{"id":"https://openalex.org/W4378781867","doi":"https://doi.org/10.1371/journal.pcbi.1011173","title":"Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection","display_name":"Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection","publication_year":2023,"publication_date":"2023-05-30","ids":{"openalex":"https://openalex.org/W4378781867","doi":"https://doi.org/10.1371/journal.pcbi.1011173","pmid":"https://pubmed.ncbi.nlm.nih.gov/37253076"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011173","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.1011173","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003216699","display_name":"Junya Sunagawa","orcid":"https://orcid.org/0000-0001-7608-4253"},"institutions":[{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Junya Sunagawa","raw_affiliation_strings":["Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido, Japan"],"raw_orcid":"https://orcid.org/0000-0001-7608-4253","affiliations":[{"raw_affiliation_string":"Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido, Japan","institution_ids":["https://openalex.org/I205349734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057319500","display_name":"Ryo Komorizono","orcid":"https://orcid.org/0000-0002-7610-7985"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryo Komorizono","raw_affiliation_strings":["Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001166064","display_name":"Hyeongki Park","orcid":"https://orcid.org/0009-0002-6507-0731"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hyeongki Park","raw_affiliation_strings":["interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014625355","display_name":"William S. Hart","orcid":"https://orcid.org/0000-0002-2504-6860"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"William S. Hart","raw_affiliation_strings":["Mathematical Institute, University of Oxford, Oxford, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematical Institute, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004524783","display_name":"Robin N. Thompson","orcid":"https://orcid.org/0000-0001-8545-5212"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robin N. Thompson","raw_affiliation_strings":["Mathematics Institute, University of Warwick, Coventry, United Kingdom","Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-8545-5212","affiliations":[{"raw_affiliation_string":"Mathematics Institute, University of Warwick, Coventry, United Kingdom","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054250729","display_name":"Akiko Makino","orcid":"https://orcid.org/0000-0001-9628-2126"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Akiko Makino","raw_affiliation_strings":["Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan","Laboratory of RNA Viruses, Graduate School of Biostudies, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Laboratory of RNA Viruses, Graduate School of Biostudies, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019725294","display_name":"Keiz\u014d Tomonaga","orcid":"https://orcid.org/0000-0003-0405-7103"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Keizo Tomonaga","raw_affiliation_strings":["Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan","Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan","Laboratory of RNA Viruses, Graduate School of Biostudies, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Laboratory of RNA Viruses, Department of Virus Research, Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Laboratory of RNA Viruses, Graduate School of Biostudies, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054895255","display_name":"Shingo Iwami","orcid":"https://orcid.org/0000-0002-1780-350X"},"institutions":[{"id":"https://openalex.org/I135598925","display_name":"Kyushu University","ror":"https://ror.org/00p4k0j84","country_code":"JP","type":"education","lineage":["https://openalex.org/I135598925"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210110652","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210134095","display_name":"Science Groove (Japan)","ror":"https://ror.org/040tczt20","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210134095"]},{"id":"https://openalex.org/I42570316","display_name":"Japanese Foundation For Cancer Research","ror":"https://ror.org/00bv64a69","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I42570316"]},{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shingo Iwami","raw_affiliation_strings":["Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan","Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan","Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan","NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan","Science Groove Inc., Fukuoka, Japan","interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan"],"raw_orcid":"https://orcid.org/0000-0002-1780-350X","affiliations":[{"raw_affiliation_string":"Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan","institution_ids":["https://openalex.org/I135598925"]},{"raw_affiliation_string":"Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan","institution_ids":["https://openalex.org/I4210110652"]},{"raw_affiliation_string":"NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan","institution_ids":["https://openalex.org/I42570316"]},{"raw_affiliation_string":"Science