{"id":"https://openalex.org/W4388201622","doi":"https://doi.org/10.7554/elife.84384.sa2","title":"Author response: Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks","display_name":"Author response: Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks","publication_year":2023,"publication_date":"2023-05-03","ids":{"openalex":"https://openalex.org/W4388201622","doi":"https://doi.org/10.7554/elife.84384.sa2"},"language":"en","primary_location":{"id":"doi:10.7554/elife.84384.sa2","doi":"https://doi.org/10.7554/elife.84384.sa2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7554/elife.84384.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"},"volume":null,"type":"peer-review","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dx.doi.org/10.7554/elife.84384.sa2","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023847954","display_name":"Arturo Torres Ortiz","orcid":"https://orcid.org/0000-0002-2492-0958","observed_orcids":["https://orcid.org/0000-0002-2492-0958"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Arturo Torres Ortiz","raw_affiliation_strings":["Department of Infection, Immunity and Inflammation, University College London","Department of Infectious Diseases, Imperial College London"],"raw_orcid":"https://orcid.org/0000-0002-2492-0958","affiliations":[{"raw_affiliation_string":"Department of Infection, Immunity and Inflammation, University College London","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Department of Infectious Diseases, Imperial College London","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068968591","display_name":"Michelle Kendall","orcid":"https://orcid.org/0000-0001-7344-7071","observed_orcids":["https://orcid.org/0000-0001-7344-7071"]},"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":false,"raw_author_name":"Michelle Kendall","raw_affiliation_strings":["Department of Statistics, University of Warwick"],"raw_orcid":"https://orcid.org/0000-0001-7344-7071","affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Warwick","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036864905","display_name":"Nathaniel Storey","orcid":"https://orcid.org/0000-0001-5942-4674","observed_orcids":["https://orcid.org/0000-0001-5942-4674"]},"institutions":[{"id":"https://openalex.org/I2800129641","display_name":"Great Ormond Street Hospital","ror":"https://ror.org/00zn2c847","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800129641","https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nathaniel Storey","raw_affiliation_strings":["Department of Microbiology, Great Ormond Street Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Great Ormond Street Hospital","institution_ids":["https://openalex.org/I2800129641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010792409","display_name":"James Hatcher","orcid":"https://orcid.org/0000-0003-2417-346X","observed_orcids":["https://orcid.org/0000-0003-2417-346X"]},"institutions":[{"id":"https://openalex.org/I2800129641","display_name":"Great Ormond Street Hospital","ror":"https://ror.org/00zn2c847","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800129641","https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James Hatcher","raw_affiliation_strings":["Department of Microbiology, Great Ormond Street Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Great Ormond Street Hospital","institution_ids":["https://openalex.org/I2800129641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044511474","display_name":"Helen Dunn","orcid":"https://orcid.org/0000-0002-7033-5143","observed_orcids":["https://orcid.org/0000-0002-7033-5143"]},"institutions":[{"id":"https://openalex.org/I2800129641","display_name":"Great Ormond Street Hospital","ror":"https://ror.org/00zn2c847","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800129641","https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Helen Dunn","raw_affiliation_strings":["Department of Microbiology, Great Ormond Street Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Great Ormond Street Hospital","institution_ids":["https://openalex.org/I2800129641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052349075","display_name":"Sunando Roy","orcid":"https://orcid.org/0000-0001-5968-9111","observed_orcids":["https://orcid.org/0000-0001-5968-9111"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sunando Roy","raw_affiliation_strings":["Department of Infection, Immunity and Inflammation, University College London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infection, Immunity and Inflammation, University College London","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109832744","display_name":"Rachel J. Williams","orcid":"https://orcid.org/0000-0001-8057-5063","observed_orcids":["https://orcid.org/0000-0001-8057-5063"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rachel Williams","raw_affiliation_strings":["UCL Genomics, University College London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCL Genomics, University College London","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084763274","display_name":"Charlotte A. Williams","orcid":"https://orcid.org/0000-0002-8586-8444","observed_orcids":["https://orcid.org/0000-0002-8586-8444"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Charlotte Williams","raw_affiliation_strings":["UCL Genomics, University College London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCL Genomics, University College London","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040571548","display_name":"Richard A. Goldstein","orcid":"https://orcid.org/0000-0001-5148-4672","observed_orcids":["https://orcid.org/0000-0001-5148-4672"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard A Goldstein","raw_affiliation_strings":["UCL Genomics, University College London"],"raw_orcid":"https://orcid.org/0000-0001-5148-4672","affiliations":[{"raw_affiliation_string":"UCL Genomics, University College London","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042745262","display_name":"Xavier Didelot","orcid":"https://orcid.org/0000-0003-1885-500X","observed_orcids":["https://orcid.org/0000-0003-1885-500X"]},"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":false,"raw_author_name":"Xavier Didelot","raw_affiliation_strings":["Department of Statistics, University of Warwick"],"raw_orcid":"https://orcid.org/0000-0003-1885-500X","affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Warwick","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006255142","display_name":"Kathryn