{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:39:30Z","timestamp":1787567970911,"version":"build-2736575974"},"reference-count":43,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T00:00:00Z","timestamp":1734998400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T00:00:00Z","timestamp":1734998400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T00:00:00Z","timestamp":1734998400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2021M3H9A2097227"],"award-info":[{"award-number":["NRF-2021M3H9A2097227"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2022R1A2C3008162"],"award-info":[{"award-number":["NRF-2022R1A2C3008162"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["RS-2023-00220840"],"award-info":[{"award-number":["RS-2023-00220840"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","award":["RS-2023-00265923"],"award-info":[{"award-number":["RS-2023-00265923"]}],"id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF: 2021M3A9I2080490"],"award-info":[{"award-number":["NRF: 2021M3A9I2080490"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003710","name":"Korea Health Industry Development Institute","doi-asserted-by":"publisher","award":["RS-2024-00406488"],"award-info":[{"award-number":["RS-2024-00406488"]}],"id":[{"id":"10.13039\/501100003710","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    An unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the receptor binding motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in variants of concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 were detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible at\n                    <jats:ext-link ext-link-type=\"uri\" xlink:href=\"https:\/\/ai-ve.org\">https:\/\/ai-ve.org<\/jats:ext-link>\n                    to provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.\n                  <\/jats:p>","DOI":"10.7554\/elife.99833","type":"journal-article","created":{"date-parts":[[2024,10,21]],"date-time":"2024-10-21T10:25:15Z","timestamp":1729506315000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.99833","source":"Crossref","is-referenced-by-count":3,"title":["Accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis"],"prefix":"10.7554","volume":"13","author":[{"given":"Jongkeun","family":"Park","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"WonJong","family":"Choi","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Do Young","family":"Seong","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Seungpil","family":"Jeong","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Ju Young","family":"Lee","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Hyo Jeong","family":"Park","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Dae Sun","family":"Chung","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Kijong","family":"Yi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05apxxy63","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate School of Medical Science and Engineering, Korea Advanced Institute and Technology","place":["Daejeon, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Uijin","family":"Kim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01wjejq96","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Ga-Yeon","family":"Yoon","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01wjejq96","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Hyeran","family":"Kim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biomedical Sciences, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Taehoon","family":"Kim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biomedical Sciences, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Sooyeon","family":"Ko","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Chemical and Biological Engineering, Seoul National University","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Eun Jeong","family":"Min","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4067-4715","authenticated-orcid":true,"given":"Hyun-Soo","family":"Cho","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01wjejq96","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"given":"Nam-Hyuk","family":"Cho","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/04h9pn542","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biomedical Sciences, Seoul National University College of Medicine","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/00cb3km46","id-type":"ROR","asserted-by":"publisher"}],"name":"Seoul National University Bundang Hospital","place":["Seongnam, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7816-1299","authenticated-orcid":true,"given":"Dongwan","family":"Hong","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medical Informatics, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Precision Medicine Research Center, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea","place":["Seoul, Republic of Korea"]},{"id":[{"id":"https:\/\/ror.org\/01fpnj063","id-type":"ROR","asserted-by":"publisher"}],"name":"CMC Institute for Basic Medical Science, the Catholic Medical Center of The Catholic University of Korea","place":["Seoul, Republic of Korea"]},{"name":"INNOONE","place":["Seoul, Republic of Korea"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2024,12,24]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.1016\/j.medidd.2021.100086","type":"journal-article","article-title":"The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant","volume":"10","author":"Ali","year":"2021","journal-title":"Medicine in Drug Discovery"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1016\/j.csbj.2019.06.022","type":"journal-article","article-title":"Evolutionary stability of salt bridges hints its contribution to stability of proteins","volume":"17","author":"Ban","year":"2019","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.bbrc.2021.08.036","type":"journal-article","article-title":"Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion","volume":"574","author":"Baral","year":"2021","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"8201","DOI":"10.1021\/acs.jpcb.0c03716","type":"journal-article","article-title":"Interdiction of protein folding for