scholar
• Brest, P., Refae, S., Mograbi, B., Hofman, P., & Milano, G. (2020). Host polymorphisms May impact SARS-CoV-2 infectivity. Trends in Genetics: TIG, 36(11), 813–815. https://doi.org/10.1016/j.tig.2020.08.003
   PubMed Web of Science ®Google Scholar
• Build structural models for several variants of SARS-CoV-2 RBD | Zenodo. (2021). https://zenodo.org/record/4780600#.YegDDf7MKMp [Accessed: 19 January 2022a].
   Google Scholar
• Callaway, E., & Ledford, H. (2021). How bad is Omicron? What scientists know so far. Nature, 600(7888), 197–199. https://doi.org/10.1038/d41586-021-03614-z
   PubMed Web of Science ®Google Scholar
• Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., De Marco, A., di Iulio, J., Zatta, F., Kaiser, H., Noack, J., Farhat, N., Czudnochowski, N., Havenar-Daughton, C., Sprouse, K. R., Dillen, J. R., Powell, A. E., … Corti, D. (2022). Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature, 602(7898), 664–670. https://doi.org/10.1038/s41586-021-04386-2
   PubMed Web of Science ®Google Scholar
• Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., Wang, J., Wang, Y., Niu, X., Yang, S., Liang, H., Sun, H., Li, T., Yu, Y., Cui, Q., … Xie, X. S. (2022). Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature, 602(7898), 657–663. https://doi.org/10.1038/s41586-021-04385-3
   PubMed Web of Science ®Google Scholar
• CDC COVID-19 Response Team. (2021). SARS-CoV-2 B.1.1.529 (Omicron) variant: United States, December 1–8, 2021. MMWR. Morbidity and Mortality Weekly Report, 70(50), 1731–1734. https://doi.org/10.15585/mmwr.mm7050e1
   PubMed Web of Science ®Google Scholar
• Cele, S., Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., Wilkinson, E., Naidoo, Y., Karim, F., Ganga, Y., Khan, K., Bernstein, M., Balazs, A. B., Gosnell, B. I., Hanekom, W., Moosa, M.-Y S., Lessells, R. J., de Oliveira, T., & Sigal, A, COMMIT-KZN Team. (2021a). Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature, 593(7857), 142–146. https://doi.org/10.1101/2021.01.26.21250224
   PubMed Web of Science ®Google Scholar
• Cele, S., Jackson, L., Khoury, D. S., Khan, K., & Moyo-Gwete, T. (2021b). SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. https://doi.org/10.1101/2021.12.08.21267417
   Google Scholar
• Chen, J., Gao, K., Wang, R., Nguyen, D. D., & Wei, G.-W. (2021b). Review of COVID-19 antibody therapies. Annual Review of Biophysics, 50(1), 1–30. https://doi.org/10.1146/annurev-biophys-062920-063711
   PubMedGoogle Scholar
• Chen, P., Nirula, A., Heller, B., Gottlieb, R. L., Boscia, J., Morris, J., Huhn, G., Cardona, J., Mocherla, B., Stosor, V., Shawa, I., Adams, A. C., Van Naarden, J., Custer, K. L., Shen, L., Durante, M., Oakley, G., Schade, A. E., Sabo, J., … Skovronsky, D. M. BLAZE-1 Investigators. (2021c). SARS-CoV-2 neutralizing antibody LY-CoV555 in outpatients with Covid-19. The New England Journal of Medicine, 384(3), 229–237. https://doi.org/10.1056/NEJMoa2029849
   PubMed Web of Science ®Google Scholar
• Chen, F., Zhang, Y., Li, X., Li, W., Liu, X., & Xue, X. (2021a). The impact of ACE2 polymorphisms on COVID-19 disease: Susceptibility, severity, and therapy. Frontiers in Cellular and Infection Microbiology, 11, 753721. https://doi.org/10.3389/fcimb.2021.753721
   PubMed Web of Science ®Google Scholar
• Chi, X., Yan, R., Zhang, J., Zhang, G., Zhang, Y., Hao, M., Zhang, Z., Fan, P., Dong, Y., Yang, Y., Chen, Z., Guo, Y., Zhang, J., Li, Y., Song, X., Chen, Y., Xia, L., Fu, L., Hou, L., … Chen, W. (2020). A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science (New York, N.Y.), 369(6504), 650–655. https://doi.org/10.1126/science.abc6952
   PubMed Web of Science ®Google Scholar
• Choi, Y., Hua, C., Sentman, C. L., Ackerman, M. E., & Bailey-Kellogg, C. (2015). Antibody humanization by structure-based computational protein design. mAbs, 7(6), 1045–1057. https://doi.org/10.1080/19420862.2015.1076600
   PubMed Web of Science ®Google Scholar
• Colson, P., Delerce, J., Burel, E., Dahan, J., Jouffret, A., Fenollar, F., Yahi, N., Fantini, J., La Scola, B., & Raoult, D. (2021). Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein. https://doi.org/10.1101/2021.12.24.21268174
   Google Scholar
• da Silva, F. L. B., Lund, M., Jönsson, B., & Akesson, T. (2006). On the complexation of proteins and polyelectrolytes. The Journal of Physical Chemistry. B, 110(9), 4459–4464. https://doi.org/10.1021/jp054880l
   PubMed Web of Science ®Google Scholar
• Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., Wenseleers, T., Gimma, A., Waites, W., Wong, K. L. M., van Zandvoort, K., Silverman, J. D., Diaz-Ordaz, K., Keogh, R., Eggo, R. M., … Edmunds, W. J. CMMID COVID-19 Working Group. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372(6538), eabg3055. https://doi.org/10.1126/science.abg3055
   PubMed Web of Science ®Google Scholar
• Dejnirattisai, W., Huo, J., Zhou, D., Zahradník, J., Supasa, P., Liu, C., Duyvesteyn, H. M. E., Ginn, H. M., Mentzer, A. J., Tuekprakhon, A., Nutalai, R., Wang, B., Dijokaite, A., Khan, S., Avinoam, O., Bahar, M., Skelly, D., Adele, S., Johnson, S. A., … Screaton, G. R. ISARIC4C Consortium. (2022). SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell, 185(3), 467–484. https://doi.org/10.1016/j.cell.2021.12.046
   PubMed Web of Science ®Google Scholar
• Dejnirattisai, W., Shaw, R. H., Supasa, P., Liu, C., Stuart, A. S., Pollard, A. J., Liu, X., Lambe, T., Crook, D., Stuart, D. I., Mongkolsapaya, J., Nguyen-Van-Tam, J. S., Snape, M. D., & Screaton, G. R. (2021). Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by post-immunisation serum. The Lancet. https://doi.org/10.1016/S0140-6736(21)02844-0
   Google Scholar
• Delboni, L. A., & Barroso da Silva, F. L. (2016). On the complexation of whey proteins. Food Hydrocolloids. 55, 89–99. https://doi.org/10.1016/j.foodhyd.2015.11.010
   Web of Science ®Google Scholar
• Denner, J. (2020). SARS-CoV-2 and enhancing antibodies. Journal of Clinical Virology : The Official Publication of the Pan American Society for Clinical Virology, 128, 104424. https://doi.org/10.1016/j.jcv.2020.104424
   PubMed Web of Science ®Google Scholar
• Deshpande, A., Harris, B. D., Martinez-Sobrido, L., Kobie, J. J., & Walter, M. R. (2021). Epitope classification and RBD binding properties of neutralizing antibodies against SARS-CoV-2 variants of concern. Frontiers in Immunology, 12, 691715. https://doi.org/10.3389/fimmu.2021.691715
   PubMed Web of Science ®Google Scholar
• Desingu, Nagarajan& Dhama, 2022: Desingu, P.A., Nagarajan, K. and Dhama, K. (2022). Emergence of Omicron third lineage BA.3 and its importance. J Med Virol, 94, 1808–1810. https://doi.org/10.1002/jmv.27601
   Google Scholar
• Destro, F., & Barolo, M. (2022). A review on the modernization of pharmaceutical development and manufacturing: Trends, perspectives, and the role of mathematical modeling. International Journal of Pharmaceutics, 620, 121715. https://doi.org/10.1016/j.ijpharm.2022.121715
   PubMed Web of Science ®Google Scholar
• Dimitrov, D. S. (2003). The secret life of ACE2 as a receptor for the SARS virus. Cell, 115(6), 652–653. https://doi.org/10.1016/S0092-8674(03)00976-0
   PubMed Web of Science ®Google Scholar
• Dolgin, E. (2022). Omicron thwarts some of the world’s most-used COVID vaccines. Nature, 601(7893), 311–311. https://doi.org/10.1038/d41586-022-00079-6
   PubMed Web of Science ®Google Scholar
• Du, L., He, Y., Zhou, Y., Liu, S., Zheng, B.-J., & Jiang, S. (2009). The spike protein of SARS-CoV: a target for vaccine and therapeutic development. Nature Reviews. Microbiology, 7(3), 226–236. https://doi.org/10.1038/nrmicro2090
   PubMed Web of Science ®Google Scholar
• Dulbecco, R., Vogt, M., & Strickland, A. G. R. (1956). A study of the basic aspects of neutralization of two animal viruses, Western equine encephalitis virus and poliomyelitis virus. Virology, 2(2), 162–205. https://doi.org/10.1016/0042-6822(56)90017-4
   PubMed Web of Science ®Google Scholar
