Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant

Adams, P.D., Afonine, P.V., Bunko´ czi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). Phenix: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221. https://doi.org/10. 1107/S0907444909052925.

Arora, P., Kempf, A., Nehlmeier, I., Schulz, S.R., Cossmann, A., Stankov, M.V., Ja€ck, H.M., Behrens, G.M.N., Po¨ hlmann, S., and Hoffmann, M. (2022). Augmented neutralisation resistance of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5. Lancet Infect. Dis. 22, 1117–1118. https://doi. org/10.1016/S1473-3099(22)00422-4.

Barnes, C.O., Jette, C.A., Abernathy, M.E., Dam, K.A., Esswein, S.R., Gristick, H.B., Malyutin, A.G., Sharaf, N.G., Huey-Tubman, K.E., Lee, Y.E., et al. (2020). SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682–687. https://doi.org/10.1038/s41586-020-2852-1.

Bruel, T., Hadjadj, J., Maes, P., Planas, D., Seve, A., Staropoli, I., Guivel- Benhassine, F., Porrot, F., Bolland, W.H., Nguyen, Y., et al. (2022). Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies. Nat. Med. 28, 1297–1302. https://doi.org/10. 1038/s41591-022-01792-5.

Cao, Y., Song, W., Wang, L., Liu, P., Yue, C., Jian, F., Yu, Y., Yisimayi, A., Wang, P., Wang, Y., et al. (2022). Characterizations of enhanced infectivity and antibody evasion of Omicron BA.2.75. Preprint at bioRxiv. https://doi. org/10.1101/2022.07.18.500332.

Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., et al. (2021). Omicron escapes the majority of existing SARS- CoV-2 neutralizing antibodies. Preprint at bioRxiv. https://doi.org/10.1101/ 2021.12.07.470392.

Cao, Y., Yisimayi, A., Jian, F., Song, W., Xiao, T., Wang, L., Du, S., Wang, J., Li, Q., Chen, X., et al. (2022). BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 608, 593–602. https://doi.org/10.1038/s41586- 022-04980-y.

Capella-Gutie´ rrez, S., Silla-Mart´ınez, J.M., and Gabaldo´ n, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973. https://doi.org/10.1093/bioinformatics/ btp348.

Cardone, G., Heymann, J.B., and Steven, A.C. (2013). One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226–236. https://doi.org/10.1016/j.jsb.2013.08.002.

Cele, S., Jackson, L., Khoury, D.S., Khan, K., Moyo-Gwete, T., Tegally, H., San, J.E., Cromer, D., Scheepers, C., Amoako, D.G., et al. (2021). Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature 602, 654–656. https://doi.org/10.1038/d41586-41021-03824-41585.

Cerutti, G., Guo, Y., Zhou, T., Gorman, J., Lee, M., Rapp, M., Reddem, E.R., Yu, J., Bahna, F., Bimela, J., et al. (2021). Potent SARS-CoV-2 neutralizing an- tibodies directed against spike N-terminal domain target a single Supersite. Cell Host Microbe 29, 819–833.e7. https://doi.org/10.1016/j.chom.2021. 03.005.

Chan, K.K., Dorosky, D., Sharma, P., Abbasi, S.A., Dye, J.M., Kranz, D.M., Herbert, A.S., and Procko, E. (2020). Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2. Science 369, 1261– 1265. https://doi.org/10.1126/science.abc0870.

Chen, S., Zhou, Y., Chen, Y., and Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. https://doi.org/10.1093/ bioinformatics/bty560.

Chi, X., Yan, R., Zhang, J., Zhang, G., Zhang, Y., Hao, M., Zhang, Z., Fan, P., Dong, Y., Yang, Y., et al. (2020). A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650–655. https://doi.org/10.1126/science.abc6952.

Cingolani, P., Platts, A., Wang, L.L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X., and Ruden, D.M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80–92. https://doi.org/10.4161/fly.19695.

