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

. 2022 Nov 09 ; 30 (11) : 1540-1555.e15. [epub] 20221018

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid36272413
Odkazy

PubMed 36272413
PubMed Central PMC9578327
DOI 10.1016/j.chom.2022.10.003
PII: S1931-3128(22)00516-9
Knihovny.cz E-zdroje

The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.

Center for iPS Cell Research and Application Kyoto University Kyoto Japan

Center for iPS Cell Research and Application Tokyo Japan

Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel

Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel; 1st Medical Faculty at Biocev Charles University Vestec Prague Czechia

Department of Cancer Pathology Faculty of Medicine Hokkaido University Sapporo Japan

Department of Cancer Pathology Faculty of Medicine Hokkaido University Sapporo Japan; Institute for Chemical Reaction Design and Discovery Hokkaido University Sapporo Japan

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

Department of Medicinal Sciences Graduate School of Pharmaceutical Sciences Kyushu University Fukuoka Japan

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

Department of Microbiology and Immunology Faculty of Medicine Hokkaido University Sapporo Japan; Laboratory of Virus Control Research Institute for Microbial Diseases Osaka University Suita Japan

Department of Veterinary Science Faculty of Agriculture University of Miyazaki Miyazaki Japan; Graduate School of Medicine and Veterinary Medicine University of Miyazaki Miyazaki Japan

Department of Veterinary Science Faculty of Agriculture University of Miyazaki Miyazaki Japan; Graduate School of Medicine and Veterinary Medicine University of Miyazaki Miyazaki Japan; Center for Animal Disease Control University of Miyazaki Miyazaki Japan

Division of Infection and immunity Joint Research Center for Human Retrovirus infection Kumamoto University Kumamoto Japan

Division of International Research Promotion International Institute for Zoonosis Control Hokkaido University Sapporo Japan

Division of Molecular Pathobiology International Institute for Zoonosis Control Hokkaido University Sapporo Japan

Division of Molecular Pathobiology International Institute for Zoonosis Control Hokkaido University Sapporo Japan; Division of International Research Promotion International Institute for Zoonosis Control Hokkaido University Sapporo Japan; One Health Research Center Hokkaido University Sapporo Japan

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

Division of Molecular Virology and Genetics Joint Research Center for Human Retrovirus infection Kumamoto University Kumamoto Japan; Department of Clinical Pathology Faculty of Medicine Suez Canal University Ismailia Egypt

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

Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan; Graduate School of Medicine The University of Tokyo Tokyo Japan

Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan; Graduate School of Medicine The University of Tokyo Tokyo 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; Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan; Collaboration Unit for Infection Joint Research Center for Human Retrovirus infection Kumamoto University Kumamoto Japan; CREST Japan Science and Technology Agency Kawaguchi Japan

Global Station for Biosurfaces and Drug Discovery Hokkaido University Sapporo Japan; Division of Pathogen Structure International Institute for Zoonosis Control Hokkaido University Sapporo Japan

Graduate School of Biomedical and Health Sciences Hiroshima University Hiroshima Japan

HiLung Inc Kyoto Japan

Institute for Genetic Medicine Hokkaido University Sapporo Japan

Interpark Kuramochi Clinic Utsunomiya Japan; Department of Global Health Promotion Tokyo Medical and Dental University Tokyo Japan

Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan

Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan; Global Station for Biosurfaces and Drug Discovery Hokkaido University Sapporo Japan; Division of Pathogen Structure International Institute for Zoonosis Control Hokkaido University Sapporo Japan

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

One Health Research Center Hokkaido University Sapporo Japan; International Collaboration Unit International Institute for Zoonosis Control Hokkaido University Sapporo Japan; Division of Risk Analysis and Management International Institute for Zoonosis Control Hokkaido University Sapporo Japan

Tokyo Metropolitan Institute of Public Health Tokyo Japan

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Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.W., Kapral G.J., Grosse-Kunstleve R.W., et al. Phenix: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 2010;66:213–221. doi: 10.1107/S0907444909052925. PubMed DOI PMC

Arora P., Kempf A., Nehlmeier I., Schulz S.R., Cossmann A., Stankov M.V., Jäck H.M., Behrens G.M.N., Pöhlmann S., Hoffmann M. Augmented neutralisation resistance of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5. Lancet Infect. Dis. 2022;22:1117–1118. doi: 10.1016/S1473-3099(22)00422-4. PubMed DOI PMC

