{"id":"https://openalex.org/W4409450771","doi":"https://doi.org/10.1371/journal.pcbi.1012960","title":"Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2","display_name":"Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2","publication_year":2025,"publication_date":"2025-04-15","ids":{"openalex":"https://openalex.org/W4409450771","doi":"https://doi.org/10.1371/journal.pcbi.1012960","pmid":"https://pubmed.ncbi.nlm.nih.gov/40233303"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012960","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012960","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012960&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012960&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020801823","display_name":"Emma B. Hodcroft","orcid":"https://orcid.org/0000-0002-0078-2212"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210135124","display_name":"Institute of Social and Preventive Medicine","ror":"https://ror.org/038esz880","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2802229882","https://openalex.org/I4210135124","https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Emma B Hodcroft","raw_affiliation_strings":["Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-0078-2212","affiliations":[{"raw_affiliation_string":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I4210135124"]},{"raw_affiliation_string":"Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093036523","display_name":"Martin Wohlfender","orcid":"https://orcid.org/0000-0002-5252-0484"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I4210135124","display_name":"Institute of Social and Preventive Medicine","ror":"https://ror.org/038esz880","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2802229882","https://openalex.org/I4210135124","https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Martin S Wohlfender","raw_affiliation_strings":["Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland","Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5252-0484","affiliations":[{"raw_affiliation_string":"Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I4210135124"]},{"raw_affiliation_string":"Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037559147","display_name":"Richard A. Neher","orcid":"https://orcid.org/0000-0003-2525-1407"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Richard A Neher","raw_affiliation_strings":["Biozentrum, University of Basel, Basel, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2525-1407","affiliations":[{"raw_affiliation_string":"Biozentrum, University of Basel, Basel, Switzerland","institution_ids":["https://openalex.org/I1850255"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012831704","display_name":"Julien Riou","orcid":"https://orcid.org/0000-0002-3808-2852"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I4210135124","display_name":"Institute of Social and Preventive Medicine","ror":"https://ror.org/038esz880","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2802229882","https://openalex.org/I4210135124","https://openalex.org/I97565354"]},{"id":"https://openalex.org/I4210149340","display_name":"Centre universitaire de m\u00e9decine g\u00e9n\u00e9rale et sant\u00e9 publique, Lausanne","ror":"https://ror.org/04mcdza51","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I4210149340"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Julien Riou","raw_affiliation_strings":["Department of Epidemiology and Health Systems, Unisant\u00e9, Center for Primary Care and Public Health & University of Lausanne, Lausanne, Switzerland","Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Health Systems, Unisant\u00e9, Center for Primary Care and Public Health & University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I4210149340"]},{"raw_affiliation_string":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I4210135124"]},{"raw_affiliation_string":"Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046525106","display_name":"Christian L. Althaus","orcid":"https://orcid.org/0000-0002-5230-6760"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I4210135124","display_name":"Institute of Social and Preventive Medicine","ror":"https://ror.org/038esz880","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2802229882","https://openalex.org/I4210135124","https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Christian L Althaus","raw_affiliation_strings":["Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-5230-6760","affiliations":[{"raw_affiliation_string":"Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I4210135124"]},{"raw_affiliation_string":"Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5020801823"],"corresponding_institution_ids":["https://openalex.org/I118564535","https://openalex.org/I12708293","https://openalex.org/I4210135124"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.5845,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.94956251,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"21","issue":"4","first_page":"e1012960","last_page":"e1012960"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9998999834060669,"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/T10410","display_name":"COVID-19 epidemiological