Deguchi, S., Tsuda, M., Kosugi, K., Sakamoto, A., Mimura, N., Negoro, R., Sano, E., Nobe, T., Maeda, K., Kusuhara, H., et al. (2021). Usability of polydi- methylsiloxane-based microfluidic devices in pharmaceutical research using human hepatocytes. ACS Biomater. Sci. Eng. 7, 3648–3657. https://doi.org/ 10.1021/acsbiomaterials.1c00642.

Dejnirattisai, W., Huo, J., Zhou, D., Zahradnı´k, J., Supasa, P., Liu, C., Duyvesteyn, H.M.E., Ginn, H.M., Mentzer, A.J., Tuekprakhon, A., et al. (2022). SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 185, 467–484.e15. https://doi.org/10. 1016/j.cell.2021.12.046.

Dong, J., Zost, S.J., Greaney, A.J., Starr, T.N., Dingens, A.S., Chen, E.C., Chen, R.E., Case, J.B., Sutton, R.E., Gilchuk, P., et al. (2021). Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat. Microbiol. 6, 1233–1244. https://doi.org/10.1038/s41564-021-00972-2.

Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132. https://doi. org/10.1107/S0907444904019158.

Ferreira, I.A.T.M., Kemp, S.A., Datir, R., Saito, A., Meng, B., Rakshit, P., Takaori-Kondo, A., Kosugi, Y., Uriu, K., Kimura, I., et al. (2021). SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. J. Infect. Dis. 224, 989–994. https://doi.org/10.1093/infdis/jiab368.

Garcia-Beltran, W.F., Lam, E.C., St. Denis, K., Nitido, A.D., Garcia, Z.H., Hauser, B.M., Feldman, J., Pavlovic, M.N., Gregory, D.J., Poznansky, M.C., et al. (2021). Multiple SARS-CoV-2 variants escape neutralization by vac- cine-induced humoral immunity. Cell 184, 2372–2383.e9. https://doi.org/10. 1016/j.cell.2021.03.013.

GitHub (2022). BA.2 sublineage with S:K147E, W152R, F157L, I210V, G257S, D339H, G446S, N460K, R493Q (73 seq as of 2022-06-29, mainly India) (June 21, 2022). https://github.com/cov-lineages/pango-designation/issues/773.

Goddard, T.D., Huang, C.C., Meng, E.C., Pettersen, E.F., Couch, G.S., Morris, J.H., and Ferrin, T.E. (2018). UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25. https://doi.org/10.1002/ pro.3235.

Gotoh, S., Ito, I., Nagasaki, T., Yamamoto, Y., Konishi, S., Korogi, Y., Matsumoto, H., Muro, S., Hirai, T., Funato, M., et al. (2014). Generation of alve- olar epithelial spheroids via isolated progenitor cells from human pluripotent stem cells. Stem Cell Rep. 3, 394–403. https://doi.org/10.1016/j.stemcr. 2014.07.005.

Gruell, H., Vanshylla, K., Korenkov, M., Tober-Lau, P., Zehner, M., Mu€nn, F., Janicki, H., Augustin, M., Schommers, P., Sander, L.E., et al. (2022). SARS- CoV-2 Omicron sublineages exhibit distinct antibody escape patterns. Cell Host Microbe 30, 1231–1241.e6. https://doi.org/10.1016/j.chom.2022.07.002.

Hachmann, N.P., Miller, J., Collier, A.Y., Ventura, J.D., Yu, J., Rowe, M., Bondzie, E.A., Powers, O., Surve, N., Hall, K., et al. (2022). Neutralization escape by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, and BA.5. N. Engl. J. Med. 387, 86–88. https://doi.org/10.1056/NEJMc2206576.

Harvey, W.T., Carabelli, A.M., Jackson, B., Gupta, R.K., Thomson, E.C., Harrison, E.M., Ludden, C., Reeve, R., Rambaut, A., et al.; COVID-19 Genomics UK (COG-UK) Consortium (2021). SARS-CoV-2 variants, spike mu- tations and immune escape. Nat. Rev. Microbiol. 19, 409–424. https://doi.org/ 10.1038/s41579-021-00573-0.