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. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020;588:682–687. doi: 10.1038/s41586-020-2852-1. 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., et al. Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies. Nat. Med. 2022;28:1297–1302. doi: 10.1038/s41591-022-01792-5. PubMed DOI

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

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

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

Capella-Gutiérrez S., Silla-Martínez J.M., Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

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

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. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature. 2021;602:654–656. doi: 10.1038/d41586-41021-03824-41585. PubMed DOI PMC

Cerutti G., Guo Y., Zhou T., Gorman J., Lee M., Rapp M., Reddem E.R., Yu J., Bahna F., Bimela J., et al. Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single Supersite. Cell Host Microbe. 2021;29:819–833.e7. doi: 10.1016/j.chom.2021.03.005. PubMed DOI PMC

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

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

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

Cingolani P., Platts A., Wang L.L., Coon M., Nguyen T., Wang L., Land S.J., Lu X., Ruden D.M. 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) 2012;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., et al. Usability of polydimethylsiloxane-based microfluidic devices in pharmaceutical research using human hepatocytes. ACS Biomater. Sci. Eng. 2021;7:3648–3657. doi: 10.1021/acsbiomaterials.1c00642. PubMed DOI

Dejnirattisai W., Huo J., Zhou D., Zahradník J., Supasa P., Liu C., Duyvesteyn H.M.E., Ginn H.M., Mentzer A.J., Tuekprakhon A., et al. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell. 2022;185:467–484.e15. doi: 10.1016/j.cell.2021.12.046. PubMed DOI PMC

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. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nat. Microbiol. 2021;6:1233–1244. doi: 10.1038/s41564-021-00972-2. PubMed DOI PMC

Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. PubMed DOI

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. SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. J. Infect. Dis. 2021;224:989–994. doi: 10.1093/infdis/jiab368. PubMed DOI PMC

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. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell. 2021;184:2372–2383.e9. doi: 10.1016/j.cell.2021.03.013. PubMed DOI PMC

GitHub 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) 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., Ferrin T.E. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 2018;27:14–25. doi: 10.1002/pro.3235. PubMed DOI PMC

Gotoh S., Ito I., Nagasaki T., Yamamoto Y., Konishi S., Korogi Y., Matsumoto H., Muro S., Hirai T., Funato M., et al. Generation of alveolar epithelial spheroids via isolated progenitor cells from human pluripotent stem cells. Stem Cell Rep. 2014;3:394–403. doi: 10.1016/j.stemcr.2014.07.005. PubMed DOI PMC

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

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. Neutralization escape by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, and BA.5. N. Engl. J. Med. 2022;387:86–88. doi: 10.1056/NEJMc2206576. PubMed DOI PMC

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 SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 2021;19:409–424. doi: 10.1038/s41579-021-00573-0. PubMed DOI PMC

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

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

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. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science. 2020;369:1501–1505. doi: 10.1126/science.abd0826. PubMed DOI PMC

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

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

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

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

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. A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Nat. Commun. 2021;12:288. doi: 10.1038/s41467-020-20602-5. PubMed DOI PMC

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

Kimura I., Yamasoba D., Nasser H., Zahradnik J., Kosugi Y., Wu J., Nagata K., Uriu K., Tanaka Y.L., Ito J., et al. SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. Preprint at bioRxiv. 2022 doi: 10.1101/2022.1104.1103.486864. PubMed DOI PMC

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

Kislaya I., Casaca P., Borges V., et al. 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. 2022 doi: 10.1101/2022.1107.1125.22277996. DOI

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

Konishi S., Gotoh S., Tateishi K., Yamamoto Y., Korogi Y., Nagasaki T., Matsumoto H., Muro S., Hirai T., Ito I., et al. Directed induction of functional multi-ciliated cells in proximal airway epithelial spheroids from human pluripotent stem cells. Stem Cell Rep. 2016;6:18–25. doi: 10.1016/j.stemcr.2015.11.010. PubMed DOI PMC

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

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094–3100. doi: 10.1093/bioinformatics/bty191. PubMed DOI PMC

Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;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 The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

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

Liu L., Wang P., Nair M.S., Yu J., Rapp M., Wang Q., Luo Y., Chan J.F., Sahi V., Figueroa A., et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature. 2020;584:450–456. doi: 10.1038/s41586-020-2571-7. PubMed DOI

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

Lok S.M. An NTD Supersite of attack. Cell Host Microbe. 2021;29:744–746. doi: 10.1016/j.chom.2021.04.010. PubMed DOI PMC