Groove Inc., Fukuoka, Japan","institution_ids":["https://openalex.org/I4210134095"]},{"raw_affiliation_string":"interdisciplinary Biology Laboratory (iBLab), Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061789335","display_name":"Ryo Yamaguchi","orcid":"https://orcid.org/0000-0003-3545-7513"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["CA","JP"],"is_corresponding":true,"raw_author_name":"Ryo Yamaguchi","raw_affiliation_strings":["Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido, Japan","Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada"],"raw_orcid":"https://orcid.org/0000-0003-3545-7513","affiliations":[{"raw_affiliation_string":"Department of Advanced Transdisciplinary Science, Hokkaido University, Sapporo, Hokkaido, Japan","institution_ids":["https://openalex.org/I205349734"]},{"raw_affiliation_string":"Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5001166064","https://openalex.org/A5003216699","https://openalex.org/A5004524783","https://openalex.org/A5014625355","https://openalex.org/A5019725294","https://openalex.org/A5054250729","https://openalex.org/A5054895255","https://openalex.org/A5057319500","https://openalex.org/A5061789335"],"corresponding_institution_ids":["https://openalex.org/I135598925","https://openalex.org/I141945490","https://openalex.org/I205349734","https://openalex.org/I22299242","https://openalex.org/I39555362","https://openalex.org/I40120149","https://openalex.org/I4210110652","https://openalex.org/I4210134095","https://openalex.org/I42570316","https://openalex.org/I60134161"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.7012,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.85690407,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"5","first_page":"e1011173","last_page":"e1011173"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T12047","display_name":"Viral Infections and Vectors","score":0.9980999827384949,"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.7892249822616577},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"Viral evolution","score":0.7856465578079224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7118645906448364},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.703234076499939},{"id":"https://openalex.org/keywords/viral-load","display_name":"Viral load","score":0.7003762722015381},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.58272385597229},{"id":"https://openalex.org/keywords/rna-virus","display_name":"RNA virus","score":0.45901551842689514},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.4468560516834259},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.418459951877594},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.41731345653533936},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17557299137115479},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1288902461528778},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12601768970489502}],"concepts":[{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.7892249822616577},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.7856465578079224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7118645906448364},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.703234076499939},{"id":"https://openalex.org/C142462285","wikidata":"https://www.wikidata.org/wiki/Q2528140","display_name":"Viral load","level":3,"score":0.7003762722015381},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.58272385597229},{"id":"https://openalex.org/C2779174946","wikidata":"https://www.wikidata.org/wiki/Q751911","display_name":"RNA virus","level":4,"score":0.45901551842689514},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.4468560516834259},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.418459951877594},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.41731345653533936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17557299137115479},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1288902461528778},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12601768970489502},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014777","descriptor_name":"Virus Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011173","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:37253076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37253076","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:10256155","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10256155","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10256155/pdf/pcbi.1011173.pdf","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"},{"id":"pmh:oai:wrap.warwick.ac.uk:176444","is_oa":true,"landing_page_url":null,"pdf_url":"https://wrap.warwick.ac.uk/176444/1/journal.pcbi.1011173.pdf","source":{"id":"https://openalex.org/S4306400665","display_name":"Warwick Research Archive Portal (University of Warwick)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39555362","host_organization_name":"University of Warwick","host_organization_lineage":["https://openalex.org/I39555362"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:27aaac16964c40b09bf10cebe518fa3f","is_oa":true,"landing_page_url":"https://doaj.org/article/27aaac16964c40b09bf10cebe518fa3f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 5, p e1011173 