{"id":"https://openalex.org/W7123352006","doi":"https://doi.org/10.1371/journal.pcbi.1013582","title":"Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning","display_name":"Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning","publication_year":2026,"publication_date":"2026-01-12","ids":{"openalex":"https://openalex.org/W7123352006","doi":"https://doi.org/10.1371/journal.pcbi.1013582","pmid":"https://pubmed.ncbi.nlm.nih.gov/41525306"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013582","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013582","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013582","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008573424","display_name":"Zengmiao Wang","orcid":"https://orcid.org/0000-0001-6954-6069"},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zengmiao Wang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122860842","display_name":"Ziqin Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqin Zhou","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122845517","display_name":"Junfu Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfu Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Beihang University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040940220","display_name":"Lingyue Yang","orcid":"https://orcid.org/0000-0002-5336-2895"},"institutions":[{"id":"https://openalex.org/I184843921","display_name":"Hebei University of Technology","ror":"https://ror.org/018hded08","country_code":"CN","type":"education","lineage":["https://openalex.org/I184843921"]},{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingyue Yang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","School of Artificial Intelligence, Hebei University of Technology, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]},{"raw_affiliation_string":"School of Artificial Intelligence, Hebei University of Technology, Tianjin, China","institution_ids":["https://openalex.org/I184843921"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhirui Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhirui Zhang","raw_affiliation_strings":["School of Statistics, Beijing Normal University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Statistics, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I25254941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122866225","display_name":"Weina Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weina Xu","raw_affiliation_strings":["School of Computer Science and Engineering, Beihang University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122898092","display_name":"Zeming Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeming Liu","raw_affiliation_strings":["School of Computer Science and Engineering, Beihang University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122874509","display_name":"Yuxi Ge","orcid":null},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxi Ge","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122847311","display_name":"Liang Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I184843921","display_name":"Hebei University of Technology","ror":"https://ror.org/018hded08","country_code":"CN","type":"education","lineage":["https://openalex.org/I184843921"]},{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Yang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","School of Artificial Intelligence, Hebei University of Technology, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]},{"raw_affiliation_string":"School of Artificial Intelligence, Hebei University of Technology, Tianjin, China","institution_ids":["https://openalex.org/I184843921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122844406","display_name":"Xiaoli Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I4210161151","display_name":"Beijing Center for Disease Prevention and Control","ror":"https://ror.org/058dc0w16","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210161151"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoli Wang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","School of Public Health, Capital Medical University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","institution_ids":["https://openalex.org/I4210161151"]},{"raw_affiliation_string":"Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"School of Public Health, Capital Medical University, Beijing, China","institution_ids":["https://openalex.org/I183519381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122866887","display_name":"Peng Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I4210161151","display_name":"Beijing Center for Disease Prevention and Control","ror":"https://ror.org/058dc0w16","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210161151"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Yang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","School of Public Health, Capital Medical University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","institution_ids":["https://openalex.org/I4210161151"]},{"raw_affiliation_string":"Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"School of Public Health, Capital Medical University, Beijing, China","institution_ids":["https://openalex.org/I183519381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122892132","display_name":"Quanyi Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I4210161151","display_name":"Beijing Center for Disease Prevention and Control","ror":"https://ror.org/058dc0w16","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210161151"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quanyi Wang","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","School of Public Health, Capital Medical University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Center for Disease Prevention and Control, Beijing, China","institution_ids":["https://openalex.org/I4210161151"]},{"raw_affiliation_string":"Beijing