{"id":"https://openalex.org/W2980386288","doi":"https://doi.org/10.1101/814673","title":"The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study","display_name":"The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study","publication_year":2019,"publication_date":"2019-10-22","ids":{"openalex":"https://openalex.org/W2980386288","doi":"https://doi.org/10.1101/814673","mag":"2980386288"},"language":"en","primary_location":{"id":"doi:10.1101/814673","doi":"https://doi.org/10.1101/814673","is_oa":true,"landing_page_url":"https://doi.org/10.1101/814673","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/10/22/814673.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/10/22/814673.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072330537","display_name":"Michael A. Martin","orcid":"https://orcid.org/0000-0002-9689-4066","observed_orcids":["https://orcid.org/0000-0002-9689-4066"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael A. Martin","raw_affiliation_strings":["Department of Biology, Emory University, Atlanta, GA, USA","Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA","Department of Biology, Emory University","Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Biology, Emory University","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060771136","display_name":"Drishti Kaul","orcid":"https://orcid.org/0000-0002-0451-8486","observed_orcids":["https://orcid.org/0000-0002-0451-8486"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Drishti Kaul","raw_affiliation_strings":["Infectious Diseases, The J. Craig Venter Institute, La Jolla, California, USA","Infectious Diseases, The J. Craig Venter Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Diseases, The J. Craig Venter Institute, La Jolla, California, USA","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"Infectious Diseases, The J. Craig Venter Institute","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040276909","display_name":"Gene S. Tan","orcid":"https://orcid.org/0000-0002-8965-1509","observed_orcids":["https://orcid.org/0000-0002-8965-1509","https://orcid.org/0000-0002-0975-0719"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gene S. Tan","raw_affiliation_strings":["Division of Infectious Diseases, Department of Medicine, University California San Diego, La Jolla, California, USA","Infectious Diseases, The J. Craig Venter Institute, La Jolla, California, USA","Division of Infectious Diseases, Department of Medicine, University California San Diego","Infectious Diseases, The J. Craig Venter Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, University California San Diego, La Jolla, California, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Infectious Diseases, The J. Craig Venter Institute, La Jolla, California, USA","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"Division of Infectious Diseases, Department of Medicine, University California San Diego","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Infectious Diseases, The J. Craig Venter Institute","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007833163","display_name":"Christopher W. Woods","orcid":"https://orcid.org/0000-0001-7240-2453","observed_orcids":["https://orcid.org/0000-0001-7240-2453"]},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher W. Woods","raw_affiliation_strings":["Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA","Center for Applied Genomics and Precision Medicine, Duke University School of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210126298"]},{"raw_affiliation_string":"Center for Applied Genomics and Precision Medicine, Duke University School of Medicine","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210126298"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063407314","display_name":"Katia Koelle","orcid":"https://orcid.org/0000-0002-0254-6141","observed_orcids":["https://orcid.org/0000-0002-0254-6141"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katia Koelle","raw_affiliation_strings":["Department of Biology, Emory University, Atlanta, GA, USA","Department of Biology, Emory University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Emory University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Biology, Emory University","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5072330537"],"corresponding_institution_ids":["https://openalex.org/I150468666"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":7,"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/T10167","display_name":"Influenza Virus Research Studies","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T10167","display_name":"Influenza Virus Research