Hashiguchi, T., Ose, T., Kubota, M., Maita, N., Kamishikiryo, J., Maenaka, K., and Yanagi, Y. (2011). Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM. Nat. Struct. Mol. Biol. 18, 135–141. https://doi.org/ 10.1038/nsmb.1969.

Hashimoto, R., Takahashi, J., Shirakura, K., Funatsu, R., Kosugi, K., Deguchi, S., Yamamoto, M., Tsunoda, Y., Morita, M., Muraoka, K., et al. (2022). SARS- CoV-2 disrupts the respiratory vascular barrier by suppressing Claudin-5 expression. Sci. Adv. 8, eabo6783. https://doi.org/10.1126/sciadv.abo6783.

Hsieh, C.L., Goldsmith, J.A., Schaub, J.M., DiVenere, A.M., Kuo, H.C.,

Javanmardi, K., Le, K.C., Wrapp, D., Lee, A.G., Liu, Y., et al. (2020). Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 369, 1501–1505. https://doi.org/10.1126/science.abd0826.

Jackson, C.B., Farzan, M., Chen, B., and Choe, H. (2022). Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 23, 3–20. https://doi. org/10.1038/s41580-021-00418-x.

Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L.E., Brookes, D.H., Wilson, L., Chen, J., Liles, K., et al. (2018). Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128. https://doi. org/10.1002/pro.3280.

Khan, K., Karim, F., Ganga, Y., Bernstein, M., Jule, Z., Reedoy, K., Cele, S., Lustig, G., Amoako, D., Wolter, N., et al. (2022). Omicron sub-lineages BA.4/ BA.5 escape BA.1 infection elicited neutralizing immunity. Preprint at medRxiv. https://doi.org/10.1101/2022.1104.1129.22274477.

Khare, S., Gurry, C., Freitas, L., Schultz, M.B., Bach, G., Diallo, A., Akite, N., Ho, J., Lee, R.T., Yeo, W., et al. (2021). GISAID’s role in pandemic response. China CDC Wkly. 3, 1049–1051. https://doi.org/10.46234/ccdcw2021.255.

Kim, C., Ryu, D.K., Lee, J., Kim, Y.I., Seo, J.M., Kim, Y.G., Jeong, J.H., Kim, M.,

Kim, J.I., Kim, P., et al. (2021). A therapeutic neutralizing antibody targeting re- ceptor binding domain of SARS-CoV-2 spike protein. Nat. Commun. 12, 288. https://doi.org/10.1038/s41467-020-20602-5.

Kimura, I., Kosugi, Y., Wu, J., Zahradnik, J., Yamasoba, D., Butlertanaka, E.P., Tanaka, Y.L., Uriu, K., Liu, Y., Morizako, N., et al. (2022a). The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep. 38, 110218. https://doi.org/10.1016/j.celrep.2021.110218.

Kimura, I., Yamasoba, D., Nasser, H., Zahradnik, J., Kosugi, Y., Wu, J., Nagata, K., Uriu, K., Tanaka, Y.L., Ito, J., et al. (2022b). SARS-CoV-2 spike S375F mu- tation characterizes the Omicron BA.1 variant. Preprint at bioRxiv. https://doi. org/10.1101/2022.1104.1103.486864.

Kimura, I., Yamasoba, D., Tamura, T., Nao, N., Suzuki, T., Oda, Y., Mitoma, S., Ito, J., Nasser, H., Zahradnik, J., et al. (2022c). Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.4 and BA.5. Cell 185, 2103– 2115.e19. https://doi.org/10.1016/j.cell.2022.1009.1018.

Kislaya, I., Casaca, P., Borges, V., et al. (2022). SARS-CoV-2 BA.5 vaccine breakthrough risk and severity compared with BA.2: a case-case and cohort study using electronic health records in Portugal. Preprint at medRxiv. https://doi.org/10.1101/2022.1107.1125.22277996.

