Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.

1st Medical Faculty at Biocev Charles University Vestec Prague Czechia

AMED CREST Japan Agency for Medical Research and Development Tokyo Japan

Bioinformation and DDBJ Center National Institute of Genetics Mishima Japan

Center for Animal Disease Control University of Miyazaki Miyazaki Japan

Center for iPS Cell Research and Application Kyoto University Kyoto Japan

Collaboration Unit for Infection Joint Research Center for Human Retrovirus infection Kumamoto University Kumamoto Japan

CREST Japan Science and Technology Agency Saitama Japan

Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel

Department of Clinical Pathology Faculty of Medicine Suez Canal University Ismailia Egypt

Department of Hematology and Oncology Graduate School of Medicine Kyoto University Kyoto Japan

Department of Microbiology and Immunology Faculty of Medicine Hokkaido University Sapporo Japan

Department of Molecular Life Science Tokai University School of Medicine Isehara Japan

Department of Veterinary Science Faculty of Agriculture University of Miyazaki Miyazaki Japan

Division of Molecular Virology and Genetics Joint Research Center for Human Retrovirus infection Kumamoto University Kumamoto Japan

Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan

Faculty of Medicine Kobe University Kobe Japan

Graduate School of Biomedical and Health Sciences Hiroshima University Hiroshima Japan

Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan

Graduate School of Medicine and Veterinary Medicine University of Miyazaki Miyazaki Japan

Graduate School of Medicine The University of Tokyo Tokyo Japan

Institute for Genetic Medicine Hokkaido University Sapporo Japan

Institute for Vaccine Research and Development Hokkaido University Sapporo Japan

International Research Center for Infectious Diseases The Institute of Medical Science The University of Tokyo Tokyo Japan

International Vaccine Design Center The Institute of Medical Science The University of Tokyo Tokyo Japan

Laboratory of Medical Virology Institute for Life and Medical Sciences Kyoto University Kyoto Japan

Laboratory of Virus Control Research Institute for Microbial Diseases Osaka University Suita Japan

Tokyo Metropolitan Institute of Public Health Tokyo Japan

Zobrazit více v PubMed

WHO . 2022. Tracking SARS-CoV-2 variants. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants

Suzuki R, Yamasoba D, Kimura I, Wang L, Kishimoto M, Ito J, Morioka Y, Nao N, Nasser H, Uriu K, Kosugi Y, Tsuda M, Orba Y, Sasaki M, Shimizu R, Kawabata R, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Sawa H, Ikeda T, Irie T, Matsuno K, Tanaka S, Fukuhara T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature 603:700–705. doi:10.1038/s41586-022-04462-1 PubMed DOI PMC

Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, Uriu K, Tsuda M, Zahradnik J, Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K, Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L, Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A, Shimada T, Nakada T-A, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii KJ, Schreiber G, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T, Ikeda T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Edited by Sawa H., Saito A., Irie T., Tanaka S., Matsuno K., Fukuhara T., and Ikeda T.. Cell 185:2103–2115. doi:10.1016/j.cell.2022.04.035 PubMed DOI PMC

Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Mølbak K, Møller CH, Skov RL, Krause TG, Rasmussen M, Sieber RN, Johannesen TB, Lillebaek T, Fonager J, Fomsgaard A, Møller FT, Stegger M, Overvad M, Spiess K, Mortensen LH. 2022. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark. Nat Commun 13:5760. doi:10.1038/s41467-022-33498-0 PubMed DOI PMC

Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium . 2022. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature 603:706–714. doi:10.1038/s41586-022-04474-x PubMed DOI PMC

Kimura I, Yamasoba D, Nasser H, Zahradnik J, Kosugi Y, Wu J, Nagata K, Uriu K, Tanaka YL, Ito J, Shimizu R, Tan TS, Butlertanaka EP, Asakura H, Sadamasu K, Yoshimura K, Ueno T, Takaori-Kondo A, Schreiber G, Toyoda M, Shirakawa K, Irie T, Saito A, Nakagawa S, Ikeda T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. iScience 25:105720. doi:10.1016/j.isci.2022.105720 PubMed DOI PMC