• Durmaz, V., Köchl, K., Singh, A., Hetmann, M., Parigger, L., Krassnigg, A., Nutz, D., Korsunsky, A., König, C., Chang, L., Krebs, M., Bassetto, R., Pavkov-Keller, T., Resch, V., Gruber, K., Steinkellner, G., & Gruber, C. C. (2021). Structural-bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild-type reference. https://doi.org/10.21203/rs.3.rs-1153124/v1
   Google Scholar
• Du, L., Yang, Y., & Zhang, X. (2021). Neutralizing antibodies for the prevention and treatment of COVID-19. Cellular & Molecular Immunology, 18(10), 2293–2306. https://doi.org/10.1038/s41423-021-00752-2
   PubMed Web of Science ®Google Scholar
• Edara, V. V., Norwood, C., Floyd, K., Lai, L., Davis-Gardner, M. E., Hudson, W. H., Mantus, G., Nyhoff, L. E., Adelman, M. W., Fineman, R., Patel, S., Byram, R., Gomes, D. N., Michael, G., Abdullahi, H., Beydoun, N., Panganiban, B., McNair, N., Hellmeister, K., … Suthar, M. S. (2021). Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. Cell Host & Microbe, 29(4), 516–521.e3. https://doi.org/10.1016/j.chom.2021.03.009
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Weiss, R. M., Terwilliger, T. C., & Wilcox, W. (1982). Hydrophobic moments and protein structure. Faraday Symposia of the Chemical Society, 17, 109. https://doi.org/10.1039/fs9821700109
   Google Scholar
• England, R. J. A., Homer, J. J., Knight, L. C., & Ell, S. R. (1999). Nasal pH measurement: a reliable and repeatable parameter. Clinical Otolaryngology and Allied Sciences, 24(1), 67–68. https://doi.org/10.1046/j.1365-2273.1999.00223.x
   PubMed Web of Science ®Google Scholar
• Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling using modeller. Current Protocols in Bioinformatics, 15(1) https://doi.org/10.1002/0471250953.bi0506s15
   Google Scholar
• Ford, C. T., Jacob Machado, D., & Janies, D. A. (2022). Predictions of the SARS-CoV-2 Omicron variant (B.1.1.529) spike protein receptor-binding domain structure and neutralizing antibody interactions. Frontiers in Virology, 2, 830202. https://doi.org/10.3389/fviro.2022.830202
   Google Scholar
• Fratev, F. (2021). N501Y and K417N mutations in the spike protein of SARS-CoV-2 alter the interactions with both hACE2 and human-derived antibody: A free energy of perturbation retrospective study. Journal of Chemical Information and Modeling, 61(12), 6079–6084. https://doi.org/10.1021/acs.jcim.1c01242
   PubMed Web of Science ®Google Scholar
• Gan, H. H., Zinno, J., Piano, F., & Gunsalus, K. C. (2022). Omicron Spike protein has a positive electrostatic surface that promotes ACE2 recognition and antibody escape. https://doi.org/10.1101/2022.02.13.480261
   Google Scholar
• Gandhi, R. T., Malani, P. N., & del Rio, C. (2022). COVID-19 therapeutics for nonhospitalized patients. JAMA, 327(7), 617. https://doi.org/10.1001/jama.2022.0335
   PubMed Web of Science ®Google Scholar
• Gao, S., & Zhang, L. (2020). ACE2 partially dictates the host range and tropism of SARS-CoV-2. Computational and Structural Biotechnology Journal, 18, 4040–4047. https://doi.org/10.1016/j.csbj.2020.11.032
   PubMed Web of Science ®Google Scholar
• Germain, R. N., Meier-Schellersheim, M., Nita-Lazar, A., & Fraser, I. D. C. (2011). Systems biology in immunology: A computational modeling perspective. Annual Review of Immunology, 29(1), 527–585. https://doi.org/10.1146/annurev-immunol-030409-101317
   PubMedGoogle Scholar
• Giron, C. C., Laaksonen, A., & Barroso da Silva, F. L. (2020). On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2. Virus Research, 285, 198021. https://doi.org/10.1016/j.virusres.2020.198021
   PubMed Web of Science ®Google Scholar
• Giron, C. C., Laaksonen, A., & Barroso da Silva, F. L. (2021). Up state of the SARS-COV-2 spike homotrimer favors an increased virulence for new variants. Frontiers in Medical Technology, 3, 694347. https://doi.org/10.3389/fmedt.2021.694347
   PubMedGoogle Scholar
• Gómez, J., Albaiceta, G. M., García-Clemente, M., López-Larrea, C., Amado-Rodríguez, L., Lopez-Alonso, I., Hermida, T., Enriquez, A. I., Herrero, P., Melón, S., Alvarez-Argüelles, M. E., Boga, J. A., Rojo-Alba, S., Cuesta-Llavona, E., Alvarez, V., Lorca, R., & Coto, E. (2020). Angiotensin-converting enzymes (ACE, ACE2) gene variants and COVID-19 outcome. Gene, 762, 145102. https://doi.org/10.1016/j.gene.2020.145102
   PubMed Web of Science ®Google Scholar
• Grant, O. C., Montgomery, D., Ito, K., & Woods, R. J. (2020a). 3D Models of glycosylated SARS-CoV-2 spike protein suggest challenges and opportunities for vaccine development. https://doi.org/10.1101/2020.04.07.030445
   Google Scholar
• Grant, O. C., Montgomery, D., Ito, K., & Woods, R. J. (2020b). Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Scientific Reports, 10(1), 14991. https://doi.org/10.1038/s41598-020-71748-7
   PubMed Web of Science ®Google Scholar
• Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021). Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host & Microbe, 29(3), 463–476.e6. https://doi.org/10.1016/j.chom.2021.02.003
   PubMed Web of Science ®Google Scholar
• Hachim, A., Kavian, N., & Valkenburg, S. A. (2021). Antibody landscapes of SARS-CoV-2 can reveal novel vaccine and diagnostic targets. Current Opinion in Virology, 50, 139–146. https://doi.org/10.1016/j.coviro.2021.08.006
   PubMed Web of Science ®Google Scholar
• Halfmann, P. J., Iida, S., Iwatsuki-Horimoto, K., Maemura, T., Kiso, M., Scheaffer, S. M., Darling, T. L., Joshi, A., Loeber, S., Singh, G., Foster, S. L., Ying, B., Case, J. B., Chong, Z., Whitener, B., Moliva, J., Floyd, K., Ujie, M., Nakajima, N., … Kawaoka, Y. Consortium Mount Sinai Pathogen Surveillance (PSP) Study Group. (2022). SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature, 603(7902), 687–692. https://doi.org/10.1038/s41586-022-04441-6
   PubMed Web of Science ®Google Scholar
• Han, P., Li, L., Liu, S., Wang, Q., Zhang, D., Xu, Z., Han, P., Li, X., Peng, Q., Su, C., Huang, B., Li, D., Zhang, R., Tian, M., Fu, L., Gao, Y., Zhao, X., Liu, K., Qi, J., Gao, G. F., & Wang, P. (2022). Receptor binding and complex structures of human ACE2 to spike RBD from Omicron and Delta SARS-CoV-2. Cell, 185(4), 630–640. https://doi.org/10.1016/j.cell.2022.01.001
   PubMed Web of Science ®Google Scholar
• Hanai, T. (2022). Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility. Talanta, 240, 123206. https://doi.org/10.1016/j.talanta.2022.123206
   PubMed Web of Science ®Google Scholar
• Harrison, A. G., Lin, T., & Wang, P. (2020). Mechanisms of SARS-CoV-2 Transmission and Pathogenesis. Trends in Immunology, 41(12), 1100–1115. https://doi.org/10.1016/j.it.2020.10.004
   PubMed Web of Science ®Google Scholar
• Hastie, K. M., Li, H., Bedinger, D., Schendel, S. L., Dennison, S. M., Li, K., Rayaprolu, V., Yu, X., Mann, C., Zandonatti, M., Diaz Avalos, R., Zyla, D., Buck, T., Hui, S., Shaffer, K., Hariharan, C., Yin, J., Olmedillas, E., Enriquez, A., … Saphire, E. O. CoVIC-DB Team1. (2021). Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study. Science (New York, N.Y.), 374(6566), 472–478. https://doi.org/10.1126/science.abh2315
   PubMed Web of Science ®Google Scholar
• Hoffmann, M., Arora, P., Groß, R., Seidel, A., Hörnich, B. F., Hahn, A. S., Krüger, N., Graichen, L., Hofmann-Winkler, H., Kempf, A., Winkler, M. S., Schulz, S., Jäck, H.-M., Jahrsdörfer, B., Schrezenmeier, H., Müller, M., Kleger, A., Münch, J., & Pöhlmann, S. (2021a). SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell, 184(9), 2384–2393.e12. https://doi.org/10.1016/j.cell.2021.03.036
   PubMed Web of Science ®Google Scholar
• Hoffmann, M., Krüger, N., Schulz, S., Cossmann, A., Rocha, C., Kempf, A., Nehlmeier, I., Graichen, L., Moldenhauer, A.-S., Winkler, M. S., Lier, M., Dopfer-Jablonka, A., Jäck, H.-M., Behrens, G. M. N., & Pöhlmann, S. (2021b). The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic. Cell, 185(3), 447–456. https://doi.org/10.1016/j.cell.2021.12.032
   PubMed Web of Science ®Google Scholar
• Hu, J., Peng, P., Cao, X., Wu, K., Chen, J., Wang, K., Tang, N., & Huang, A. (2022). Increased immune escape of the new SARS-CoV-2 variant of concern Omicron. Cellular & Molecular Immunology, 19(2), 293–295. https://doi.org/10.1038/s41423-021-00836-z