Research Center for Respiratory Infectious Diseases, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"School of Public Health, Capital Medical University, Beijing, China","institution_ids":["https://openalex.org/I183519381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000800848","display_name":"Yunlong Cao","orcid":"https://orcid.org/0000-0001-5918-1078"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunlong Cao","raw_affiliation_strings":["Biomedical Pioneering Innovation Center, Peking University, Beijing, China","Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China","School of Life Sciences, Peking University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Pioneering Innovation Center, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"raw_affiliation_string":"School of Life Sciences, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122855615","display_name":"Yuanfang Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanfang Guo","raw_affiliation_strings":["School of Computer Science and Engineering, Beihang University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026792205","display_name":"Tian Huaiyu","orcid":null},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]},{"id":"https://openalex.org/I4210146364","display_name":"National Marine Environmental Forecasting Center","ror":"https://ror.org/047hznt06","country_code":"CN","type":"government","lineage":["https://openalex.org/I211433327","https://openalex.org/I4210127390","https://openalex.org/I4210146364"]},{"id":"https://openalex.org/I4210166112","display_name":"State Key Laboratory of Remote Sensing Science","ror":"https://ror.org/05wzjqa24","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210166112"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaiyu Tian","raw_affiliation_strings":["Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Joint International Research Laboratory of Catastrophe Simulation and Systemic Risk Governance, School of National Safety and Emergency Management, Beijing Normal University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-4466-0858","affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Surveillance, Early Warning and Pathogen Research on Emerging Infectious Diseases, Beijing Research Center for Respiratory Infectious Diseases, State Key Laboratory of Remote Sensing and Digital Earth, Center for Global Change and Public Health, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210166112","https://openalex.org/I25254941"]},{"raw_affiliation_string":"National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Joint International Research Laboratory of Catastrophe Simulation and Systemic Risk Governance, School of National Safety and Emergency Management, Beijing Normal University, Beijing, China","institution_ids":["https://openalex.org/I4210146364"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5008573424"],"corresponding_institution_ids":["https://openalex.org/I25254941","https://openalex.org/I4210166112"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0722519,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"e1013582","last_page":"e1013582"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.4205000102519989,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.4205000102519989,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.2574999928474426,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.08370000123977661,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genetic-fitness","display_name":"Genetic Fitness","score":0.667900025844574},{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.6039999723434448},{"id":"https://openalex.org/keywords/evolutionary-dynamics","display_name":"Evolutionary dynamics","score":0.5889999866485596},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5188000202178955},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4999000132083893},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.4016999900341034},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.3921000063419342},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.3894999921321869},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.38100001215934753}],"concepts":[{"id":"https://openalex.org/C2910387474","wikidata":"https://www.wikidata.org/wiki/Q331710","display_name":"Genetic Fitness","level":3,"score":0.667900025844574},{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.6039999723434448},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.5889999866485596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.520799994468689},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5188000202178955},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4999000132083893},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4401000142097473},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.4016999900341034},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.39590001106262207},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.3921000063419342},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.3894999921321869},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.38100001215934753},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.36419999599456787},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.35659998655319214},{"id":"https://openalex.org/C3018558359","wikidata":"https://www.wikidata.org/wiki/Q1660157","display_name":"Immune escape","level":3,"score":0.3395000100135803},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.33379998803138733},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.305400013923645},{"id":"https://openalex.org/C2777648638","wikidata":"https://www.wikidata.org/wiki/Q57751738","display_name":"Coronavirus","level":5,"score":0.3012999892234802},{"id":"https://openalex.org/C2781251061","wikidata":"https://www.wikidata.org/wiki/Q5416089","display_name":"Evasion (ethics)","level":3,"score":0.295199990272522},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.2890999913215637},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.28600001335144043},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.28540000319480896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2851000130176544},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.2831000089645386},{"id":"https://openalex.org/C126701199","wikidata":"https://www.wikidata.org/wiki/Q264224","display_name":"Complex dynamics","level":2,"score":0.2554999887943268},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2549000084400177}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056084","descriptor_name":"Genetic Fitness","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1013582","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013582","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41525306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41525306","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12810920","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12810920/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013582","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013582","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8213661909103394,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2866663875","display_name":null,"funder_award_id":"2233300001","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5099478260","display_name":null,"funder_award_id":"2021ZD0111201","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"},{"id":"https://openalex.org/G7292151899","display_name":null,"funder_award_id":"82204160, 62272020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1971769921","https://openalex.org/W1972928030","https://openalex.org/W1975272103","https://openalex.org/W2016592339","https://openalex.org/W2030332043","https://openalex.org/W2092500478","https://openalex.org/W2094993886","https://openalex.org/W2587970647","https://openalex.org/W3043124965","https://openalex.org/W3048714202","https://openalex.org/W3111599922","https://openalex.org/W3121000782","https://openalex.org/W3127329393","https://openalex.org/W3127852352","https://openalex.org/W3133511640","https://openalex.org/W3135257712","https://openalex.org/W3193526107","https://openalex.org/W3193682077","https://openalex.org/W4200344940","https://openalex.org/W4200601232","https://openalex.org/W4205815466","https://openalex.org/W4207077414","https://openalex.org/W4220807057","https://openalex.org/W4226443473","https://openalex.org/W4281383093","https://openalex.org/W4281939105","https://openalex.org/W4282942003","https://openalex.org/W4283026725","https://openalex.org/W4283331799","https://openalex.org/W4283646162","https://openalex.org/W4309306331","https://openalex.org/W4309469480","https://openalex.org/W4310957931","https://openalex.org/W4311822700","https://openalex.org/W4317436860","https://openalex.org/W4320491837","https://openalex.org/W4320497972","https://openalex.org/W4320857368","https://openalex.org/W4362609000","https://openalex.org/W4366496918","https://openalex.org/W4366824094","https://openalex.org/W4376642822","https://openalex.org/W4380577051","https://openalex.org/W4385415878","https://openalex.org/W4385618176","https://openalex.org/W4385665291","https://openalex.org/W4385776975","https://openalex.org/W4390394037","https://openalex.org/W4394694607","https://openalex.org/W4399528993","https://openalex.org/W4400279796","https://openalex.org/W4402132679","https://openalex.org/W4404124403"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1,10,50,111,123,137,149,158],"heterogeneity":[2],"of":[3,54,92,113,153,162],"population-level":[4],"viral":[5,14,51,154],"fitness":[6,52,87,93,105,155],"dynamics,":[7],"which":[8],"reflect":[9],"interplay":[11],"between":[12],"intrinsic":[13],"properties":[15],"and":[16,33,71,88,116,157],"population":[17],"immunity,":[18],"is":[19],"critical":[20],"for":[21,47],"pandemic":[22],"preparedness.":[23],"However,":[24],"how":[25],"these":[26],"dynamics":[27,53,156],"vary":[28],"across":[29,75],"diverse":[30],"immune":[31,72,98,108,129],"backgrounds":[32],"mutational":[34],"landscapes":[35],"remain":[36],"poorly":[37],"characterized.":[38],"We":[39],"present":[40],"Geno-GNN,":[41,80],"a":[42],"graph":[43],"representation":[44],"learning":[45],"approach":[46],"retrospectively":[48],"characterizing":[49],"severe":[55],"acute":[56],"respiratory":[57],"syndrome":[58],"coronavirus":[59],"2":[60,67],"(SARS-CoV-2).":[61],"Geno-GNN":[62],"accurately":[63],"predicts":[64],"angiotensin-converting":[65],"enzyme":[66],"(ACE2)":[68],"binding":[69],"affinity":[70,115,118,142],"escape":[73],"potential":[74],"multiple":[76],"external":[77],"datasets.":[78],"Using":[79],"we":[81],"identified":[82],"temporal":[83],"patterns":[84],"in":[85],"SARS-CoV-2":[86,133],"detected":[89],"varying":[90],"rates":[91],"change":[94],"associated":[95],"with":[96,127],"distinct":[97],"backgrounds.":[99],"Virtual":[100],"mutation":[101],"scanning":[102],"revealed":[103],"two":[104],"trajectories:":[106],"broad":[107],"evasion":[109],"at":[110,120],"cost":[112],"ACE2":[114,117,141],"maintenance":[119],"or":[121],"above":[122],"Wuhan-Hu-1":[124],"level":[125],"along":[126],"moderate":[128],"escape.":[130],"Notably,":[131],"real-world":[132],"variants":[134],"predominantly":[135],"followed":[136],"latter":[138],"trajectory,":[139],"sustaining":[140],"via":[143],"fixed":[144],"mutations.":[145],"These":[146],"findings":[147],"underscore":[148],"heterogeneous,":[150],"immune-contextualized":[151],"nature":[152],"complex":[159],"evolutionary":[160],"pathways":[161],"SARS-CoV-2.":[163]},"counts_by_year":[],"updated_date":"2026-01-14T23:40:02.550235","created_date":"2026-01-14T00:00:00"}