Li L, Liao H, Meng Y, Li W, Han P, Liu K, Wang Q, Li D, Zhang Y, Wang L, Fan Z, Zhang Y, Wang Q, Zhao X, Sun Y, Huang N, Qi J, Gao GF. 2022. Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell 185:2952–2960. doi:10.1016/j.cell.2022.06.023 PubMed DOI PMC

Starr TN, Greaney AJ, Stewart CM, Walls AC, Hannon WW, Veesler D, Bloom JD. 2022. Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains. PLoS Pathog 18:e1010951. doi:10.1371/journal.ppat.1010951 PubMed DOI PMC

Takashita E, Kinoshita N, Yamayoshi S, Sakai-Tagawa Y, Fujisaki S, Ito M, Iwatsuki-Horimoto K, Halfmann P, Watanabe S, Maeda K, Imai M, Mitsuya H, Ohmagari N, Takeda M, Hasegawa H, Kawaoka Y. 2022. Efficacy of antiviral agents against the SARS-CoV-2 Omicron subvariant BA.2. N Engl J Med 386:1475–1477. doi:10.1056/NEJMc2201933 PubMed DOI PMC

Case JB, Mackin S, Errico JM, Chong Z, Madden EA, Whitener B, Guarino B, Schmid MA, Rosenthal K, Ren K, Dang HV, Snell G, Jung A, Droit L, Handley SA, Halfmann PJ, Kawaoka Y, Crowe JE, Fremont DH, Virgin HW, Loo Y-M, Esser MT, Purcell LA, Corti D, Diamond MS. 2022. Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains. Nat Commun 13:3824. doi:10.1038/s41467-022-31615-7 PubMed DOI PMC

Uraki R, Kiso M, Iida S, Imai M, Takashita E, Kuroda M, Halfmann PJ, Loeber S, Maemura T, Yamayoshi S, Fujisaki S, Wang Z, Ito M, Ujie M, Iwatsuki-Horimoto K, Furusawa Y, Wright R, Chong Z, Ozono S, Yasuhara A, Ueki H, Sakai-Tagawa Y, Li R, Liu Y, Larson D, Koga M, Tsutsumi T, Adachi E, Saito M, Yamamoto S, Hagihara M, Mitamura K, Sato T, Hojo M, Hattori S-I, Maeda K, Valdez R, Okuda M, Murakami J, Duong C, Godbole S, Douek DC, Maeda K, Watanabe S, Gordon A, Ohmagari N, Yotsuyanagi H, Diamond MS, Hasegawa H, Mitsuya H, Suzuki T, Kawaoka Y, IASO study team . 2022. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron/BA.2. Nature 607:119–127. doi:10.1038/s41586-022-04856-1 PubMed DOI PMC

Tamura T, Yamasoba D, Oda Y, Ito J, Kamasaki T, Nao N, Hashimoto R, Fujioka Y, Suzuki R, Wang L, Ito H, Kimura I, Yokota I, Kishimoto M, Tsuda M, Sawa H, Yoshimatsu K, Ohba Y, Yamamoto Y, Nagamoto T, Kanamune J, Matsuno K, Takayama K, Tanaka S, Sato K, Fukuhara T, The Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5. Microbiology. doi:10.1101/2022.08.05.502758 PubMed DOI PMC

Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao N-Y, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. 2022. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in Southern Africa. Nature 603:679–686. doi:10.1038/s41586-022-04411-y PubMed DOI PMC

Kimura I, Yamasoba D, Tamura T, Nao N, Suzuki T, Oda Y, Mitoma S, Ito J, Nasser H, Zahradnik J, Uriu K, Fujita S, Kosugi Y, Wang L, Tsuda M, Kishimoto M, Ito H, Suzuki R, Shimizu R, Begum MM, Yoshimatsu K, Kimura KT, Sasaki J, Sasaki-Tabata K, Yamamoto Y, Nagamoto T, Kanamune J, Kobiyama K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Shirakawa K, Takaori-Kondo A, Kuramochi J, Schreiber G, Ishii KJ, Hashiguchi T, Ikeda T, Saito A, Fukuhara T, Tanaka S, Matsuno K, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.4 and BA.5. Cell 185:3992–4007. doi:10.1016/j.cell.2022.09.018 PubMed DOI PMC