studies","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9937999844551086,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5131610035896301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4522271454334259},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3827272951602936}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5131610035896301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4522271454334259},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3827272951602936}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000635","qualifier_name":"transmission","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005858","descriptor_name":"Germany","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005858","descriptor_name":"Germany","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D005858","descriptor_name":"Germany","qualifier_ui":"Q000453","qualifier_name":"epidemiology","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":"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":"D013557","descriptor_name":"Switzerland","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D013557","descriptor_name":"Switzerland","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D013557","descriptor_name":"Switzerland","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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":"D050936","descriptor_name":"Basic Reproduction Number","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D050936","descriptor_name":"Basic Reproduction Number","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D050936","descriptor_name":"Basic Reproduction Number","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058873","descriptor_name":"Pandemics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1012960","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012960","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012960&type=printable","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:40233303","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40233303","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:serval.unil.ch:BIB_90B0681CC1AD","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_90B0681CC1AD","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"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, vol. 21, no. 4, pp. e1012960","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unil.ch:iris/269971","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/269971","pdf_url":"https://iris.unil.ch/bitstreams/a0e9e195-04d8-46a4-94da-8d10125b3825/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12040226","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12040226","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"},{"id":"pmh:doi:10.48620/87898","is_oa":false,"landing_page_url":"https://boris-portal.unibe.ch/handle/20.500.12422/210174","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"pmh:oai:RePEc:plo:pcbi00:1012960","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012960","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:1c5199ec8bf74da6a8a0c37565a81b85","is_oa":true,"landing_page_url":"https://doaj.org/article/1c5199ec8bf74da6a8a0c37565a81b85","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 21, Iss 4, p e1012960 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012960","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012960","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012960&type=printable","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","display_name":"Good health and well-being","score":0.8199999928474426}],"awards":[{"id":"https://openalex.org/G1183610800","display_name":"Evolution, persistence, and spread of endemic viruses","funder_award_id":"211225","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G1481412291","display_name":null,"funder_award_id":"101095619","funder_id":"https://openalex.org/F4320334322","funder_display_name":"HORIZON EUROPE Framework Programme"},{"id":"https://openalex.org/G1876066754","display_name":"Efficient and rapidly SCAlable EU-wide evidence-driven Pandemic response plans through dynamic Epidemic data assimilation","funder_award_id":"101095619","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2979637270","display_name":"Forschungspauschale Forschungsratspr\u00e4sident SNF","funder_award_id":"189498","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G323265177","display_name":"Tracking the COVID-19 epidemic in Switzerland: phylogenetics and epidemiological modeling","funder_award_id":"196046","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5726979388","display_name":"Epidemic intelligence to minimize 2019-nCoV\u2019s public health, economic and social impact in Europe","funder_award_id":"101003688","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6365289800","display_name":null,"funder_award_id":"101003688","funder_id":"https://openalex.org/F4320338448","funder_display_name":"HORIZON EUROPE European Innovation Council"},{"id":"https://openalex.org/G6948791793","display_name":null,"funder_award_id":"189498","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310992","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321099","display_name":"Bundesamt f\u00fcr Gesundheit","ror":"https://ror.org/01qtc5416"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null},{"id":"https://openalex.org/F4320335238","display_name":"Staatssekretariat f\u00fcr Bildung, Forschung und Innovation","ror":"https://ror.org/01kw63t33"},{"id":"https://openalex.org/F4320338448","display_name":"HORIZON EUROPE European Innovation Council","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409450771.pdf","grobid_xml":"https://content.openalex.org/works/W4409450771.