   PubMed Web of Science ®Google Scholar
• Hu, W., Zhang, Y., Fei, P., Zhang, T., Yao, D., Gao, Y., Liu, J., Chen, H., Lu, Q., Mudianto, T., Zhang, X., Xiao, C., Ye, Y., Sun, Q., Zhang, J., Xie, Q., Wang, P.-H., Wang, J., Li, Z., Lou, J., & Chen, W. (2021). Mechanical activation of spike fosters SARS-CoV-2 viral infection. Cell Research, 31(10), 1047–1060. https://doi.org/10.1038/s41422-021-00558-x
   PubMed Web of Science ®Google Scholar
• Hwang, S., Baek, S.-H., & Park, D. (2022). Interaction analysis of the spike protein of delta and Omicron variants of SARS-CoV-2 with hACE2 and eight monoclonal antibodies using the fragment molecular orbital method. Journal of Chemical Information and Modeling, 62(7), 1771–1782. https://doi.org/10.1021/acs.jcim.2c00100
   PubMed Web of Science ®Google Scholar
• Hyltegren, K., Polimeni, M., Skepö, M., & Lund, M. (2020). Integrating all-atom and coarse-grained simulations: Toward understanding of IDPs at surfaces. Journal of Chemical Theory and Computation, 16(3), 1843–1853. https://doi.org/10.1021/acs.jctc.9b01041
   PubMed Web of Science ®Google Scholar
• Ibrahim, B., McMahon, D. P., Hufsky, F., Beer, M., Deng, L., Mercier, P. L., Palmarini, M., Thiel, V., & Marz, M. (2018). A new era of virus bioinformatics. Virus Research, 251, 86–90. https://doi.org/10.1016/j.virusres.2018.05.009
   PubMed Web of Science ®Google Scholar
• Ireson, N. J., Tait, J. S., MacGregor, G. A., & Baker, E. H. (2001). Comparison of nasal pH values in black and white individuals with normal and high blood pressure. Clinical Science (London, England: 1979), 100(3), 327–333. https://doi.org/10.1042/CS20000259
   PubMed Web of Science ®Google Scholar
• Ishikawa, T., Ozono, H., Akisawa, K., Hatada, R., Okuwaki, K., & Mochizuki, Y. (2021). Interaction analysis on the SARS-CoV-2 spike protein receptor binding domain using visualization of the interfacial electrostatic complementarity. The Journal of Physical Chemistry Letters, 12(46), 11267–11272. https://doi.org/10.1021/acs.jpclett.1c02788
   PubMed Web of Science ®Google Scholar
• Iyer, S. (2021). Apart, together: reflections on the COVID-19 pandemic. Trends in Microbiology, 29(12), 1049–1051. https://doi.org/10.1016/j.tim.2021.09.009
   PubMed Web of Science ®Google Scholar
• Jafary, F., Jafari, S., & Ganjalikhany, M. R. (2021). In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Scientific Reports, 11(1), 6927. https://doi.org/10.1038/s41598-021-86380-2
   PubMed Web of Science ®Google Scholar
• Jawad, B., Adhikari, P., Podgornik, R., & Ching, W.-Y. (2022). Binding interactions between receptor-binding domain of spike protein and human angiotensin converting enzyme-2 in omicron variant. The Journal of Physical Chemistry Letters, 13(17), 3915–3921. https://doi.org/10.1021/acs.jpclett.2c00423
   PubMed Web of Science ®Google Scholar
• Jaworski, J. P. (2021). Neutralizing monoclonal antibodies for COVID-19 treatment and prevention. Biomedical Journal, 44(1), 7–17. https://doi.org/10.1016/j.bj.2020.11.011
   PubMed Web of Science ®Google Scholar
• Jurado de Carvalho, S., Ghiotto, R. C. T., & Barroso da Silva, F. L. (2006). Monte Carlo and modified Tanford − Kirkwood results for macromolecular electrostatics calculations. The Journal of Physical Chemistry. B, 110(17), 8832–8839. https://doi.org/10.1021/jp054891e
   PubMed Web of Science ®Google Scholar
• Khan, K., Karim, F., Cele, S., San, J. E., & Lustig, G. (2021b). Omicron infection enhances neutralizing immunity against the Delta variant. https://doi.org/10.1101/2021.12.27.21268439
   Google Scholar
• Khan, A., Zia, T., Suleman, M., Khan, T., Ali, S. S., Abbasi, A. A., Mohammad, A., & Wei, D. (2021a). Higher infectivity of the SARS‐CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology, 236(10), 7045–7057. https://doi.org/10.1002/jcp.30367
   PubMed Web of Science ®Google Scholar
• Khetan, R., Curtis, R., Deane, C. M., Hadsund, J. T., Kar, U., Krawczyk, K., Kuroda, D., Robinson, S. A., Sormanni, P., Tsumoto, K., Warwicker, J., & Martin, A. C. R. (2022). Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. mAbs, 14(1), 2020082. https://doi.org/10.1080/19420862.2021.2020082
   PubMed Web of Science ®Google Scholar
• King, A. C., Woods, M., Liu, W., Lu, Z., Gill, D., & Krebs, M. R. H. (2011). High-throughput measurement, correlation analysis, and machine-learning predictions for pH and thermal stabilities of Pfizer-generated antibodies. Protein Science : a Publication of the Protein Society, 20(9), 1546–1557. https://doi.org/10.1002/pro.680
   PubMed Web of Science ®Google Scholar
• Kirkwood, J. G., & Shumaker, J. B. (1952). Forces between protein molecules in solution arising from fluctuations in proton charge and configuration. Proceedings of the National Academy of Sciences of the United States of America, 38(10), 863–871. https://doi.org/10.1073/pnas.38.10.863
   PubMed Web of Science ®Google Scholar
• Klasse, P. J. (2014). Neutralization of virus infectivity by antibodies: old problems in new perspectives. Advances in Biology, 2014, 1–24. https://doi.org/10.1155/2014/157895
   Google Scholar
• Kozlov, M. (2021). Omicron overpowers key COVID antibody treatments in early tests. Nature, d41586-021-03829–0. https://doi.org/10.1038/d41586-021-03829-0
   Google Scholar
• Kozlov, M. (2022). How does Omicron spread so fast? A high viral load isn’t the answer. Nature, d41586-022-00129-z. https://doi.org/10.1038/d41586-022-00129-z
   Google Scholar
• Kumar, R., Murugan, N. A., & Srivastava, V. (2022). Improved binding affinity of omicron’s spike protein for the human angiotensin-converting enzyme 2 receptor is the key behind its increased virulence. International Journal of Molecular Sciences, 23(6), 3409. https://doi.org/10.3390/ijms23063409
   PubMed Web of Science ®Google Scholar
• Kumar, S., Plotnikov, N. V., Rouse, J. C., & Singh, S. K. (2018a). Biopharmaceutical Informatics: supporting biologic drug development via molecular modelling and informatics. The Journal of Pharmacy and Pharmacology, 70(5), 595–608. https://doi.org/10.1111/jphp.12700
   PubMed Web of Science ®Google Scholar
• Kumar, A., Prasoon, P., Kumari, C., Pareek, V., Faiq, M. A., Narayan, R. K., Kulandhasamy, M., & Kant, K. (2021). SARS‐CoV‐2‐specific virulence factors in COVID‐19. Journal of Medical Virology, 93(3), 1343–1350. https://doi.org/10.1002/jmv.26615
   PubMed Web of Science ®Google Scholar
• Kumar, S., Roffi, K., Tomar, D. S., Cirelli, D., Luksha, N., Meyer, D., Mitchell, J., Allen, M. J., & Li, L. (2018b). Rational optimization of a monoclonal antibody for simultaneous improvements in its solution properties and biological activity A. Protein Engineering, Design & Selection : PEDS, 31(7-8), 313–325. https://doi.org/10.1093/protein/gzy020
   PubMed Web of Science ®Google Scholar
• Kupferschmidt, K. (2021a). New mutations raise specter of ‘immune escape. Science (New York, N.Y.), 371(6527), 329–330. https://doi.org/10.1126/science.371.6527.329
   PubMed Web of Science ®Google Scholar
• Kupferschmidt, K. (2021b). Where did ‘weird’ Omicron come from? Science, 374(6572), 1179–1179. https://doi.org/10.1126/science.acx9738
   PubMed Web of Science ®Google Scholar
• Lan, J., He, X., Ren, Y., Wang, Z., Zhou, H., Fan, S., Zhu, C., Liu, D., Shao, B., Liu, T.-Y., Wang, Q., Zhang, L., Ge, J., Wang, T., & Wang, X. (2022). Structural and computational insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction. https://doi.org/10.1101/2022.01.03.474855
   Google Scholar
• Laurini, E., Marson, D., Aulic, S., Fermeglia, M., & Pricl, S. (2020). Computational alanine scanning and structural analysis of the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 complex. ACS Nano, 14(9), 11821–11830. https://doi.org/10.1021/acsnano.0c04674
   PubMed Web of Science ®Google Scholar
• Leach, A. R. (2001). Molecular modelling: principles and applications. 2nd ed. Prentice Hall.