Saito A, Irie T, Suzuki R, Maemura T, Nasser H, Uriu K, Kosugi Y, Shirakawa K, Sadamasu K, Kimura I, Ito J, Wu J, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Loeber S, Tsuda M, Wang L, Ozono S, Butlertanaka EP, Tanaka YL, Shimizu R, Shimizu K, Yoshimatsu K, Kawabata R, Sakaguchi T, Tokunaga K, Yoshida I, Asakura H, Nagashima M, Kazuma Y, Nomura R, Horisawa Y, Yoshimura K, Takaori-Kondo A, Imai M, Tanaka S, Nakagawa S, Ikeda T, Fukuhara T, Kawaoka Y, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 602:300–306. doi:10.1038/s41586-021-04266-9 PubMed DOI PMC

Nasser H, Shimizu R, Ito J, Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Sato K, Ikeda T. 2022. Monitoring fusion kinetics of viral and target cell membranes in living cells using a SARS-CoV-2 spike-protein-mediated membrane fusion assay. STAR Protoc 3:101773. doi:10.1016/j.xpro.2022.101773 PubMed DOI PMC

Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang K-Y, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, OPTIC Consortium, ISARIC4C Consortium, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. 2022. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 185:467–484. doi:10.1016/j.cell.2021.12.046 PubMed DOI PMC

Bruel T, Hadjadj J, Maes P, Planas D, Seve A, Staropoli I, Guivel-Benhassine F, Porrot F, Bolland W-H, Nguyen Y, Casadevall M, Charre C, Péré H, Veyer D, Prot M, Baidaliuk A, Cuypers L, Planchais C, Mouquet H, Baele G, Mouthon L, Hocqueloux L, Simon-Loriere E, André E, Terrier B, Prazuck T, Schwartz O. 2022. Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies. Nat Med 28:1297–1302. doi:10.1038/s41591-022-01792-5 PubMed DOI

Cao Y, Yisimayi A, Jian F, Song W, Xiao T, Wang L, Du S, Wang J, Li Q, Chen X, Yu Y, Wang P, Zhang Z, Liu P, An R, Hao X, Wang Y, Wang J, Feng R, Sun H, Zhao L, Zhang W, Zhao D, Zheng J, Yu L, Li C, Zhang N, Wang R, Niu X, Yang S, Song X, Chai Y, Hu Y, Shi Y, Zheng L, Li Z, Gu Q, Shao F, Huang W, Jin R, Shen Z, Wang Y, Wang X, Xiao J, Xie XS. 2022. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 608:593–602. doi:10.1038/s41586-022-04980-y PubMed DOI PMC

Zhou H, Dcosta BM, Landau NR, Tada T. 2022. Resistance of SARS-CoV-2 Omicron BA.1 and BA.2 variants to vaccine-elicited sera and therapeutic monoclonal antibodies. Viruses 14:1334. doi:10.3390/v14061334 PubMed DOI PMC

Torii S, Ono C, Suzuki R, Morioka Y, Anzai I, Fauzyah Y, Maeda Y, Kamitani W, Fukuhara T, Matsuura Y. 2021. Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction. Cell Rep 35:109014. doi:10.1016/j.celrep.2021.109014 PubMed DOI PMC

Matsuyama S, Nao N, Shirato K, Kawase M, Saito S, Takayama I, Nagata N, Sekizuka T, Katoh H, Kato F, Sakata M, Tahara M, Kutsuna S, Ohmagari N, Kuroda M, Suzuki T, Kageyama T, Takeda M. 2020. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc Natl Acad Sci U S A 117:7001–7003. doi:10.1073/pnas.2002589117 PubMed DOI PMC

Hashimoto R, Takahashi J, Shirakura K, Funatsu R, Kosugi K, Deguchi S, Yamamoto M, Tsunoda Y, Morita M, Muraoka K, Tanaka M, Kanbara T, Tanaka S, Tamiya S, Tokunoh N, Kawai A, Ikawa M, Ono C, Tachibana K, Kondoh M, Obana M, Matsuura Y, Ohsumi A, Noda T, Yamamoto T, Yoshioka Y, Torisawa Y-S, Date H, Fujio Y, Nagao M, Takayama K, Okada Y. 2022. SARS-CoV-2 disrupts the respiratory vascular barrier by suppressing Claudin-5 expression. Sci Adv 8:eabo6783. doi:10.1126/sciadv.abo6783 PubMed DOI PMC