therapeutic drug development in SARS CoV-2","volume":"124","author":"Bergasa-Caceres","year":"2020","journal-title":"The Journal of Physical Chemistry. B"},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vead022","type":"journal-article","article-title":"MutaGAN: A sequence-to-sequence GAN framework to predict mutations of evolving protein populations","volume":"9","author":"Berman","year":"2023","journal-title":"Virus Evolution"},{"key":"bib6","doi-asserted-by":"publisher","DOI":"10.3390\/biom12111665","type":"journal-article","article-title":"In silico protein folding prediction of covid-19 mutations and variants","volume":"12","author":"Bhowmick","year":"2022","journal-title":"Biomolecules"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"4597","DOI":"10.1016\/j.cell.2023.08.026","type":"journal-article","article-title":"SARS-CoV-2 variants evolve convergent strategies to remodel the host response","volume":"186","author":"Bouhaddou","year":"2023","journal-title":"Cell"},{"key":"bib8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28865-w","type":"journal-article","article-title":"Improved prediction of protein-protein interactions using AlphaFold2","volume":"13","author":"Bryant","year":"2022","journal-title":"Nature Communications"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.1016\/j.bpj.2021.02.007","type":"journal-article","article-title":"Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction","volume":"120","author":"Cao","year":"2021","journal-title":"Biophysical Journal"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/s41586-021-04385-3","type":"journal-article","article-title":"Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies","volume":"602","author":"Cao","year":"2022","journal-title":"Nature"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41588-022-01033-y","type":"journal-article","article-title":"Global landscape of SARS-CoV-2 genomic surveillance and data sharing","volume":"54","author":"Chen","year":"2022","journal-title":"Nature Genetics"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","type":"journal-article","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1016\/j.cell.2022.01.001","type":"journal-article","article-title":"Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2","volume":"185","author":"Han","year":"2022","journal-title":"Cell"},{"key":"bib14","type":"software","article-title":"AIVE","volume-title":"Software Heritage","author":"Honglab-Research","year":"2023","unstructured":"Honglab-Research. 2023. AIVE. Software Heritage. swh:1:rev:095b018c31384e0e20bf1c643bed7dd5fbd40414. https:\/\/archive.softwareheritage.org\/swh:1:dir:a319c5add134b653f2ef21419067d71292d86b3f;origin=https:\/\/github.com\/Honglab-Research\/AIVE;visit=swh:1:snp:591f6175be9f2f00c66184fa1878725609ecfcd3;anchor=swh:1:rev:095b018c31384e0e20bf1c643bed7dd5fbd40414."},{"key":"bib15","type":"software","article-title":"AIVE-prediction","volume-title":"Software Heritage","author":"Honglab-Research","year":"2024","unstructured":"Honglab-Research. 2024. AIVE-prediction. Software Heritage. swh:1:rev:9401d4b10b4e73656721583c0fa000bcbcb3aa6e. https:\/\/archive.softwareheritage.org\/swh:1:dir:7dcacb61c2ba57e13ce44670682421e064348e94;origin=https:\/\/github.com\/Honglab-Research\/AIVE-prediction;visit=swh:1:snp:43ee045b188b050cc9af87db2f4dca13ecf17543;anchor=swh:1:rev:9401d4b10b4e73656721583c0fa000bcbcb3aa6e."},{"key":"bib16","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-021-01611-2","type":"journal-article","article-title":"The key amino acids of E protein involved in early flavivirus infection: viral entry","volume":"18","author":"Hu","year":"2021","journal-title":"Virology Journal"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"4122","DOI":"10.1111\/febs.14941","type":"journal-article","article-title":"Hydrophobic surface residues can stabilize a protein through improved water-protein interactions","volume":"286","author":"Islam","year":"2019","journal-title":"The FEBS Journal"},{"key":"bib18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38188-z","type":"journal-article","article-title":"Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant","volume":"14","author":"Ito","year":"2023","journal-title":"Nature Communications"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41586-021-03237-4","type":"journal-article","article-title":"Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis","volume":"591","author":"Johnson","year":"2021","journal-title":"Nature"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","type":"journal-article","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1186\/1745-7580-6-S1-S2","type":"journal-article","article-title":"pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes","volume":"6 Suppl 1","author":"Khan","year":"2010","journal-title":"Immunome Research"},{"key":"bib22","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-023-02035-z","type":"journal-article","article-title":"SARS-CoV-2 receptor-binding domain deep mutational AlphaFold2 structures","volume":"10","author":"Kilim","year":"2023","journal-title":"Scientific Data"},{"key":"bib23","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01381-18","type":"journal-article","article-title":"Mutations in the spike protein of middle east respiratory syndrome coronavirus transmitted in korea increase resistance to antibody-mediated neutralization","volume":"93","author":"Kleine-Weber","year":"2019","journal-title":"Journal of Virology"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1096\/fasebj.9.7.7737462","type":"journal-article","article-title":"The hydrophobic effect in protein folding","volume":"9","author":"Lins","year":"1995","journal-title":"FASEB Journal"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1038\/s41562-021-01122-8","type":"journal-article","article-title":"A global database of COVID-19 vaccinations","volume":"5","author":"Mathieu","year":"2021","journal-title":"Nature Human Behaviour"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1016\/j.jmb.2011.02.053","type":"journal-article","article-title":"Contribution of hydrophobic interactions to protein stability","volume":"408","author":"Pace","year":"2011","journal-title":"Journal