   Google Scholar
• Li, F. (2016). Structure, function, and evolution of coronavirus spike proteins. Annual Review of Virology, 3(1), 237–261. https://doi.org/10.1146/annurev-virology-110615-042301
   PubMed Web of Science ®Google Scholar
• Li, J. Z., & Gandhi, R. T. (2022). Realizing the potential of anti–SARS-CoV-2 monoclonal antibodies for COVID-19 management. JAMA, 327(5), 427. https://doi.org/10.1001/jama.2021.19994
   PubMed Web of Science ®Google Scholar
• Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., Yu, J., Chik, K. K.-H., Yuen, T. T.-T., Yoon, C., To, K. K.-W., Chen, H., Yin, M. T., Sobieszczyk, M. E., Huang, Y., … Ho, D. D. (2021a). Striking antibody evasion manifested by the omicron variant of SARS-CoV-2. Nature, 602(7898), 676–681. https://doi.org/10.1038/s41586-021-04388-0
   PubMed Web of Science ®Google Scholar
• Liu, Y., Soh, W. T., Kishikawa, J.-I., Hirose, M., Nakayama, E. E., Li, S., Sasai, M., Suzuki, T., Tada, A., Arakawa, A., Matsuoka, S., Akamatsu, K., Matsuda, M., Ono, C., Torii, S., Kishida, K., Jin, H., Nakai, W., Arase, N., … Arase, H. (2021b). An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies. Cell, 184(13), 3452–3466.e18. https://doi.org/10.1016/j.cell.2021.05.032
   PubMed Web of Science ®Google Scholar
• Lousa, D., Soares, C., & Barroso Da Silva, F. L. (2022). EDITORIAL: Computational approaches to foster innovation in the treatment and diagnosis of infectious diseases. Frontiers in Medical Technology, 4, 841088. https://doi.org/10.3389/fmedt.2022.841088
   PubMedGoogle Scholar
• Lu, L., Mok, B. W.-Y., Chen, L.-L., Chan, J. M.-C., Tsang, O. T.-Y., Lam, B. H.-S., Chuang, V. W.-M., Chu, A. W.-H., Chan, W.-M., Ip, J. D., Chan, B. P.-C., Zhang, R., Yip, C. C.-Y., Cheng, V. C.-C., Chan, K.-H., Jin, D.-Y., Hung, I. F.-N., Yuen, K.-Y., Chen, H., & To, K. K.-W. (2021). Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. Clinical Infectious Diseases, ciab1041. https://doi.org/10.1093/cid/ciab1041
   Google Scholar
• Lupala, C. S., Ye, Y., Chen, H., Su, X.-D., & Liu, H. (2022). Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor. Biochemical and Biophysical Research Communications, 590, 34–41. https://doi.org/10.1016/j.bbrc.2021.12.079
   PubMed Web of Science ®Google Scholar
• Maher, M. C., Bartha, I., Weaver, S., di Iulio, J., Ferri, E., Soriaga, L., Lempp, F. A., Hie, B. L., Bryson, B., Berger, B., Robertson, D. L., Snell, G., Corti, D., Virgin, H. W., Kosakovsky Pond, S. L., & Telenti, A. (2022). Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science Translational Medicine, 14(633) https://doi.org/10.1126/scitranslmed.abk3445
   Google Scholar
• Mallapaty, S., Callaway, E., Kozlov, M., Ledford, H., Pickrell, J., & Van Noorden, R. (2021). How COVID vaccines shaped 2021 in eight powerful charts. Nature, 600(7890), 580–583. https://doi.org/10.1038/d41586-021-03686-x
   PubMed Web of Science ®Google Scholar
• Mannar, D., Saville, J. W., Zhu, X., Srivastava, S. S., Berezuk, A. M., Tuttle, K. S., Marquez, A. C., Sekirov, I., & Subramaniam, S. (2022). SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex. Science (New York, N.Y.), 375(6582), 760–764. https://doi.org/10.1126/science.abn7760
   PubMed Web of Science ®Google Scholar
• Marovich, M., Mascola, J. R., & Cohen, M. S. (2020). Monoclonal antibodies for prevention and treatment of COVID-19. JAMA, 324(2), 131–132. https://doi.org/10.1001/jama.2020.10245
   PubMed Web of Science ®Google Scholar
• Mascolo, S., Carleo, M. A., Contieri, M., Izzo, S., Perna, A., De Luca, A., & Esposito, V. (2021). SARS‐CoV‐2 and inflammatory responses: From mechanisms to the potential therapeutic use of intravenous immunoglobulin. Journal of Medical Virology, 93(5), 2654–2661. https://doi.org/10.1002/jmv.26651
   PubMed Web of Science ®Google Scholar
• Maslo, C., Friedland, R., Toubkin, M., Laubscher, A., Akaloo, T., & Kama, B. (2022). Characteristics and outcomes of hospitalized patients in South Africa during the COVID-19 omicron wave compared with previous waves. JAMA, 327(6), 583–584. https://doi.org/10.1001/jama.2021.24868
   PubMed Web of Science ®Google Scholar
• McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., Powell, A. E., Croll, T. I., Nix, J., Virgin, H. W., Corti, D., Snell, G., & Veesler, D. (2022). Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science (New York, N.Y.), 375(6583), 864–868. https://doi.org/10.1126/science.abn8652
   PubMed Web of Science ®Google Scholar
• McEwan, W. A., & James, L. C. (2015). TRIM21-dependent intracellular antibody neutralization of virus infection. In: Progress in Molecular Biology and Translational Science (129, 167–187). Elsevier. https://doi.org/10.1016/bs.pmbts.2014.10.006
   Google Scholar
• Mendonça, D. C., Macedo, J. N., Guimarães, S. L., Barroso da Silva, F. L., Cassago, A., Garratt, R. C., Portugal, R. V., & Araujo, A. P. U. (2019). A revised order of subunits in mammalian septin complexes. Cytoskeleton (Hoboken, N.J.), 76(9–10), 457–466. https://doi.org/10.1002/cm.21569
   PubMed Web of Science ®Google Scholar
• Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., Zepeda, S. K., Papa, G., Kemp, S. A., Ikeda, T., Toyoda, M., Tan, T. S., Kuramochi, J., Mitsunaga, S., Ueno, T., … Gupta, R. K, Ecuador-COVID19 Consortium. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature, 603(7902), 706–714. https://doi.org/10.1038/s41586-022-04474-x
   PubMed Web of Science ®Google Scholar
• Metzger, C., Lienhard, R., Seth-Smith, H. M. B., Roloff, T., Wegner, F., Sieber, J., Bel, M., Greub, G., & Egli, A. (2021). PCR performance in the SARS-CoV-2 Omicron variant of concern? Swiss Medical Weekly, 151, w30120–50. https://doi.org/10.4414/smw.2021.w30120
   PubMed Web of Science ®Google Scholar
• Möhlendick, B., Schönfelder, K., Breuckmann, K., Elsner, C., Babel, N., Balfanz, P., Dahl, E., Dreher, M., Fistera, D., Herbstreit, F., Hölzer, B., Koch, M., Kohnle, M., Marx, N., Risse, J., Schmidt, K., Skrzypczyk, S., Sutharsan, S., Taube, C., … Kribben, A. (2021). ACE2 polymorphism and susceptibility for SARS-CoV-2 infection and severity of COVID-19. Pharmacogenetics and Genomics, 31(8), 165–171. https://doi.org/10.1097/FPC.0000000000000436
   PubMed Web of Science ®Google Scholar
• Morton, S. P., & Phillips, J. L. (2020). Computational electrostatics predict variations in SARS-CoV-2 spike and human ACE2 interactions. https://doi.org/10.1101/2020.04.30.071175
   Google Scholar
• Mullard, A. (2021). FDA approves 100th monoclonal antibody product. Nature Reviews. Drug Discovery, 20(7), 491–495. https://doi.org/10.1038/d41573-021-00079-7
   PubMed Web of Science ®Google Scholar
• Nanda, H., Datta, S. A. K., Heinrich, F., Lösche, M., Rein, A., Krueger, S., & Curtis, J. E. (2010). Electrostatic interactions and binding orientation of HIV-1 matrix studied by neutron reflectivity. Biophysical Journal, 99(8), 2516–2524. https://doi.org/10.1016/j.bpj.2010.07.062
   PubMed Web of Science ®Google Scholar
• Narayanan, H., Dingfelder, F., Condado Morales, I., Patel, B., Heding, K. E., Bjelke, J. R., Egebjerg, T., Butté, A., Sokolov, M., Lorenzen, N., & Arosio, P. (2021). Design of biopharmaceutical formulations accelerated by machine learning. Molecular Pharmaceutics, 18(10), 3843–3853. https://doi.org/10.1021/acs.molpharmaceut.1c00469
   PubMed Web of Science ®Google Scholar