Saito A, Tamura T, Zahradnik J, Deguchi S, Tabata K, Anraku Y, Kimura I, Ito J, Yamasoba D, Nasser H, Toyoda M, Nagata K, Uriu K, Kosugi Y, Fujita S, Shofa M, Monira Begum M, Shimizu R, Oda Y, Suzuki R, Ito H, Nao N, Wang L, Tsuda M, Yoshimatsu K, Kuramochi J, Kita S, Sasaki-Tabata K, Fukuhara H, Maenaka K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Ueno T, Schreiber G, Takaori-Kondo A, Shirakawa K, Sawa H, Irie T, Hashiguchi T, Takayama K, Matsuno K, Tanaka S, Ikeda T, Fukuhara T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant. Cell Host Microbe 30:1540–1555. doi:10.1016/j.chom.2022.10.003 PubMed DOI PMC

McGrath ME, Xue Y, Dillen C, Oldfield L, Assad-Garcia N, Zaveri J, Singh N, Baracco L, Taylor LJ, Vashee S, Frieman MB. 2022. SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis. Proc Natl Acad Sci U S A 119:e2204717119. doi:10.1073/pnas.2204717119 PubMed DOI PMC

Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. 2022. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun 13:4337. doi:10.1038/s41467-022-31930-z PubMed DOI PMC

Silvas JA, Vasquez DM, Park J-G, Chiem K, Allué-Guardia A, Garcia-Vilanova A, Platt RN, Miorin L, Kehrer T, Cupic A, Gonzalez-Reiche AS, Bakel H van, García-Sastre A, Anderson T, Torrelles JB, Ye C, Martinez-Sobrido L. 2021. Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 human ACE2 transgenic mice. J Virol 95:e0040221. doi:10.1128/JVI.00402-21 PubMed DOI PMC

Nemudryi A, Nemudraia A, Wiegand T, Nichols J, Snyder DT, Hedges JF, Cicha C, Lee H, Vanderwood KK, Bimczok D, Jutila MA, Wiedenheft B. 2021. SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7A that limits immune suppression. Cell Rep 35:109197. doi:10.1016/j.celrep.2021.109197 PubMed DOI PMC

Kohyama M, Suzuki T, Nakai W, Ono C, Matsuoka S, Iwatani K, Liu Y, Sakai Y, Nakagawa A, Tomii K, Ohmura K, Okada M, Matsuura Y, Ohshima S, Maeda Y, Okamoto T, Arase H. 2023. SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses. Int Immunol 35:43–52. doi:10.1093/intimm/dxac044 PubMed DOI PMC

Zahradník J, Nunvar J, Schreiber G. 2022. Perspectives: SARS-CoV-2 spike convergent evolution as a guide to explore adaptive advantage. Front Cell Infect Microbiol 12:748948. doi:10.3389/fcimb.2022.748948 PubMed DOI PMC

Upadhyay V, Patrick C, Lucas A, Mallela KMG. 2022. Convergent evolution of multiple mutations improves the viral fitness of SARS-CoV-2 variants by balancing positive and negative selection. Biochemistry 61:963–980. doi:10.1021/acs.biochem.2c00132 PubMed DOI

Focosi D, McConnell S, Casadevall A. 2022. The Omicron variant of concern: diversification and convergent evolution in spike protein, and escape from anti-spike monoclonal antibodies. Drug Resist Updat 65:100882. doi:10.1016/j.drup.2022.100882 PubMed DOI PMC

Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, Williamson C, Hsiao N, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Crandall K. 2022. Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact spike function. Evol biol 39. doi:10.1093/molbev/msac061 PubMed DOI PMC

Chen D-Y, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O’Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. 2023. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature 615:143–150. doi:10.1038/s41586-023-05697-2 PubMed DOI

Pastorio C, Zech F, Noettger S, Jung C, Jacob T, Sanderson T, Sparrer KMJ, Kirchhoff F. 2022. Determinants of spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Cell Host Microbe 30:1255–1268. doi:10.1016/j.chom.2022.07.006 PubMed DOI PMC

Ozono S, Zhang Y, Ode H, Sano K, Tan TS, Imai K, Miyoshi K, Kishigami S, Ueno T, Iwatani Y, Suzuki T, Tokunaga K. 2021. SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat Commun 12:848. doi:10.1038/s41467-021-21118-2 PubMed DOI PMC