Kondo, N., Miyauchi, K., and Matsuda, Z. (2011). Monitoring viral-mediated membrane fusion using fluorescent reporter methods. Curr. Protoc. Cell Biol. Chapter. Unit 26.9. https://doi.org/10.1002/0471143030.cb2609s50.

Konishi, S., Gotoh, S., Tateishi, K., Yamamoto, Y., Korogi, Y., Nagasaki, T., Matsumoto, H., Muro, S., Hirai, T., Ito, I., et al. (2016). Directed induction of functional multi-ciliated cells in proximal airway epithelial spheroids from hu- man pluripotent stem cells. Stem Cell Rep. 6, 18–25. https://doi.org/10. 1016/j.stemcr.2015.11.010.

Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215–220. https://doi.org/ 10.1038/s41586-020-2180-5.

Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100. https://doi.org/10.1093/bioinformatics/bty191.

Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760. https://doi.org/ 10.1093/bioinformatics/btp324.

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R.; 1000 Genome Project Data Processing Subgroup (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. https://doi.org/10.1093/bioinformatics/ btp352.

Liu, L., Iketani, S., Guo, Y., Chan, J.F., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M.S., et al. (2021). Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature 602, 676–681. https://doi.org/ 10.1038/d41586-41021-03826-41583.

Liu, L., Wang, P., Nair, M.S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J.F., Sahi, V., Figueroa, A., et al. (2020). Potent neutralizing antibodies against mul- tiple epitopes on SARS-CoV-2 spike. Nature 584, 450–456. https://doi.org/10. 1038/s41586-020-2571-7.

Liu, Y., Arase, N., Kishikawa, J.-i., Hirose, M., Li, S., Tada, A., Matsuoka, S., Arakawa, A., Akamatsu, K., Ono, C., et al. (2021). The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines. Preprint at bioRxiv. https://doi.org/10.1101/2021.1108.1122.457114.

Lok, S.M. (2021). An NTD Supersite of attack. Cell Host Microbe 29, 744–746. https://doi.org/10.1016/j.chom.2021.04.010.

Lyke, K.E., Atmar, R.L., Islas, C.D., Posavad, C.M., Szydlo, D., Paul Chourdhury, R., Deming, M.E., Eaton, A., Jackson, L.A., Branche, A.R., et al. (2022). Rapid decline in vaccine-boosted neutralizing antibodies against SARS-CoV-2 Omicron variant. Cell Rep. Med. 3, 100679. https://doi.org/10. 1016/j.xcrm.2022.100679.

Matsuyama, S., Nao, N., Shirato, K., Kawase, M., Saito, S., Takayama, I., Nagata, N., Sekizuka, T., Katoh, H., Kato, F., et al. (2020). Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc. Natl. Acad. Sci. USA 117, 7001–7003. https://doi.org/10.1073/pnas.2002589117.

McCallum, M., De Marco, A., Lempp, F.A., Tortorici, M.A., Pinto, D., Walls, A.C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021). N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell 184, 2332–2347.e16. https://doi.org/10.1016/j.cell.2021.03.028.

Meng, B., Abdullahi, A., Ferreira, I.A.T.M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P.P., Fatihi, S., Rathore, S., et al. (2022). Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fuso- genicity. Nature 603, 706–714. https://doi.org/10.1038/s41586-022-04474-x.

Mirdita, M., Schu€tze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., and Steinegger, M. (2022). ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682. https://doi.org/10.1038/s41592-022-01488-1.

Mittal, A., Khattri, A., and Verma, V. (2022). Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants. PLOS Pathog. 18. e1010260. https://doi.org/10.1371/journal.ppat.1010260.

Motozono, C., Toyoda, M., Zahradnik, J., Saito, A., Nasser, H., Tan, T.S., Ngare, I., Kimura, I., Uriu, K., Kosugi, Y., et al. (2021). SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 29, 1124–1136.e11. https://doi.org/10.1016/j.chom.2021.06.006.