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1042757214","https://openalex.org/W1965457228","https://openalex.org/W2094740420","https://openalex.org/W2110204999","https://openalex.org/W2130227690","https://openalex.org/W2160253520","https://openalex.org/W2320882304","https://openalex.org/W2482029392","https://openalex.org/W2577537660","https://openalex.org/W2605343262","https://openalex.org/W2753818523","https://openalex.org/W3004026249","https://openalex.org/W3008760660","https://openalex.org/W3013907808","https://openalex.org/W3015538318","https://openalex.org/W3015792206","https://openalex.org/W3020184843","https://openalex.org/W3022825990","https://openalex.org/W3026427469","https://openalex.org/W3027806553","https://openalex.org/W3030518044","https://openalex.org/W3048874187","https://openalex.org/W3055859021","https://openalex.org/W3087356468","https://openalex.org/W3092945599","https://openalex.org/W3096084589","https://openalex.org/W3107304136","https://openalex.org/W3112934818","https://openalex.org/W3114257716","https://openalex.org/W3126894445","https://openalex.org/W3132630010","https://openalex.org/W3139378956","https://openalex.org/W3155317409","https://openalex.org/W3165173849","https://openalex.org/W3181358231","https://openalex.org/W3190179650","https://openalex.org/W3194572293","https://openalex.org/W3197037893","https://openalex.org/W3198153170","https://openalex.org/W3215610096","https://openalex.org/W4290648800","https://openalex.org/W4291448064","https://openalex.org/W4310520627","https://openalex.org/W4312067632","https://openalex.org/W4378211593","https://openalex.org/W4378715587","https://openalex.org/W4378781879","https://openalex.org/W4385802596","https://openalex.org/W4386085719","https://openalex.org/W4389042267","https://openalex.org/W4393412447","https://openalex.org/W4393864525"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"The":[0,66],"wealth":[1],"of":[2,22,43,68,97,100,113,132,154,177,181,213,239,256,273,285,287,313],"genomic":[3,139,280],"data":[4,140],"that":[5,168,294],"was":[6,71],"generated":[7],"during":[8],"the":[9,20,33,41,51,95,98,110,114,130,178,188,229,240,247,254,271,290,298,305,308],"COVID-19":[10],"pandemic":[11],"provides":[12],"an":[13,237],"exceptional":[14],"opportunity":[15],"to":[16,29,72,77,228,267,300],"obtain":[17],"information":[18,269],"on":[19,171,270],"transmission":[21,226,272,306],"SARS-CoV-2.":[23],"Specifically,":[24],"there":[25],"is":[26],"great":[27],"interest":[28],"better":[30],"understand":[31],"how":[32],"effective":[34],"reproduction":[35],"number":[36],"[Formula:":[37,79,133,182,190],"see":[38,80,134,183,191],"text]":[39,81,135,184,192],"and":[40,60,63,82,116,136,166,185,202,223,243,276,307],"overdispersion":[42,309],"secondary":[44,311],"cases,":[45],"which":[46,105,217],"can":[47],"be":[48],"quantified":[49],"by":[50,199],"negative":[52],"binomial":[53],"dispersion":[54],"parameter":[55],"k,":[56,186],"changed":[57],"over":[58],"time":[59],"across":[61],"regions":[62],"viral":[64,85,108],"variants.":[65],"aim":[67],"our":[69,295],"study":[70,262],"develop":[73],"a":[74,91,125,147,264],"Bayesian":[75,126],"framework":[76],"infer":[78,268],"k":[83,137,203,214],"from":[84,138,163],"sequence":[86,102],"data.":[87,281],"First,":[88],"we":[89,106,120,151,292],"developed":[90],"mathematical":[92],"model":[93,123,145,235],"for":[94,221],"distribution":[96,180],"size":[99],"identical":[101,155],"clusters,":[103],"in":[104,146,157,161,215,232,289,310],"integrated":[107],"transmission,":[109],"mutation":[111],"rate":[112],"virus,":[115],"incomplete":[117],"case-detection.":[118],"Second,":[119],"implemented":[121],"this":[122,144],"within":[124],"inference":[127],"framework,":[128],"allowing":[129],"estimation":[131,238],"only.":[141],"We":[142,173,208],"validated":[143],"simulation":[148],"study.":[149],"Third,":[150],"identified":[152],"clusters":[153],"sequences":[156,160,286],"all":[158],"SARS-CoV-2":[159],"2021":[162],"Switzerland,":[164],"Denmark,":[165],"Germany":[167],"were":[169],"available":[170],"GISAID.":[172],"obtained":[174,198,249],"monthly":[175],"estimates":[176,193,197,212,248],"posterior":[179],"with":[187,205],"resulting":[189],"slightly":[194],"lower":[195],"than":[196],"other":[200,230,314],"methods,":[201],"comparable":[204],"previous":[206],"results.":[207],"found":[209],"comparatively":[210],"higher":[211],"Denmark":[216],"suggests":[218],"less":[219],"opportunities":[220],"superspreading":[222],"more":[224],"controlled":[225],"compared":[227],"countries":[231],"2021.":[233],"Our":[234,261],"included":[236],"case":[241],"detection":[242],"sampling":[244],"probability,":[245],"but":[246],"had":[250],"large":[251],"uncertainty,":[252],"reflecting":[253],"difficulty":[255],"estimating":[257],"these":[258],"parameters":[259],"simultaneously.":[260],"presents":[263],"novel":[265],"method":[266,296],"infectious":[274],"diseases":[275],"its":[277],"heterogeneity":[278],"using":[279],"With":[282],"increasing":[283],"availability":[284],"pathogens":[288],"future,":[291],"expect":[293],"has":[297],"potential":[299],"provide":[301],"new":[302],"insights":[303],"into":[304],"cases":[312],"pathogens.":[315]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}