Ferreira I, Kemp SA, Datir R, Saito A, Meng B, Rakshit P, Takaori-Kondo A, Kosugi Y, Uriu K, Kimura I, Shirakawa K, Abdullahi A, Agarwal A, Ozono S, Tokunaga K, Sato K, Gupta RK, CITIID-NIHR BioResource COVID-19 Collaboration, Indian SARS-CoV-2 Genomics Consortium, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2021. SARS-CoV-2 B.1.617 mutations L452R and E484Q are not synergistic for antibody evasion. J Infect Dis 224:989–994. doi:10.1093/infdis/jiab368 PubMed DOI PMC

Fujita S, Kosugi Y, Kimura I, Yamasoba D, Sato K. 2022. Structural insight into the resistance of the SARS-CoV-2 Omicron BA.4 and BA.5 variants to Cilgavimab. Viruses 14:2677. doi:10.3390/v14122677 PubMed DOI PMC

Majumdar S, Sarkar R. 2022. Mutational and phylogenetic analyses of the two lineages of the Omicron variant. J Med Virol 94:1777–1779. doi:10.1002/jmv.27558 PubMed DOI PMC

Wang L, Cheng G. 2022. Sequence analysis of the emerging SARS-CoV-2 variant Omicron in South Africa. J Med Virol 94:1728–1733. doi:10.1002/jmv.27516 PubMed DOI

Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. 2015. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003. doi:10.1093/ve/vev003 PubMed DOI PMC

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. doi:10.1093/molbev/mst010 PubMed DOI PMC

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530–1534. doi:10.1093/molbev/msaa131 PubMed DOI PMC

Yu G, Lam TT-Y, Zhu H, Guan Y. 2018. Two methods for mapping and visualizing associated data on phylogeny using Ggtree. Mol Biol Evol 35:3041–3043. doi:10.1093/molbev/msy194 PubMed DOI PMC

Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, Akite N, Ho J, Lee RT, Yeo W, Curation Team GC, Maurer-Stroh S. 2021. GISAID's role in pandemic response. China CDC Wkly 3:1049–1051. doi:10.46234/ccdcw2021.255 PubMed DOI PMC

Aksamentov I, Roemer C, Hodcroft EB, Neher RA. 2021. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw 6:3773. doi:10.21105/joss.03773 DOI

Gu Z, Eils R, Schlesner M. 2016. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32:2847–2849. doi:10.1093/bioinformatics/btw313 PubMed DOI

Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, Ikeda T, Nakagawa S, Ueno T, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2021. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Edited by Ikeda T., Nakagawa S., Ueno T., and Sato K.. Cell Host Microbe 29:1124–1136. doi:10.1016/j.chom.2021.06.006 PubMed DOI PMC

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

Peleg Y, Unger T. 2014. Application of the restriction-free (RF) cloning for multicomponents assembly. Methods Mol Biol 1116:73–87. doi:10.1007/978-1-62703-764-8_6 PubMed DOI

Zahradník J, Marciano S, Shemesh M, Zoler E, Harari D, Chiaravalli J, Meyer B, Rudich Y, Li C, Marton I, Dym O, Elad N, Lewis MG, Andersen H, Gagne M, Seder RA, Douek DC, Schreiber G. 2021. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol 6:1188–1198. doi:10.1038/s41564-021-00954-4 PubMed DOI

Kondo N, Miyauchi K, Matsuda Z. 2011. Monitoring viral-mediated membrane fusion using fluorescent reporter methods. Curr Protoc Cell Biol Chapter 26:Unit. doi:10.1002/0471143030.cb2609s50 PubMed DOI

Uriu K, Kimura I, Shirakawa K, Takaori-Kondo A, Nakada T-A, 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. N Engl J Med 385:2397–2399. doi:10.1056/NEJMc2114706 PubMed DOI PMC

Uriu K, Cárdenas P, Muñoz E, Barragan V, Kosugi Y, Shirakawa K, Takaori-Kondo A, Sato K, Ecuador-COVID19 Consortium, The Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Characterization of the immune resistance of severe acute respiratory syndrome Coronavirus 2 Mu variant and the robust immunity induced by Mu infection. J Infect Dis 226:1200–1203. doi:10.1093/infdis/jiac053 PubMed DOI PMC

Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, Motozono C, Saito A, Nakagawa S, Sato K, The Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. The SARS-CoV-2 lambda variant exhibits enhanced infectivity and immune resistance. Edited by Motozono C., Saito A., Nakagawa S., and Sato K.. Cell Rep 38:110218. doi:10.1016/j.celrep.2021.110218 PubMed DOI PMC

Yamasoba D, Kosugi Y, Kimura I, Fujita S, Uriu K, Ito J, Sato K, Genotype to Phenotype Japan (G2P-Japan) Consortium . 2022. Neutralisation sensitivity of SARS-CoV-2 Omicron subvariants to therapeutic monoclonal antibodies. Lancet Infect Dis 22:942–943. doi:10.1016/S1473-3099(22)00365-6 PubMed DOI PMC

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

Zahradník J, Dey D, Marciano S, Kolářová L, Charendoff CI, Subtil A, Schreiber G. 2021. A protein-engineered, enhanced yeast display platform for rapid evolution of challenging targets. ACS Synth Biol 10:3445–3460. doi:10.1021/acssynbio.1c00395 PubMed DOI PMC

Breitsprecher D, Fung PA, Tschammer N. 2018. Improving biosensor assay development by determining sample quality with Tycho NT.6. Nat Methods 15:298–298. doi:10.1038/nmeth.f.406 DOI

Ito J, Suzuki R, Uriu K, Itakura Y, Zahradnik J, Kimura KT, Deguchi S, Wang L, Lytras S, Tamura T, Kida I, Nasser H, Shofa M, Begum MM, Tsuda M, Oda Y, Suzuki T, Sasaki J, Sasaki-Tabata K, Fujita S, Yoshimatsu K, Ito H, Nao N, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Kuramochi J, Schreiber G, Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito A, Matsuno K, Takayama K, Hashiguchi T, Tanaka S, Fukuhara T, Ikeda T, Sato K. 2023. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nat Commun 14:2671. doi:10.1038/s41467-023-38188-z PubMed DOI PMC

Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, Nasser H, Shofa M, Oda Y, Lytras S, Nao N, Itakura Y, Deguchi S, Suzuki R, Wang L, Begum MM, Kita S, Yajima H, Sasaki J, Sasaki-Tabata K, Shimizu R, Tsuda M, Kosugi Y, Fujita S, Pan L, Sauter D, Yoshimatsu K, Suzuki S, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Schreiber G, Maenaka K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Hashiguchi T, Ikeda T, Fukuhara T, Saito A, Tanaka S, Matsuno K, Takayama K, Sato K. 2023. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun 14:2800. doi:10.1038/s41467-023-38435-3 PubMed DOI PMC

Reed LJ, Muench H. 1938. A simple method of estimating fifty percent endpoints. Am J Epidemiol 27:493–497. doi:10.1093/oxfordjournals.aje.a118408 DOI

Chen S, Zhou Y, Chen Y, Gu J. 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi:10.1093/bioinformatics/bty560 PubMed DOI PMC

Li H, Durbin R. 2009. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754–1760. doi:10.1093/bioinformatics/btp324 PubMed DOI PMC

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

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 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. doi:10.4161/fly.19695 PubMed DOI PMC

Deguchi S, Tsuda M, Kosugi K, Sakamoto A, Mimura N, Negoro R, Sano E, Nobe T, Maeda K, Kusuhara H, Mizuguchi H, Yamashita F, Torisawa YS, Takayama K. 2021. Usability of polydimethylsiloxane-based microfluidic devices in pharmaceutical research using human hepatocytes. ACS Biomater Sci Eng 7:3648–3657. doi:10.1021/acsbiomaterials.1c00642 PubMed DOI

Sano E, Suzuki T, Hashimoto R, Itoh Y, Sakamoto A, Sakai Y, Saito A, Okuzaki D, Motooka D, Muramoto Y, Noda T, Takasaki T, Sakuragi J-I, Minami S, Kobayashi T, Yamamoto T, Matsumura Y, Nagao M, Okamoto T, Takayama K. 2022. Cell response analysis in SARS-CoV-2 infected bronchial organoids. Commun Biol 5:516. doi:10.1038/s42003-022-03499-2 PubMed DOI PMC