Studies","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.006399999838322401,"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/T11243","display_name":"Respiratory viral infections research","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/h3n2","display_name":"H3N2","score":0.9610000252723694},{"id":"https://openalex.org/keywords/defective-viral-genomes","display_name":"defective viral genomes","score":0.9990000128746033},{"id":"https://openalex.org/keywords/genetic-drift","display_name":"genetic drift","score":0.8230000138282776},{"id":"https://openalex.org/keywords/viral-population-dynamics","display_name":"viral population dynamics","score":0.593999981880188},{"id":"https://openalex.org/keywords/human-challenge-studies","display_name":"human challenge studies","score":0.656000018119812},{"id":"https://openalex.org/keywords/disease-severity","display_name":"disease severity","score":0.7070000171661377},{"id":"https://openalex.org/keywords/virus-titer","display_name":"viral titer","score":0.35899999737739563}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7872607707977295},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5865612030029297},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.5561891198158264},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5257535576820374},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.5220051407814026},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4980342388153076},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.45334717631340027},{"id":"https://openalex.org/C2777546802","wikidata":"https://www.wikidata.org/wiki/Q834390","display_name":"Influenza A virus","level":3,"score":0.44660618901252747},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41755348443984985},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.4149206280708313},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4013459086418152},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3861083984375},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08084899187088013},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/814673","doi":"https://doi.org/10.1101/814673","is_oa":true,"landing_page_url":"https://doi.org/10.1101/814673","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/10/22/814673.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/814673","doi":"https://doi.org/10.1101/814673","is_oa":true,"landing_page_url":"https://doi.org/10.1101/814673","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/10/22/814673.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8999999761581421}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2394953455","display_name":null,"funder_award_id":"HHSN272200900007C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3617891517","display_name":"The J. Craig Venter Institute Genome Center for Infectious Diseases","funder_award_id":"U19AI110819","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4903124716","display_name":null,"funder_award_id":"NC66001","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G7818234022","display_name":null,"funder_award_id":"W911NF-17-2-0034","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2980386288.pdf","grobid_xml":"https://content.openalex.org/works/W2980386288.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W181611061","https://openalex.org/W1478284728","https://openalex.org/W1550747493","https://openalex.org/W1587026990","https://openalex.org/W1786607516","https://openalex.org/W1795100282","https://openalex.org/W1970497184","https://openalex.org/W1971382242","https://openalex.org/W1974372768","https://openalex.org/W1984284869","https://openalex.org/W1988747748","https://openalex.org/W1995755137","https://openalex.org/W2022019185","https://openalex.org/W2023388704","https://openalex.org/W2023822106","https://openalex.org/W2036182565","https://openalex.org/W2041315270","https://openalex.org/W2043701535","https://openalex.org/W2048987737","https://openalex.org/W2051899627","https://openalex.org/W2067832820","https://openalex.org/W2071516717","https://openalex.org/W2086162889","https://openalex.org/W2086666408","https://openalex.org/W2096907185","https://openalex.org/W2098795484","https://openalex.org/W2098803005","https://openalex.org/W2101350700","https://openalex.org/W2108234281","https://openalex.org/W2112637120","https://openalex.org/W2114389380","https://openalex.org/W2116054283","https://openalex.org/W2118622042","https://openalex.org/W2127827982","https://openalex.org/W2127883868","https://openalex.org/W2130338247","https://openalex.org/W2131271579","https://openalex.org/W2134126529","https://openalex.org/W2139359573","https://openalex.org/W2145686583","https://openalex.org/W2146607614","https://openalex.org/W2154349465","https