Harris","orcid":"https://orcid.org/0000-0003-3807-9749","observed_orcids":["https://orcid.org/0000-0003-3807-9749"]},"institutions":[{"id":"https://openalex.org/I225661044","display_name":"Barts Health NHS Trust","ror":"https://ror.org/00b31g692","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I225661044"]},{"id":"https://openalex.org/I2800129641","display_name":"Great Ormond Street Hospital","ror":"https://ror.org/00zn2c847","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800129641","https://openalex.org/I2800349819"]},{"id":"https://openalex.org/I2801259928","display_name":"Royal London Hospital","ror":"https://ror.org/019my5047","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I225661044","https://openalex.org/I2801259928"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kathryn Harris","raw_affiliation_strings":["Department of Microbiology, Great Ormond Street Hospital","Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Great Ormond Street Hospital","institution_ids":["https://openalex.org/I2800129641"]},{"raw_affiliation_string":"Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust","institution_ids":["https://openalex.org/I225661044","https://openalex.org/I2801259928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070647783","display_name":"Judith Breuer","orcid":"https://orcid.org/0000-0001-8246-0534","observed_orcids":["https://orcid.org/0000-0001-8246-0534"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Judith Breuer","raw_affiliation_strings":["Department of Infection, Immunity and Inflammation, University College London"],"raw_orcid":"https://orcid.org/0000-0001-8246-0534","affiliations":[{"raw_affiliation_string":"Department of Infection, Immunity and Inflammation, University College London","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042365397","display_name":"Louis Grandjean","orcid":"https://orcid.org/0000-0002-1457-8327","observed_orcids":["https://orcid.org/0000-0002-1457-8327"]},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Louis Grandjean","raw_affiliation_strings":["Department of Infection, Immunity and Inflammation, University College London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infection, Immunity and Inflammation, University College London","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3000,"currency":"USD","value_usd":2500},"apc_paid":{"value":3000,"currency":"USD","value_usd":2500},"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"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":0.9506999850273132,"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":0.9506999850273132,"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/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.013799999840557575,"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":0.010099999606609344,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/sars-cov-2","display_name":"SARS-CoV-2","score":0.9980000257492065},{"id":"https://openalex.org/keywords/covid-19","display_name":"COVID-19 pandemic","score":0.9340000152587891},{"id":"https://openalex.org/keywords/within-host-viral-diversity","display_name":"within-host viral diversity","score":0.8669999837875366},{"id":"https://openalex.org/keywords/viral-subpopulations","display_name":"viral subpopulations","score":0.8009999990463257},{"id":"https://openalex.org/keywords/phylogenetic-reconstruction","display_name":"phylogenetic inference","score":0.8659999966621399},{"id":"https://openalex.org/keywords/genomic-epidemiology","display_name":"genomic epidemiology","score":0.6159999966621399},{"id":"https://openalex.org/keywords/hospital-outbreak","display_name":"hospital outbreak","score":0.6819999814033508},{"id":"https://openalex.org/keywords/contact-tracing","display_name":"contact tracing","score":0.5709999799728394},{"id":"https://openalex.org/keywords/genome-sequencing","display_name":"genome sequencing","score":0.4429999887943268}],"concepts":[{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.7982251644134521},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.6383547782897949},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6292191743850708},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.616685152053833},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.6050563454627991},{"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":0.5727601051330566},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.562797486782074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5142054557800293},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.45640695095062256},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.44537854194641113},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.4219365119934082},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.34829676151275635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2064187228679657},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.19984042644500732},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.14392709732055664},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14112815260887146},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.06641140580177307},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.05258217453956604},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.04750627279281616},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.04268428683280945},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.03928735852241516},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.03632357716560364},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.03576508164405823}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.7554/elife.84384.sa2","doi":"https://doi.org/10.7554/elife.84384.sa2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7554/elife.84384.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"}],"best_oa_location":{"id":"doi:10.7554/elife.84384.sa2","doi":"https://doi.org/10.7554/elife.84384.sa2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7554/elife.84384.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4386910567","https://openalex.org/W4210766426","https://openalex.org/W4387652881","https://openalex.org/W4379966847","https://openalex.org/W4401393818","https://openalex.org/W4310156776","https://openalex.org/W3025626435","https://openalex.org/W4366819684","https://openalex.org/W3164125857","https://openalex.org/W3175889053"],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-11-02T09:45:03.842371","created_date":"2023-11-02T00:00:00"}