• Neamtu, A., Mocci, F., Laaksonen, A., & Barroso da Silva, F. L. (2022). Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. https://doi.org/10.1101/2022.01.04.474958
   Google Scholar
• Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453. https://doi.org/10.1016/0022-2836(70)90057-4
   PubMed Web of Science ®Google Scholar
• Nguyen, H., Lan, P. D., Nissley, D. A., O'Brien, E. P., & Li, M. S. (2021). Electrostatic interactions explain the higher binding affinity of the CR3022 antibody for SARS-CoV-2 than the 4A8 antibody. The Journal of Physical Chemistry. B, 125(27), 7368–7379. https://doi.org/10.1021/acs.jpcb.1c03639
   PubMed Web of Science ®Google Scholar
• Nie, C., Sahoo, A. K., Herrmann, A., Ballauff, M., Netz, R. R., & Haag, R. (2022). Charge Matters: Mutations in Omicron variant favor binding to cells. ChemBioChem. 23(6) https://doi.org/10.1002/cbic.202100681
   Google Scholar
• O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, 7(2), veab064. https://doi.org/10.1093/ve/veab064
   PubMed Web of Science ®Google Scholar
• Ortega, J. T., Jastrzebska, B., & Rangel, H. R. (2021). Omicron SARS-CoV-2 variant spike protein shows an increased affinity to the human ACE2 receptor: An in silico analysis. Pathogens, 11(1), 45. https://doi.org/10.3390/pathogens11010045
   PubMed Web of Science ®Google Scholar
• Ou, J., Lan, W., Wu, X., Zhao, T., Duan, B., Yang, P., Ren, Y., Quan, L., Zhao, W., Seto, D. and Chodosh, J. (2022). Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events. Signal Transduction and Targeted Therapy, 7(1), 1–9.
   Google Scholar
• Park, Y.-J., De Marco, A., Starr, T. N., Liu, Z., Pinto, D., Walls, A. C., Zatta, F., Zepeda, S. K., Bowen, J. E., Sprouse, K. R., Joshi, A., Giurdanella, M., Guarino, B., Noack, J., Abdelnabi, R., Foo, S.-Y C., Rosen, L. E., Lempp, F. A., Benigni, F., … Veesler, D. (2022). Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. Science, 375(6579), eabm8143–454. https://doi.org/10.1126/science.abm8143
   Web of Science ®Google Scholar
• Parums, D. V. (2021). Editorial: Revised World Health Organization (WHO) terminology for variants of concern and variants of interest of SARS-CoV-2. Medical Science Monitor, 27 https://doi.org/10.12659/MSM.933622
   Google Scholar
• Peckham, H., de Gruijter, N. M., Raine, C., Radziszewska, A., Ciurtin, C., Wedderburn, L. R., Rosser, E. C., Webb, K., & Deakin, C. T. (2020). Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission. Nature Communications, 11(1), 6317. https://doi.org/10.1038/s41467-020-19741-6
   PubMed Web of Science ®Google Scholar
• Pereira, F., Tosta, S., Lima, M. M., Reboredo de Oliveira da Silva, L., Nardy, V. B., Gómez, M. K. A., Lima, J. G., Fonseca, V., de Oliveira, T., Lourenço, J., Alcantara, L. C., Jr., Giovanetti, M., & Leal, A. (2021). Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report. Journal of Medical Virology, 93(9), 5523–5526. https://doi.org/10.1002/jmv.27086
   PubMed Web of Science ®Google Scholar
• Pérez-Then, E., Lucas, C., Monteiro, V. S., Miric, M., & Brache, V. (2021). Immunogenicity of heterologous BNT162b2 booster in fully vaccinated individuals with CoronaVac against SARS-CoV-2 variants Delta and Omicron: the Dominican Republic Experience. https://doi.org/10.1101/2021.12.27.21268459
   Google Scholar
• Persson, B. A., Lund, M., Forsman, J., Chatterton, D. E. W., & Åkesson, T. (2010). Molecular evidence of stereo-specific lactoferrin dimers in solution. Biophysical Chemistry, 151(3), 187–189. https://doi.org/10.1016/j.bpc.2010.06.005
   PubMed Web of Science ®Google Scholar
• Petrides, D., Carmichael, D., Siletti, C., & Koulouris, A. (2014). Biopharmaceutical process optimization with simulation and scheduling tools. Bioengineering (Basel, Switzerland), 1(4), 154–187. https://doi.org/10.3390/bioengineering1040154
   PubMedGoogle Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera? A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., Peter, A., Guarino, B., Spreafico, R., Cameroni, E., Case, J. B., Chen, R. E., Havenar-Daughton, C., Snell, G., Telenti, A., … Corti, D. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 583(7815), 290–295. https://doi.org/10.1038/s41586-020-2349-y
   PubMed Web of Science ®Google Scholar
• Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., Prot, M., Gallais, F., Gantner, P., Velay, A., Le Guen, J., Kassis-Chikhani, N., Edriss, D., Belec, L., Seve, A., … Schwartz, O. (2021). Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature, 596(7871), 276–280. https://doi.org/10.1038/s41586-021-03777-9
   PubMed Web of Science ®Google Scholar
• Plante, J. A., Mitchell, B. M., Plante, K. S., Debbink, K., Weaver, S. C., & Menachery, V. D. (2021). The variant gambit: COVID-19’s next move. Cell Host & Microbe, 29(4), 508–515. https://doi.org/10.1016/j.chom.2021.02.020
   PubMed Web of Science ®Google Scholar
• Poveda-Cuevas, S. A., Etchebest, C., & Barroso da Silva, F. L. (2018). Insights into the ZIKV NS1 virology from different strains through a fine analysis of physicochemical properties. ACS Omega, 3(11), 16212–16229. https://doi.org/10.1021/acsomega.8b02081
   PubMed Web of Science ®Google Scholar
• Poveda-Cuevas, S. A., Etchebest, C., & Barroso da Silva, F. L. (2020). Identification of electrostatic epitopes in flavivirus by computer simulations: The PROCEEDpKa method. Journal of Chemical Information and Modeling, 60(2), 944–963. https://doi.org/10.1021/acs.jcim.9b00895
   PubMed Web of Science ®Google Scholar
• Poveda-Cuevas, S. A., Etchebest, C., & Barroso da Silva, F. L. (2022). Self-association features of NS1 proteins from different flaviviruses. Virus Research. https://doi.org/10.1016/j.virusres.2022.198838
   Google Scholar
• Ramaraj, T., Angel, T., Dratz, E. A., Jesaitis, A. J., & Mumey, B. (2012). Antigen–antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures. Biochimica et Biophysica Acta, 1824(3), 520–532. https://doi.org/10.1016/j.bbapap.2011.12.007
   PubMed Web of Science ®Google Scholar
• Reis, G., Dos Santos Moreira-Silva, E. A., Silva, D. C. M., Thabane, L., Milagres, A. C., Ferreira, T. S., Dos Santos, C. V. Q., de Souza Campos, V. H., Nogueira, A. M. R., de Almeida, A. P. F. G., Callegari, E. D., de Figueiredo Neto, A. D., Savassi, L. C. M., Simplicio, M. I. C., Ribeiro, L. B., Oliveira, R., Harari, O., Forrest, J. I., Ruton, H., … Mills, E. J. Together Investigators. (2022). Effect of early treatment with fluvoxamine on risk of emergency care and hospitalisation among patients with COVID-19: the TOGETHER randomised, platform clinical trial. The Lancet. Global Health, 10(1), e42–e51. https://doi.org/10.1016/S2214-109X(21)00448-4
   PubMed Web of Science ®Google Scholar
• Renn, A., Fu, Y., Hu, X., Hall, M. D., & Simeonov, A. (2020). Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2. Trends in Pharmacological Sciences, 41(11), 815–829. https://doi.org/10.1016/j.tips.2020.07.004
   PubMed Web of Science ®Google Scholar
• Rich, R. R., Shearer, W. T., Frew, A. J., Fleisher, T. A., Schroeder, H. W., & Weyand, C. M. (2019). Clinical Immunology. Elsevier. https://doi.org/10.1016/C2015-0-00344-6
   Google Scholar
• Rockett, R. J., Basile, K., Maddocks, S., Fong, W., & Agius, J. E. (2021). Resistance Conferring Mutations in SARS-CoV-2 delta following sotrovimab infusion. https://doi.org/10.1101/2021.12.18.21267628
   Google Scholar