Niwa, H., Yamamura, K., and Miyazaki, J. (1991). Efficient selection for high- expression transfectants with a novel eukaryotic vector. Gene 108, 193–199. https://doi.org/10.1016/0378-1119(91)90434-d.

Ozono, S., Zhang, Y., Ode, H., Sano, K., Tan, T.S., Imai, K., Miyoshi, K., Kishigami, S., Ueno, T., Iwatani, Y., et al. (2021). SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat. Commun. 12, 848. https://doi.org/10.1038/s41467-021-21118-2.

Ozono, S., Zhang, Y., Tobiume, M., Kishigami, S., and Tokunaga, K. (2020). Super-rapid quantitation of the production of HIV-1 harboring a luminescent peptide tag. J. Biol. Chem. 295, 13023–13030. https://doi.org/10.1074/jbc. RA120.013887.

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612. https://doi.org/10.1002/jcc.20084.

Pinto, D., Park, Y.J., Beltramello, M., Walls, A.C., Tortorici, M.A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290–295. https://doi.org/10.1038/s41586-020-2349-y.

Planas, D., Saunders, N., Maes, P., Guivel-Benhassine, F., Planchais, C., Buchrieser, J., Bolland, W.H., Porrot, F., Staropoli, I., Lemoine, F., et al. (2021). Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature 602, 671–675. https://doi.org/10.1038/d41586-41021-03827-41582.

Punjani, A., Rubinstein, J.L., Fleet, D.J., and Brubaker, M.A. (2017). cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determina- tion. Nat. Methods 14, 290–296. https://doi.org/10.1038/nmeth.4169.

Qu, P., Faraone, J., Evans, J.P., Zou, X., Zheng, Y.M., Carlin, C., Bednash, J.S., Lozanski, G., Mallampalli, R.K., Saif, L.J., et al. (2022). Neutralization of the SARS-CoV-2 omicron BA.4/5 and BA.2.12.1 Subvariants. N. Engl. J. Med. 386, 2526–2528. https://doi.org/10.1056/NEJMc2206725.

Reed, L.J., and Muench, H. (1938). A simple method of estimating fifty percent endpoints. Am. J. Hyg. 27, 493–497.

Reeves, P.J., Callewaert, N., Contreras, R., and Khorana, H.G. (2002). Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N- acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl. Acad. Sci. USA 99, 13419–13424. https://doi.org/10.1073/ pnas.212519299.

Saito, A., Irie, T., Suzuki, R., Maemura, T., Nasser, H., Uriu, K., Kosugi, Y., Shirakawa, K., Sadamasu, K., Kimura, I., et al. (2022). Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 602, 300–306. https://doi.org/10.1038/s41586-021-04266-9.

Sano, E., Suzuki, T., Hashimoto, R., Itoh, Y., Sakamoto, A., Sakai, Y., Saito, A., Okuzaki, D., Motooka, D., Muramoto, Y., et al. (2022). Cell response analysis in SARS-CoV-2 infected bronchial organoids. Commun. Biol. 5, 516. https://doi. org/10.1038/s42003-022-03499-2.

Shen, X., Chalkias, S., Feng, J., Chen, X., Zhou, H., Marshall, J.C., Girard, B., Tomassini, J.E., Aunins, A., Das, R., et al. (2022). Neutralization of SARS-CoV-2 omicron BA.2.75 after mRNA-1273 Vaccination. N. Engl. J. Med. 387, 1234–1236. https://doi.org/10.1056/NEJMc2210648.

Stalls, V., Lindenberger, J., Gobeil, S.M., Henderson, R., Parks, R., Barr, M., Deyton, M., Martin, M., Janowska, K., Huang, X., et al. (2022). Cryo-EM struc- tures of SARS-CoV-2 Omicron BA.2 spike. Cell Rep. 39, 111009. https://doi. org/10.1016/j.celrep.2022.111009.

Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. https:// doi.org/10.1093/bioinformatics/btu033.

Suryadevara, N., Shrihari, S., Gilchuk, P., VanBlargan, L.A., Binshtein, E., Zost, S.J., Nargi, R.S., Sutton, R.E., Winkler, E.S., Chen, E.C., et al. (2021). Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein. Cell 184, 2316– 2331.e15. https://doi.org/10.1016/j.cell.2021.03.029.

Suzuki, R., Yamasoba, D., Kimura, I., Wang, L., Kishimoto, M., Ito, J., Morioka, Y., Nao, N., Nasser, H., Uriu, K., et al. (2022). Attenuated fusogenicity and path- ogenicity of SARS-CoV-2 Omicron variant. Nature 603, 700–705. https://doi. org/10.1038/s41586-022-04462-1.

Takashita, E., Kinoshita, N., Yamayoshi, S., Sakai-Tagawa, Y., Fujisaki, S., Ito, M., Iwatsuki-Horimoto, K., Chiba, S., Halfmann, P., Nagai, H., et al. (2022). Efficacy of antibodies and antiviral drugs against Covid-19 Omicron variant. N. Engl. J. Med. 386, 995–998. https://doi.org/10.1056/NEJMc2119407.

Takashita, E., Kinoshita, N., Yamayoshi, S., Sakai-Tagawa, Y., Fujisaki, S., Ito, M., Iwatsuki-Horimoto, K., Halfmann, P., Watanabe, S., Maeda, K., et al. (2022). Efficacy of antiviral agents against the SARS-CoV-2 Omicron subvar- iant BA.2. N. Engl. J. Med. 386, 1475–1477. https://doi.org/10.1056/ NEJMc2201933.

Tamura, T., Yamasoba, D., Oda, Y., Ito, J., Kamasaki, T., Nao, N., Hashimoto, R., Fujioka, Y., Suzuki, R., Wang, L., et al. (2022). Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5. Preprint at bioRxiv. https://doi.org/10.1101/2022.1108.1105.502758.

Tuekprakhon, A., Nutalai, R., Dijokaite-Guraliuc, A., Zhou, D., Ginn, H.M., Selvaraj, M., Liu, C., Mentzer, A.J., Supasa, P., Duyvesteyn, H.M.E., et al. (2022). Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell 185, 2422–2433.e13. https://doi.org/10.1016/j.cell.2022. 06.005.

Uriu, K., Ca´ rdenas, P., Mun˜ oz, E., Barragan, V., Kosugi, Y., Shirakawa, K., Takaori-Kondo, A.; Ecuador-COVID19 Consortium, The Genotype to Phenotype Japan (G2P-Japan) Consortium, and Sato, K. (2022). Characterization of the immune resistance of SARS-CoV-2 Mu variant and the robust immunity induced by Mu infection. J. Infect. Dis. 226, 1200–1203. https://doi.org/10.1093/infdis/jiac053.

Uriu, K., Kimura, I., Shirakawa, K., Takaori-Kondo, A., Nakada, T.A., Kaneda, A., Nakagawa, S., and Sato, K.; Genotype to Phenotype Japan (G2P-Japan) Consortium (2021). Neutralization of the SARS-CoV-2 Mu variant by convales- cent and vaccine serum. N. Engl. J. Med. 385, 2397–2399. https://doi.org/10. 1056/NEJMc2114706.

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., and Diamond, M.S. (2022). An in- fectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by ther- apeutic monoclonal antibodies. Nat. Med. 28, 490–495. https://doi.org/10. 1038/s41591-021-01678-y.

Voss, W.N., Hou, Y.J., Johnson, N.V., Delidakis, G., Kim, J.E., Javanmardi, K., Horton, A.P., Bartzoka, F., Paresi, C.J., Tanno, Y., et al. (2021). Prevalent, pro- tective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epi- topes. Science 372, 1108–1112. https://doi.org/10.1126/science.abg5268.