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011173","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":[],"awards":[{"id":"https://openalex.org/G1524525519","display_name":"Systems Bone Biology","funder_award_id":"18KT0018","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G181872037","display_name":null,"funder_award_id":"JPMJMS2025","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G2113122299","display_name":null,"funder_award_id":"20wm0325015s0301","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G2432938456","display_name":null,"funder_award_id":"20fk0108413s0301","funder_id":"https://openalex.org/F4320337468","funder_display_name":"National Center for Emerging and Zoonotic Infectious Diseases"},{"id":"https://openalex.org/G2576085165","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G2805833997","display_name":null,"funder_award_id":"JPMJMS2025","funder_id":"https://openalex.org/F4320338247","funder_display_name":"Moonshot Research and Development Program"},{"id":"https://openalex.org/G301936887","display_name":null,"funder_award_id":"20wm0325004s0201","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G3326939414","display_name":null,"funder_award_id":"JPMJMS2021","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G3597076755","display_name":null,"funder_award_id":"19fk0108156h0001, 20fk0108140s0801, 20fk0108413s0301","funder_id":"https://openalex.org/F4320337468","funder_display_name":"National Center for Emerging and Zoonotic Infectious Diseases"},{"id":"https://openalex.org/G372768772","display_name":null,"funder_award_id":"20fk0108140s0801","funder_id":"https://openalex.org/F4320337468","funder_display_name":"National Center for Emerging and Zoonotic Infectious Diseases"},{"id":"https://openalex.org/G3985126362","display_name":null,"funder_award_id":"JP21K19909","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4730495038","display_name":"New modeling and mathematical analysis for pattern formations in life sciences","funder_award_id":"18H01139","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5368403867","display_name":null,"funder_award_id":"JPMJMS2021","funder_id":"https://openalex.org/F4320338247","funder_display_name":"Moonshot Research and Development Program"},{"id":"https://openalex.org/G5493789391","display_name":"Big data ecology for understanding host-pathogen interaction from sequence data","funder_award_id":"16H04845","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5621846355","display_name":null,"funder_award_id":"JP20H05682","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5626571485","display_name":null,"funder_award_id":"JPMJAX22AK","funder_id":"https://openalex.org/F4320338246","funder_display_name":"ACT-X"},{"id":"https://openalex.org/G5878114834","display_name":"Evolutionary Ecological Origins of Interspecific Asymmetry in Reproductive Isolation","funder_award_id":"21K15160","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6000661553","display_name":null,"funder_award_id":"JPMJAX22AK","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G603344638","display_name":null,"funder_award_id":"JPMJMS2021","funder_id":"https://openalex.org/F4320338243","funder_display_name":"JST-Mirai Program"},{"id":"https://openalex.org/G6195167763","display_name":null,"funder_award_id":"19gm1310002","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G6507334783","display_name":null,"funder_award_id":"20wm0325007h0001","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G6687757193","display_name":null,"funder_award_id":"JPMJMS2021","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6836997584","display_name":null,"funder_award_id":"19fk0108156h0001","funder_id":"https://openalex.org/F4320337468","funder_display_name":"National Center for Emerging and Zoonotic Infectious Diseases"},{"id":"https://openalex.org/G687005924","display_name":null,"funder_award_id":"20fk0108140s0801","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G718989205","display_name":null,"funder_award_id":"20H05042","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G753450732","display_name":null,"funder_award_id":"JPMJMS2021, JPMJMS2025","funder_id":"https://openalex.org/F4320338247","funder_display_name":"Moonshot Research and Development Program"},{"id":"https://openalex.org/G8455102717","display_name":null,"funder_award_id":"19fk0310114h0103","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G8544600726","display_name":null,"funder_award_id":"20wm0325012s0301","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320309791","display_name":"Suzuken Memorial Foundation","ror":"https://ror.org/03yvcwz92"},{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320318066","display_name":"Shinnihon Foundation of Advanced Medical Treatment Research","ror":null},{"id":"https://openalex.org/F4320322286","display_name":"Japan Prize Foundation","ror":"https://ror.org/01z7s7j95"},{"id":"https://openalex.org/F4320322525","display_name":"Secom Science and Technology Foundation","ror":"https://ror.org/05ggzej07"},{"id":"https://openalex.org/F4320323515","display_name":"Daiwa Securities Health Foundation","ror":"https://ror.org/007pxvx88"},{"id":"https://openalex.org/F4320327693","display_name":"Life Science Foundation of Japan","ror":null},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320337468","display_name":"National