• Rössler, A., Riepler, L., Bante, D., von Laer, D., & Kimpel, J. (2022). SARS-CoV-2 Omicron variant neutralization in serum from vaccinated and convalescent persons. The New England Journal of Medicine, 386(7), 698–700. https://doi.org/10.1056/NEJMc2119236
   PubMed Web of Science ®Google Scholar
• S. Wu-Pong & Y. Rojanasakul (eds.). (2008). Biopharmaceutical drug design and development. Humana Press. https://doi.org/10.1007/978-1-59745-532-9
   Google Scholar
• Sabino, E. C., Buss, L. F., Carvalho, M. P. S., Prete, C. A., Crispim, M. A. E., Fraiji, N. A., Pereira, R. H. M., Parag, K. V., da Silva Peixoto, P., Kraemer, M. U. G., Oikawa, M. K., Salomon, T., Cucunuba, Z. M., Castro, M. C., de Souza Santos, A. A., Nascimento, V. H., Pereira, H. S., Ferguson, N. M., Pybus, O. G., … Faria, N. R. (2021). Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. The Lancet, 397(10273), 452–455. https://doi.org/10.1016/S0140-6736(21)00183-5
   PubMed Web of Science ®Google Scholar
• Sato, H., Yokoyama, M., & Toh, H. (2013). Genomics and computational science for virus research. Frontiers in Microbiology, 4, 42. https://doi.org/10.3389/fmicb.2013.00042
   PubMed Web of Science ®Google Scholar
• Sayed, S. (2021). COVID-19 and diabetes; possible role of polymorphism and rise of telemedicine. Primary Care Diabetes, 15(1), 4–9. https://doi.org/10.1016/j.pcd.2020.08.018
   PubMed Web of Science ®Google Scholar
• Scheepers, C., Everatt, J., Amoako, D. G., Tegally, H., Wibmer, C. K., Mnguni, A., Ismail, A., Mahlangu, B., Lambson, B. E., Martin, D. P., Wilkinson, E., San, J. E., Giandhari, J., Manamela, N., Ntuli, N., Kgagudi, P., Cele, S., Richardson, S. I., Pillay, S., … Bhiman, J. N. (2022). Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Nature Communications, 13(1), 1976. https://doi.org/10.1038/s41467-022-29579-9
   PubMed Web of Science ®Google Scholar
• Schlick, T., & Portillo-Ledesma, S. (2021). Biomolecular modeling thrives in the age of technology. Nature Computational Science, 1(5), 321–331. https://doi.org/10.1038/s43588-021-00060-9
   PubMedGoogle Scholar
• Schmidt, F., Muecksch, F., Weisblum, Y., Da Silva, J., Bednarski, E., Cho, A., Wang, Z., Gaebler, C., Caskey, M., Nussenzweig, M. C., Hatziioannou, T., & Bieniasz, P. D. (2022). Plasma neutralization of the SARS-CoV-2 Omicron variant. The New England Journal of Medicine, 386(6), 599–601. https://doi.org/10.1056/NEJMc2119641
   PubMed Web of Science ®Google Scholar
• Schubert, M., Bertoglio, F., Steinke, S., Heine, P.A., Ynga-Durand, M.A., Maass, H., Sammartino, J.C., Cassaniti, I., Zuo, F., Du, L. & Korn, J. (2022). Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. BMC medicine, 20(1), 1–11.
   Web of Science ®Google Scholar
• Shah, M., & Woo, H. G. (2021). Omicron: A heavily mutated SARS-CoV-2 variant exhibits stronger binding to ACE2 and potently escapes approved COVID-19 therapeutic antibodies. Frontiers in Immunology, 12, 830527. https://doi.org/10.3389/fimmu.2021.830527
   PubMed Web of Science ®Google Scholar
• Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221–224. https://doi.org/10.1038/s41586-020-2179-y
   PubMed Web of Science ®Google Scholar
• Sharma, V. K., Patapoff, T. W., Kabakoff, B., Pai, S., Hilario, E., Zhang, B., Li, C., Borisov, O., Kelley, R. F., Chorny, I., Zhou, J. Z., Dill, K. A., & Swartz, T. E. (2014). In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability. Proceedings of the National Academy of Sciences of the United States of America, 111(52), 18601–18606. https://doi.org/10.1073/pnas.1421779112
   PubMed Web of Science ®Google Scholar
• Sharma, D., Priyadarshini, P., & Vrati, S. (2015). Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research S.P. Goff (ed.). Journal of Virology, 89(3), 1489–1501. https://doi.org/10.1128/JVI.02027-14
   PubMed Web of Science ®Google Scholar
• Simmons, G., Reeves, J. D., Rennekamp, A. J., Amberg, S. M., Piefer, A. J., & Bates, P. (2004). Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry. Proceedings of the National Academy of Sciences of the United States of America, 101(12), 4240–4245. https://doi.org/10.1073/pnas.0306446101
   PubMed Web of Science ®Google Scholar
• Sokal, A., Broketa, M., Barba-Spaeth, G., Meola, A., Fernández, I., Fourati, S., Azzaoui, I., de La Selle, A., Vandenberghe, A., Roeser, A., Bouvier-Alias, M., Crickx, E., Languille, L., Michel, M., Godeau, B., Gallien, S., Melica, G., Nguyen, Y., Zarrouk, V., … Mahévas, M. (2022). Analysis of mRNA vaccination-elicited RBD-specific memory B cells reveals strong but incomplete immune escape of the SARS-CoV-2 Omicron variant. Immunity, 55(6), 1096–1104.e4. https://doi.org/10.1016/j.immuni.2022.04.002
   PubMed Web of Science ®Google Scholar
• Starr, T. N., Greaney, A. J., Dingens, A. S., & Bloom, J. D. (2021). Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Cell Reports. Medicine, 2(4), 100255. https://doi.org/10.1016/j.xcrm.2021.100255
   PubMedGoogle Scholar
• 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., King, N. P., Veesler, D., & Bloom, J. D. (2020). Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell, 182(5), 1295–1310.e20. https://doi.org/10.1016/j.cell.2020.08.012
   PubMed Web of Science ®Google Scholar
• Suryamohan, K., Diwanji, D., Stawiski, E. W., Gupta, R., Miersch, S., Liu, J., Chen, C., Jiang, Y.-P., Fellouse, F. A., Sathirapongsasuti, J. F., Albers, P. K., Deepak, T., Saberianfar, R., Ratan, A., Washburn, G., Mis, M., Santhosh, D., Somasekar, S., Hiranjith, G. H., … Seshagiri, S. (2021). Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. Communications Biology, 4(1), 475. https://doi.org/10.1038/s42003-021-02030-3
   PubMed Web of Science ®Google Scholar
• Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021). The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews. Genetics, 22(12), 757–773. https://doi.org/10.1038/s41576-021-00408-x
   PubMed Web of Science ®Google Scholar
• Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., Mlisana, K., von Gottberg, A., Walaza, S., Allam, M., Ismail, A., Mohale, T., Glass, A. J., Engelbrecht, S., Van Zyl, G., … de Oliveira, T. (2021). Detection of a SARS-CoV-2 variant of concern in South Africa. Nature, 592(7854), 438–443. https://doi.org/10.1038/s41586-021-03402-9
   PubMed Web of Science ®Google Scholar
• Teixeira, A. A. R., Lund, M., & Barroso da Silva, F. L. (2010). Fast proton titration scheme for multiscale modeling of protein solutions. Journal of Chemical Theory and Computation, 6(10), 3259–3266. https://doi.org/10.1021/ct1003093
   PubMed Web of Science ®Google Scholar
• Tian, X., Li, C., Huang, A., Xia, S., Lu, S., Shi, Z., Lu, L., Jiang, S., Yang, Z., Wu, Y., & Ying, T. (2020). Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerging Microbes & Infections, 9(1), 382–385. https://doi.org/10.1080/22221751.2020.1729069
   PubMed Web of Science ®Google Scholar
• Tian, F., Tong, B., Sun, L., Shi, S., Zheng, B., Wang, Z., Dong, X., & Zheng, P. (2021). N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. eLife, 10, e69091. https://doi.org/10.7554/eLife.69091
   PubMed Web of Science ®Google Scholar
• Toyoshima, Y., Nemoto, K., Matsumoto, S., Nakamura, Y., & Kiyotani, K. (2020). SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Journal of Human Genetics, 65(12), 1075–1082. https://doi.org/10.1038/s10038-020-0808-9
   PubMed Web of Science ®Google Scholar
• Tracking SARS-CoV-2 Variants. https://www.who.int/emergencies/what-we-do/tracking-SARS-CoV-2-variants [Accessed: 7 January 2022b].