://openalex.org/W2158073495","https://openalex.org/W2159324451","https://openalex.org/W2159954944","https://openalex.org/W2169456326","https://openalex.org/W2527990262","https://openalex.org/W2608565547","https://openalex.org/W2762066873","https://openalex.org/W2791412679","https://openalex.org/W2801701694","https://openalex.org/W2810440784","https://openalex.org/W2896071441","https://openalex.org/W4230096730"],"related_works":["https://openalex.org/W4399261726","https://openalex.org/W4388837454","https://openalex.org/W2527990262","https://openalex.org/W7126259754","https://openalex.org/W2762066873","https://openalex.org/W3035086373","https://openalex.org/W4415833602","https://openalex.org/W4411339217","https://openalex.org/W2998742227","https://openalex.org/W1981950460"],"abstract_inverted_index":{"Abstract":[0],"The":[1,16,249],"rapid":[2],"evolution":[3,250],"of":[4,20,52,74,79,127,145,155,189,201,225,234,251,256,263,315,321,345,358,369],"influenza":[5,37,135,252,272],"is":[6,273,285,336],"an":[7,125],"important":[8,367],"contributing":[9],"factor":[10],"to":[11,42,106,118,180,209,275,330],"its":[12],"high":[13],"worldwide":[14],"incidence.":[15],"emergence":[17],"and":[18,31,91,236,260,283,295,327],"spread":[19],"genetic":[21,153,241,370],"point":[22],"mutations":[23],"has":[24,266],"been":[25,85,104,267],"thoroughly":[26],"studied":[27,268],"both":[28,165,292],"within":[29,32,169,228,293],"populations":[30,110,157,227,375],"individual":[33,115],"hosts.":[34,176],"In":[35],"addition,":[36],"viruses":[38],"are":[39,59],"also":[40],"known":[41,274,286],"generate":[43,276],"genomic":[44],"variation":[45],"during":[46,281,376],"their":[47,119,245,324,328,362],"replication":[48,75],"in":[49,64,87,112,114,130,147,244,254,269,301,333,349,372],"the":[50,77,143,152,199,223,232,237,261,297,319,343,356,366],"form":[51],"defective":[53,277],"viral":[54,214,278,381],"genomes":[55,279,290],"(DVGs).":[56],"These":[57,100],"DVGs":[58,82,128,146,162,193,197,311,348],"formed":[60],"by":[61],"internal":[62],"deletions":[63],"at":[65,296],"least":[66],"one":[67],"gene":[68,264],"segment":[69],"that":[70,240,306],"render":[71],"them":[72],"incapable":[73],"without":[76],"presence":[78,205],"wild-type":[80],"virus.":[81],"have":[83,102,304],"previously":[84],"identified":[86],"natural":[88],"human":[89,138,334,352],"infections":[90,116,378],"may":[92],"be":[93,210],"associated":[94,211],"with":[95,212,379],"less":[96],"severe":[97],"clinical":[98],"outcomes.":[99],"studies":[101,354],"not":[103,185,207,337],"able":[105],"address":[107],"how":[108,288],"DVG":[109,156,204,226,374],"evolve":[111,291],"vivo":[113],"due":[117,179],"cross-sectional":[120],"design.":[121],"Here":[122],"we":[123,183,341],"present":[124,129],"analysis":[126],"samples":[131,168,350],"from":[132,351],"two":[133],"longitudinal":[134],"A":[136],"H3N2":[137],"challenge":[139,353],"studies.":[140],"We":[141,360],"observe":[142,186],"generation":[144],"almost":[148],"all":[149],"subjects.":[150],"Although":[151],"composition":[154],"was":[158,206],"highly":[159],"variable,":[160],"identical":[161],"were":[163],"observed":[164],"between":[166,175],"multiple":[167],"single":[170,257],"hosts":[171,294,335],"as":[172,174],"well":[173,338],"Most":[177],"likely":[178],"stochastic":[181],"effects,":[182],"did":[184],"clear":[187],"instances":[188],"selection":[190],"for":[191,195],"specific":[192],"or":[194,216,308],"shorter":[196],"over":[198,231],"course":[200,233,357],"infection.":[202,359],"Furthermore,":[203],"found":[208],"peak":[213,217],"titer":[215],"symptom":[218],"scores.":[219],"Our":[220],"analyses":[221],"highlight":[222],"diversity":[224],"a":[229],"host":[230],"infection":[235],"apparent":[238],"role":[239,368],"drift":[242,371],"plays":[243],"population":[246,298],"dynamics.":[247],"Importance":[248],"virus,":[253],"terms":[255],"nucleotide":[258],"variants":[259],"reassortment":[262],"segments,":[265],"detail.":[270],"However,":[271,318],"(DVGs)":[280],"replication,":[282],"little":[284],"about":[287],"these":[289],"level.":[299],"Studies":[300],"animal":[302],"models":[303],"indicated":[305],"prophylactically":[307],"therapeutically":[309],"administered":[310],"can":[312],"impact":[313],"patterns":[314],"disease":[316,331],"progression.":[317],"formation":[320,344],"naturally-occurring":[322],"DVGs,":[323],"evolutionary":[325,363],"dynamics,":[326],"contribution":[329],"severity":[332],"understood.":[339],"Here,":[340],"identify":[342],"de":[346],"novo":[347],"throughout":[355],"analyze":[361],"trajectories,":[364],"revealing":[365],"shaping":[373],"acute":[377],"well-adapted":[380],"strains.":[382]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2019-10-25T00:00:00"}