Center for Emerging and Zoonotic Infectious Diseases","ror":"https://ror.org/04vmke174"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338243","display_name":"JST-Mirai Program","ror":null},{"id":"https://openalex.org/F4320338246","display_name":"ACT-X","ror":null},{"id":"https://openalex.org/F4320338247","display_name":"Moonshot Research and Development Program","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W136988059","https://openalex.org/W1511129506","https://openalex.org/W1520628336","https://openalex.org/W1547663347","https://openalex.org/W1659842140","https://openalex.org/W1985735834","https://openalex.org/W1986726490","https://openalex.org/W2002380506","https://openalex.org/W2003574450","https://openalex.org/W2004049741","https://openalex.org/W2004500886","https://openalex.org/W2006564892","https://openalex.org/W2008620264","https://openalex.org/W2012547638","https://openalex.org/W2022291864","https://openalex.org/W2025503453","https://openalex.org/W2025788954","https://openalex.org/W2033832533","https://openalex.org/W2037556165","https://openalex.org/W2045989152","https://openalex.org/W2046717399","https://openalex.org/W2048752816","https://openalex.org/W2062996387","https://openalex.org/W2069935119","https://openalex.org/W2070649137","https://openalex.org/W2071539584","https://openalex.org/W2073100533","https://openalex.org/W2073918065","https://openalex.org/W2097141283","https://openalex.org/W2106396133","https://openalex.org/W2112090702","https://openalex.org/W2116100710","https://openalex.org/W2120612096","https://openalex.org/W2120982899","https://openalex.org/W2130138900","https://openalex.org/W2130203599","https://openalex.org/W2142677793","https://openalex.org/W2145605402","https://openalex.org/W2146607614","https://openalex.org/W2157475700","https://openalex.org/W2163438954","https://openalex.org/W2260088441","https://openalex.org/W2306323185","https://openalex.org/W2321894563","https://openalex.org/W2535127719","https://openalex.org/W2560514568","https://openalex.org/W2567699202","https://openalex.org/W2588059836","https://openalex.org/W2595587791","https://openalex.org/W2802499388","https://openalex.org/W2883029773","https://openalex.org/W2971382621","https://openalex.org/W3015494731","https://openalex.org/W3022320324","https://openalex.org/W3035306765","https://openalex.org/W3036693799","https://openalex.org/W3045635391","https://openalex.org/W3132630010","https://openalex.org/W3153599567","https://openalex.org/W3158578082","https://openalex.org/W3164088920","https://openalex.org/W4200573720","https://openalex.org/W4205901551","https://openalex.org/W4206712614","https://openalex.org/W4211158349","https://openalex.org/W4212799904","https://openalex.org/W4212821474","https://openalex.org/W4220756778","https://openalex.org/W4229028530","https://openalex.org/W4378781867","https://openalex.org/W6605527092","https://openalex.org/W6807339262","https://openalex.org/W6962688574","https://openalex.org/W7000679336"],"related_works":["https://openalex.org/W2009307527","https://openalex.org/W2074878346","https://openalex.org/W1995324211","https://openalex.org/W3092640155","https://openalex.org/W1998441997","https://openalex.org/W2208496181","https://openalex.org/W2066247337","https://openalex.org/W2110932451","https://openalex.org/W2974674658","https://openalex.org/W2903140350"],"abstract_inverted_index":{"Viruses":[0],"evolve":[1],"in":[2,32,58,133,162,194],"infected":[3,106],"host":[4,7,96],"populations,":[5,60],"and":[6,21,45,61,86,181],"population":[8],"dynamics":[9,85],"affect":[10],"viral":[11,25,49,142,151,169,184],"evolution.":[12],"RNA":[13,37],"viruses":[14,38,69,117,180],"with":[15,111,118,138,146,166],"a":[16,22,41,46,76,112,119,134,139,147],"short":[17,135],"duration":[18,44],"of":[19,64,67,101,105,178],"infection":[20,43,84,164,190],"high":[23,120,140,159],"peak":[24,48,141,168],"load,":[26],"such":[27],"as":[28],"SARS-CoV-2,":[29],"are":[30,127],"maintained":[31,57],"human":[33,195],"populations.":[34],"By":[35],"contrast,":[36,145],"characterized":[39],"by":[40],"long":[42,163],"low":[47,125,155,167],"load":[50],"(e.g.,":[51],"borna":[52],"disease":[53],"virus)":[54],"can":[55],"be":[56,130],"nonhuman":[59],"the":[62,65,95,99,102,176],"process":[63],"evolution":[66,92,152],"persistent":[68,179,188],"has":[70],"rarely":[71],"been":[72],"explored.":[73],"Here,":[74],"using":[75],"multi-level":[77],"modeling":[78],"approach":[79],"including":[80],"both":[81],"individual-level":[82],"virus":[83,91,121,156,189],"population-scale":[87],"transmission,":[88],"we":[89],"consider":[90],"based":[93],"on":[94,175],"environment,":[97],"specifically,":[98],"effect":[100],"contact":[103,115,149],"history":[104],"hosts.":[107],"We":[108],"found":[109],"that,":[110],"highly":[113],"dense":[114],"history,":[116,150],"production":[122,157],"rate":[123],"but":[124,158,186],"accuracy":[126],"likely":[128],"to":[129,192],"optimal,":[131],"resulting":[132,161],"infectious":[136],"period":[137],"load.":[143,170],"In":[144],"low-density":[148],"is":[153],"toward":[154],"accuracy,":[160],"durations":[165],"Our":[171],"study":[172],"sheds":[173],"light":[174],"origin":[177],"why":[182],"acute":[183],"infections":[185],"not":[187],"tends":[191],"prevail":[193],"society.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