   Google Scholar
• Tso, F. Y., Lidenge, S. J., Poppe, L. K., Peña, P. B., Privatt, S. R., Bennett, S. J., Ngowi, J. R., Mwaiselage, J., Belshan, M., Siedlik, J. A., Raine, M. A., Ochoa, J. B., Garcia-Diaz, J., Nossaman, B., Buckner, L., Roberts, W. M., Dean, M. J., Ochoa, A. C., West, J. T., & Wood, C. (2021). Presence of antibody-dependent cellular cytotoxicity (ADCC) against SARS-CoV-2 in COVID-19 plasma L. Margolis (ed.). PloS One, 16(3), e0247640. https://doi.org/10.1371/journal.pone.0247640
   PubMed Web of Science ®Google Scholar
• Tuckerman, M. E. (2010). Statistical mechanics: Theory and molecular simulation. Oxford University Press.
   Google Scholar
• Ubah, O. C., Lake, E. W., Gunaratne, G. S., Gallant, J. P., Fernie, M., Robertson, A. J., Marchant, J. S., Bold, T. D., Langlois, R. A., Matchett, W. E., Thiede, J. M., Shi, K., Yin, L., Moeller, N. H., Banerjee, S., Ferguson, L., Kovaleva, M., Porter, A. J., Aihara, H., LeBeau, A. M., & Barelle, C. J. (2021). Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography. Nature Communications, 12(1), 7325. https://doi.org/10.1038/s41467-021-27611-y
   PubMed Web of Science ®Google Scholar
• Uriu, K., Kimura, I., Shirakawa, K., Takaori-Kondo, A., Nakada, T., Kaneda, A., Nakagawa, S., & Sato, K, Genotype to Phenotype Japan (G2P-Japan) Consortium. (2021). Neutralization of the SARS-CoV-2 Mu variant by convalescent and vaccine serum. The New England Journal of Medicine, 385(25), 2397–2399. https://doi.org/10.1056/NEJMc2114706
   PubMed Web of Science ®Google Scholar
• VanBlargan, L. A., Errico, J. M., Halfmann, P. J., Zost, S. J., Crowe, J. E., Purcell, L. A., Kawaoka, Y., Corti, D., Fremont, D. H., & Diamond, M. S. (2022). An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies. Nature Medicine, 28(3), 490–495. https://doi.org/10.1038/s41591-021-01678-y
   PubMed Web of Science ®Google Scholar
• Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., Choga, W. T., Colquhoun, R., Davids, M., Deforche, K., Doolabh, D., du Plessis, L., Engelbrecht, S., Everatt, J., Giandhari, J., … de Oliveira, T. (2022). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, 603(7902), 679–686. https://doi.org/10.1038/s41586-022-04411-y
   PubMed Web of Science ®Google Scholar
• Voloch, C. M., da Silva Francisco, R., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. d C., Mariani, D., da Costa, R. M., Ferreira, O. C., Cavalcanti, A. C., Frauches, T. S., de Mello, C. M. B., Leitão, I. d C., Galliez, R. M., Faffe, D. S., Castiñeiras, T. M. P. P., Tanuri, A., & de Vasconcelos, A. T. R. Covid19-UFRJ Workgroup. (2021). Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil C.R. Parrish (ed. Journal of Virology, 95(10) https://doi.org/10.1128/JVI.00119-21
   Google Scholar
• Wade, R. C., Gabdoulline, R. R., Ludemann, S. K., & Lounnas, V. (1998). Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations. Proceedings of the National Academy of Sciences of the United States of America, 95(11), 5942–5949. https://doi.org/10.1073/pnas.95.11.5942
   PubMed Web of Science ®Google Scholar
• Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
   PubMed Web of Science ®Google Scholar
• Walls, A. C., Xiong, X., Park, Y.-J., Tortorici, M. A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., Zambon, M., Rey, F. A., Corti, D., & Veesler, D. (2019). Unexpected receptor functional mimicry elucidates activation of coronavirus fusion. Cell, 176(5), 1026–1039.e15. https://doi.org/10.1016/j.cell.2018.12.028
   PubMed Web of Science ®Google Scholar
• Wang, R., Chen, J., Hozumi, Y., Yin, C., & Wei, G.-W. (2022). Emerging vaccine-breakthrough SARS-CoV-2 variants. ACS Infectious Diseases, 8(3), 546–556. https://doi.org/10.1021/acsinfecdis.1c00557
   PubMed Web of Science ®Google Scholar
• Wang, D., Ge, Y., Zhong, B., & Liu, D. (2021a). Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Computational and Structural Biotechnology Journal, 19, 1661–1671. https://doi.org/10.1016/j.csbj.2021.03.021
   PubMed Web of Science ®Google Scholar
• Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., Oliveira, T. Y., Yang, Z., Abernathy, M. E., Huey-Tubman, K. E., Hurley, A., Turroja, M., West, K. A., Gordon, K., Millard, K. G., … Nussenzweig, M. C. (2021b). mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature, 592(7855), 616–622. https://doi.org/10.1038/s41586-021-03324-6
   PubMed Web of Science ®Google Scholar
• Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K.-Y., Wang, Q., Zhou, H., Yan, J., & Qi, J. (2020). Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell, 181(4), 894–904.e9. 2020) https://doi.org/10.1016/j.cell.2020.03.045
   PubMed Web of Science ®Google Scholar
• Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Weinreich, D. M., Sivapalasingam, S., Norton, T., Ali, S., Gao, H., Bhore, R., Musser, B. J., Soo, Y., Rofail, D., Im, J., Perry, C., Pan, C., Hosain, R., Mahmood, A., Davis, J. D., Turner, K. C., Hooper, A. T., Hamilton, J. D., Baum, A., … Yancopoulos, G. D. Trial Investigators. (2021b). REGN-COV2, a neutralizing antibody cocktail, in outpatients with Covid-19. The New England Journal of Medicine, 384(3), 238–251. https://doi.org/10.1056/NEJMoa2035002
   PubMed Web of Science ®Google Scholar
• Weinreich, D. M., Sivapalasingam, S., Norton, T., Ali, S., Gao, H., Bhore, R., Xiao, J., Hooper, A. T., Hamilton, J. D., Musser, B. J., Rofail, D., Hussein, M., Im, J., Atmodjo, D. Y., Perry, C., Pan, C., Mahmood, A., Hosain, R., Davis, J. D., … Yancopoulos, G. D. (2021a). REGEN-COV antibody combination and outcomes in outpatients with Covid-19. New England Journal of Medicine, 385(23), e81. https://doi.org/10.1056/NEJMoa2108163
   PubMed Web of Science ®Google Scholar
• Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., Gaebler, C., Agudelo, M., Cho, A., Wang, Z., Gazumyan, A., Cipolla, M., Luchsinger, L., Hillyer, C. D., Caskey, M., … Bieniasz, P. D. (2020). Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife, 9, e61312. https://doi.org/10.7554/eLife.61312
   PubMed Web of Science ®Google Scholar
• West, A. P., Wertheim, J. O., Wang, J. C., Vasylyeva, T. I., Havens, J. L., Chowdhury, M. A., Gonzalez, E., Fang, C. E., Di Lonardo, S. S., Hughes, S., Rakeman, J. L., Lee, H. H., Barnes, C. O., Gnanapragasam, P. N. P., Yang, Z., Gaebler, C., Caskey, M., Nussenzweig, M. C., Keeffe, J. R., & Bjorkman, P. J. (2021). Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nature Communications, 12(1), 4886. https://doi.org/10.1038/s41467-021-25168-4