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. Rapid decline in vaccine-boosted neutralizing antibodies against SARS-CoV-2 Omicron variant. Cell Rep. Med. 2022;3:100679. doi: 10.1016/j.xcrm.2022.100679. PubMed DOI PMC

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

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. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell. 2021;184:2332–2347.e16. doi: 10.1016/j.cell.2021.03.028. PubMed DOI PMC

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. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature. 2022;603:706–714. doi: 10.1038/s41586-022-04474-x. PubMed DOI PMC

Mirdita M., Schütze K., Moriwaki Y., Heo L., Ovchinnikov S., Steinegger M. ColabFold: making protein folding accessible to all. Nat. Methods. 2022;19:679–682. doi: 10.1038/s41592-022-01488-1. PubMed DOI PMC

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

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

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

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

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

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

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. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature. 2020;583:290–295. doi: 10.1038/s41586-020-2349-y. PubMed DOI

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

Punjani A., Rubinstein J.L., Fleet D.J., Brubaker M.A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods. 2017;14:290–296. doi: 10.1038/nmeth.4169. PubMed DOI

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. Neutralization of the SARS-CoV-2 omicron BA.4/5 and BA.2.12.1 Subvariants. N. Engl. J. Med. 2022;386:2526–2528. doi: 10.1056/NEJMc2206725. PubMed DOI PMC

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

Reeves P.J., Callewaert N., Contreras R., Khorana H.G. 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. 2002;99:13419–13424. doi: 10.1073/pnas.212519299. PubMed DOI PMC

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

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

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

Stalls V., Lindenberger J., Gobeil S.M., Henderson R., Parks R., Barr M., Deyton M., Martin M., Janowska K., Huang X., et al. Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike. Cell Rep. 2022;39:111009. doi: 10.1016/j.celrep.2022.111009. PubMed DOI PMC

Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–1313. doi: 10.1093/bioinformatics/btu033. PubMed DOI PMC

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. Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein. Cell. 2021;184:2316–2331.e15. doi: 10.1016/j.cell.2021.03.029. PubMed DOI PMC

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

Takashita E., Kinoshita N., Yamayoshi S., Sakai-Tagawa Y., Fujisaki S., Ito M., Iwatsuki-Horimoto K., Chiba S., Halfmann P., Nagai H., et al. Efficacy of antibodies and antiviral drugs against Covid-19 Omicron variant. N. Engl. J. Med. 2022;386:995–998. doi: 10.1056/NEJMc2119407. 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., et al. Efficacy of antiviral agents against the SARS-CoV-2 Omicron subvariant BA.2. N. Engl. J. Med. 2022;386:1475–1477. doi: 10.1056/NEJMc2201933. PubMed DOI PMC

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

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. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell. 2022;185:2422–2433.e13. doi: 10.1016/j.cell.2022.06.005. PubMed DOI PMC

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

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 Neutralization of the SARS-CoV-2 Mu variant by convalescent and vaccine serum. N. Engl. J. Med. 2021;385:2397–2399. doi: 10.1056/NEJMc2114706. PubMed DOI PMC

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. An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies. Nat. Med. 2022;28:490–495. doi: 10.1038/s41591-021-01678-y. PubMed DOI PMC

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. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science. 2021;372:1108–1112. doi: 10.1126/science.abg5268. PubMed DOI PMC

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. Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5, & BA.5. Nature. 2022;608:603–608. doi: 10.1038/s41586-022-05053-w. PubMed DOI PMC

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

WHO Tracking SARS-CoV-2 variants (July 19, 2022) 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. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 2018;27:293–315. doi: 10.1002/pro.3330. PubMed DOI PMC

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. A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent. Nat. Struct. Mol. Biol. 2021;28:202–209. doi: 10.1038/s41594-020-00549-3. PubMed DOI PMC

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

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

Yamasoba D., Kimura I., Nasser H., Morioka Y., Nao N., Ito J., Uriu K., Tsuda M., Zahradnik J., Shirakawa K., et al. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell. 2022;185:2103–2115.e19. doi: 10.1016/j.cell.2022.04.035. PubMed DOI PMC

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

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

Zahradník J., Marciano S., Shemesh M., Zoler E., Harari D., Chiaravalli J., Meyer B., Rudich Y., Li C., Marton I., et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat. Microbiol. 2021;6:1188–1198. doi: 10.1038/s41564-021-00954-4. PubMed DOI

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