of Molecular Biology"},{"key":"bib27","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.9648","type":"journal-article","article-title":"Excessive G-U transversions in novel allele variants in SARS-CoV-2 genomes","volume":"8","author":"Panchin","year":"2020","journal-title":"PeerJ"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/s41564-021-00908-w","type":"journal-article","article-title":"The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets","volume":"6","author":"Peacock","year":"2021","journal-title":"Nature Microbiology"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","type":"journal-article","article-title":"UCSF ChimeraX: Structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Science"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1128\/JVI.01570-10","type":"journal-article","article-title":"The hydrophobic domain of infectious bronchitis virus E protein alters the host secretory pathway and is important for release of infectious virus","volume":"85","author":"Ruch","year":"2011","journal-title":"Journal of Virology"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1038\/s41586-019-1923-7","type":"journal-article","article-title":"Improved protein structure prediction using potentials from deep learning","volume":"577","author":"Senior","year":"2020","journal-title":"Nature"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"5010","DOI":"10.1111\/febs.15651","type":"journal-article","article-title":"The structural basis of accelerated host cell entry by SARS-CoV-2\u2020","volume":"288","author":"Seyran","year":"2021","journal-title":"The FEBS Journal"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/s10867-022-09615-x","type":"journal-article","article-title":"Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV","volume":"48","author":"Shekhawat","year":"2022","journal-title":"Journal of Biological Physics"},{"key":"bib34","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","type":"journal-article","article-title":"GISAID: Global initiative on sharing all influenza data - from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveillance"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1016\/j.jinf.2023.07.006","type":"journal-article","article-title":"Artificial intelligence, machine learning and deep learning: Potential resources for the infection clinician","volume":"87","author":"Theodosiou","year":"2023","journal-title":"The Journal of Infection"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1038\/s41591-023-02448-8","type":"journal-article","article-title":"Large language models in medicine","volume":"29","author":"Thirunavukarasu","year":"2023","journal-title":"Nature Medicine"},{"key":"bib37","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.698365","type":"journal-article","article-title":"Comprehensive deep mutational scanning reveals the immune-escaping hotspots of sars-cov-2 receptor-binding domain targeting neutralizing antibodies","volume":"12","author":"Tsai","year":"2021","journal-title":"Frontiers in Microbiology"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1016\/j.jmb.2015.09.014","type":"journal-article","article-title":"The haddock2.2 web server: user-friendly integrative modeling of biomolecular complexes","volume":"428","author":"van Zundert","year":"2016","journal-title":"Journal of Molecular Biology"},{"key":"bib39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2102983118","type":"journal-article","article-title":"Middle East respiratory syndrome coronavirus Spike protein variants exhibit geographic differences in virulence","volume":"118","author":"Wong","year":"2021","journal-title":"PNAS"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26703-z","type":"journal-article","article-title":"A deep learning framework identifies dimensional representations of Alzheimer\u2019s Disease from brain structure","volume":"12","author":"Yang","year":"2021","journal-title":"Nature Communications"},{"key":"bib41","doi-asserted-by":"publisher","DOI":"10.1038\/s41746-022-00742-2","type":"journal-article","article-title":"A large language model for electronic health records","volume":"5","author":"Yang","year":"2022","journal-title":"NPJ Digital Medicine"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1038\/s12276-021-00658-z","type":"journal-article","article-title":"Mutational spectrum of SARS-CoV-2 during the global pandemic","volume":"53","author":"Yi","year":"2021","journal-title":"Experimental & Molecular Medicine"},{"key":"bib43","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2022.106264","type":"journal-article","article-title":"TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution","volume":"152","author":"Zhou","year":"2023","journal-title":"Computers in Biology and Medicine"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/99833\/elife-99833-v2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/99833\/elife-99833-v2.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/99833","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:57:14Z","timestamp":1787565434000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/99833"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,24]]},"references-count":43,"alternative-id":["10.7554\/eLife.99833"],"URL":"https:\/\/doi.org\/10.7554\/elife.99833","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.06.14.598983","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.99833.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.99833.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.99833.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:a319c5add134b653f2ef21419067d71292d86b3f;origin=https:\/\/github.com\/Honglab-Research\/AIVE;visit=swh:1:snp:591f6175be9f2f00c66184fa1878725609ecfcd3;anchor=swh:1:rev:095b018c31384e0e20bf1c643bed7dd5fbd40414","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:7dcacb61c2ba57e13ce44670682421e064348e94;origin=https:\/\/github.com\/Honglab-Research\/AIVE-prediction;visit=swh:1:snp:43ee045b188b050cc9af87db2f4dca13ecf17543;anchor=swh:1:rev:9401d4b10b4e73656721583c0fa000bcbcb3aa6e","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,24]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP99833"}}