   PubMed Web of Science ®Google Scholar
• Whittaker, G. R. (2021). SARS-CoV-2 spike and its adaptable furin cleavage site. The Lancet. Microbe, 2(10), e488–e489. https://doi.org/10.1016/S2666-5247(21)00174-9
   PubMedGoogle Scholar
• Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., Rossouw, T., Boswell, M., Ueckermann, V., Meiring, S., von Gottberg, A., Cohen, C., Morris, L., Bhiman, J. N., & Moore, P. L. (2021). SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nature Medicine, 27(4), 622–625. https://doi.org/10.1038/s41591-021-01285-x
   PubMed Web of Science ®Google Scholar
• Wilhelm, A., Widera, M., Grikscheit, K., Toptan, T., Schenk, B., Pallas, C., Metzler, M., Kohmer, N., Hoehl, S., Helfritz, F. A., Wolf, T., Goetsch, U., & Ciesek, S. (2021). Reduced neutralization of SARS-CoV-2 Omicron variant by vaccine sera and monoclonal antibodies. https://doi.org/10.1101/2021.12.07.21267432
   Google Scholar
• Willett, B.J., Grove, J., MacLean, O., Wilkie, C., Logan, N., De Lorenzo, G., Furnon, W., Scott, S., Manali, M., Szemiel, A., Ashraf, S., Vink, E., Harvey, W. T., Davis, C., Orton, R., Hughes, J., Holland, P., Silva, V., Pascall, D., … & Thomson. E. C. (2022). The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism. medRxiv. https://doi.org/10.1101/2022.01.03.21268111
   Google Scholar
• World Health Organization. (2021). Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of concern. November 2021. World Health Organization. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern [Accessed: 6 January 2022].
   Google Scholar
• Xie, Y., Guo, W., Lopez-Hernadez, A., Teng, S., & Li, L. (2022). The pH effects on SARS-CoV and SARS-CoV-2 spike proteins in the process of binding to hACE2. Pathogens, 11(2), 238. https://doi.org/10.3390/pathogens11020238
   PubMed Web of Science ®Google Scholar
• Xie, X., Han, J.-B., Ma, G., Feng, X.-L., Li, X., Zou, Q.-C., Deng, Z.-H., & Zeng, J. (2021). China. Emerging SARS-CoV-2 B.1.621/Mu variant is prominently resistant to inactivated vaccine-elicited antibodies. Zoological Research, 42(6), 789–791. https://doi.org/10.24272/j.issn.2095-8137.2021.343
   PubMed Web of Science ®Google Scholar
• Xie, Y., Karki, C. B., Du, D., Li, H., Wang, J., Sobitan, A., Teng, S., Tang, Q., & Li, L. (2020). Spike proteins of SARS-CoV and SARS-CoV-2 utilize different mechanisms to bind with human ACE2. Frontiers in Molecular Biosciences, 7, 591873. https://doi.org/10.3389/fmolb.2020.591873
   PubMed Web of Science ®Google Scholar
• Yadav, R., Chaudhary, J. K., Jain, N., Chaudhary, P. K., Khanra, S., Dhamija, P., Sharma, A., Kumar, A., & Handu, S. (2021). Role of structural and non-structural proteins and therapeutic targets of SARS-CoV-2 for COVID-19. Cells, 10(4), 821. https://doi.org/10.3390/cells10040821
   PubMed Web of Science ®Google Scholar
• Yan, W., Zheng, Y., Zeng, X., He, B., & Cheng, W. (2022). Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduction and Targeted Therapy, 7(1), 26. https://doi.org/10.1038/s41392-022-00884-5
   PubMed Web of Science ®Google Scholar
• Yang, Q., Syed, A. A. S., Fahira, A., & Shi, Y. (2021a). Structural analysis of the SARS-CoV-2 Omicron variant proteins. Research (Washington, D.C.), 2021, 9769586–9769584. https://doi.org/10.34133/2021/9769586
   PubMedGoogle Scholar
• Yang, T.-J., Yu, P.-Y., Chang, Y.-C., Liang, K.-H., Tso, H.-C., Ho, M.-R., Chen, W.-Y., Lin, H.-T., Wu, H.-C., & Hsu, S.-T. D. (2021b). Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. Nature Structural & Molecular Biology, 28(9), 731–739. https://doi.org/10.1038/s41594-021-00652-z
   PubMed Web of Science ®Google Scholar
• Yu, J., Collier, A. Y., Rowe, M., Mardas, F., Ventura, J. D., Wan, H., Miller, J., Powers, O., Chung, B., Siamatu, M., Hachmann, N. P., Surve, N., Nampanya, F., Chandrashekar, A., & Barouch, D. H. (2022). Neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 Variants. The New England Journal of Medicine, 386(16), 1579–1580. https://doi.org/10.1056/NEJMc2201849
   PubMed Web of Science ®Google Scholar
• Yuan, S., Ye, Z.-W., Liang, R., Tang, K., & Zhang, A. J. (2022). The SARS-CoV-2 Omicron (B.1.1.529) variant exhibits altered pathogenicity, transmissibility, and fitness in the golden Syrian hamster model. https://doi.org/10.1101/2022.01.12.476031
   Google Scholar
• Zemla, A., Desautels, T., Lau, E. Y., Zhu, F., Arrildt, K. T., Segelke, B. W., Sundaram, S., & Faissol, D. (2021). SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a large range of neutralizing antibodies, using a rapid computational platform. https://doi.org/10.1101/2021.12.16.472843
   Google Scholar
• Zhang, W., Davis, B. D., Chen, S. S., Sincuir Martinez, J. M., Plummer, J. T., & Vail, E. (2021b). Emergence of a Novel SARS-CoV-2 Variant in Southern California. JAMA, 325(13), 1324–1326. https://doi.org/10.1001/jama.2021.1612
   PubMed Web of Science ®Google Scholar
• Zhang, J., Xiao, T., Cai, Y., Lavine, C. L., Peng, H., Zhu, H., Anand, K., Tong, P., Gautam, A., Mayer, M. L., Walsh, R. M., Rits-Volloch, S., Wesemann, D. R., Yang, W., Seaman, M. S., Lu, J., & Chen, B. (2021a). Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science (New York, N.Y.), 374(6573), 1353–1360. https://doi.org/10.1126/science.abl9463
   PubMed Web of Science ®Google Scholar
• Zhao, X., Xiong, D., Luo, S., & Duan, L. (2022). Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight. Physical Chemistry Chemical Physics: PCCP, 24(15), 8724–8737. https://doi.org/10.1039/d2cp00449f
   PubMed Web of Science ®Google Scholar
• Zhu, Z., Chakraborti, S., He, Y., Roberts, A., Sheahan, T., Xiao, X., Hensley, L. E., Prabakaran, P., Rockx, B., Sidorov, I. A., Corti, D., Vogel, L., Feng, Y., Kim, J.-O., Wang, L.-F., Baric, R., Lanzavecchia, A., Curtis, K. M., Nabel, G. J., … Dimitrov, D. S. (2007). Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceedings of the National Academy of Sciences of the United States of America, 104(29), 12123–12128. https://doi.org/10.1073/pnas.0701000104
   PubMed Web of Science ®Google Scholar
• Zuo, F., Abolhassani, H., Du, L., Piralla, A., & Bertoglio, F. (2022). Heterologous immunization with inactivated vaccine followed by mRNA booster elicits strong humoral and cellular immune responses against the SARS-CoV-2 Omicron variant. https://doi.org/10.1101/2022.01.04.22268755
   Google Scholar