Wang, Q., Guo, Y., Iketani, S., Nair, M.S., Li, Z., Mohri, H., Wang, M., Yu, J., Bowen, A.D., Chang, J.Y., et al. (2022). Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5, & BA.5. Nature 608, 603–608. https://doi.org/10.1038/s41586-022-05053-w.

Westendorf, K., Zˇentelis, S., Wang, L., Foster, D., Vaillancourt, P., Wiggin, M., Lovett, E., van der Lee, R., Hendle, J., Pustilnik, A., et al. (2022). LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Cell Rep. 39, 110812. https://doi.org/10.1016/j.celrep.2022.110812.

WHO (2022). Tracking SARS-CoV-2 variants (July 19, 2022). https://www.who. int/en/activities/tracking-SARS-CoV-2-variants.

Williams, C.J., Headd, J.J., Moriarty, N.W., Prisant, M.G., Videau, L.L., Deis, L.N., Verma, V., Keedy, D.A., Hintze, B.J., Chen, V.B., et al. (2018). MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315. https://doi.org/10.1002/pro.3330.

Xiao, T., Lu, J., Zhang, J., Johnson, R.I., McKay, L.G.A., Storm, N., Lavine, C.L., Peng, H., Cai, Y., Rits-Volloch, S., et al. (2021). A trimeric human angio- tensin-converting enzyme 2 as an anti-SARS-CoV-2 agent. Nat. Struct. Mol. Biol. 28, 202–209. https://doi.org/10.1038/s41594-020-00549-3.

Yamamoto, M., Kiso, M., Sakai-Tagawa, Y., Iwatsuki-Horimoto, K., Imai, M., Takeda, M., Kinoshita, N., Ohmagari, N., Gohda, J., Semba, K., et al. (2020). The anticoagulant nafamostat potently inhibits SARS-CoV-2 S protein-medi- ated fusion in a cell fusion assay system and viral infection in vitro in a cell- yype-dependent manner. Viruses 12, 629. https://doi.org/10.3390/ v12060629.

Yamamoto, Y., Gotoh, S., Korogi, Y., Seki, M., Konishi, S., Ikeo, S., Sone, N., Nagasaki, T., Matsumoto, H., Muro, S., et al. (2017). Long-term expansion of alveolar stem cells derived from human iPS cells in organoids. Nat. Methods 14, 1097–1106. https://doi.org/10.1038/nmeth.4448.

Yamasoba, D., Kimura, I., Nasser, H., Morioka, Y., Nao, N., Ito, J., Uriu, K., Tsuda, M., Zahradnik, J., Shirakawa, K., et al. (2022a). Virological characteris- tics of the SARS-CoV-2 Omicron BA.2 spike. Cell 185, 2103–2115.e19. https:// doi.org/10.1016/j.cell.2022.04.035.

Yamasoba, D., Kosugi, Y., Kimura, I., Fujita, S., Uriu, K., Ito, J., and Sato, K.; Genotype to Phenotype Japan (G2P-Japan) Consortium (2022b). Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies. Lancet Infect. Dis. 22, 942–943. https://doi.org/10. 1016/S1473-3099(22)00365-6.

Zahradnı´k, J., Dey, D., Marciano, S., Kola´ˇrova´ , L., Charendoff, C.I., Subtil, A., and Schreiber, G. (2021a). A protein-engineered, enhanced yeast display plat- form for rapid evolution of challenging targets. ACS Synth. Biol. 10, 3445– 3460. https://doi.org/10.1021/acssynbio.1c00395.

Zahradnı´k, J., Marciano, S., Shemesh, M., Zoler, E., Harari, D., Chiaravalli, J., Meyer, B., Rudich, Y., Li, C., Marton, I., et al. (2021b). SARS-CoV-2 variant pre- diction and antiviral drug design are enabled by RBD in vitro evolution. Nat. Microbiol. 6, 1188–1198. https://doi.org/10.1038/s41564-021-00954-4.