{"id":"https://openalex.org/W7214610062","doi":"https://doi.org/10.48550/arxiv.2609.30515","title":"Prevalence and the rate of antigenic evolution are jointly determined in an eco-evolutionary SIR model","display_name":"Prevalence and the rate of antigenic evolution are jointly determined in an eco-evolutionary SIR model","publication_year":2026,"publication_date":"2026-09-24","ids":{"openalex":"https://openalex.org/W7214610062","doi":"https://doi.org/10.48550/arxiv.2609.30515"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2609.30515","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.30515","pdf_url":"https://arxiv.org/pdf/2609.30515","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2609.30515","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5153240885","display_name":"Daniel Gomez","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gomez, Daniel","raw_affiliation_strings":["Department of Biology , University of Pennsylvania , Philadelphia , PA 19104 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology , University of Pennsylvania , Philadelphia , PA 19104 , USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073702596","display_name":"Joshua B. Plotkin","orcid":"https://orcid.org/0000-0003-2349-6304","observed_orcids":["https://orcid.org/0000-0003-2349-6304","https://orcid.org/0000-0001-6232-7613"]},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Plotkin, Joshua B.","raw_affiliation_strings":["Department of Biology , University of Pennsylvania , Philadelphia , PA 19104 , USA","Department of Mathematics and Statistics , University of New Mexico , Albuquerque , NM 87131 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology , University of Pennsylvania , Philadelphia , PA 19104 , USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Mathematics and Statistics , University of New Mexico , Albuquerque , NM 87131 , USA","institution_ids":["https://openalex.org/I169521973"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/2604","display_name":"Applied Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/2604","display_name":"Applied Mathematics"},"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":0.005400000140070915,"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/T10167","display_name":"Influenza Virus Research Studies","score":0.0010000000474974513,"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/influenza-a-virus","display_name":"influenza A virus","score":0.890999972820282},{"id":"https://openalex.org/keywords/antigenic-evolution","display_name":"antigenic evolution","score":0.796999990940094},{"id":"https://openalex.org/keywords/eco-evolutionary-dynamics","display_name":"eco-evolutionary dynamics","score":0.9210000038146973},{"id":"https://openalex.org/keywords/sir-model","display_name":"SIR model","score":0.8899999856948853},{"id":"https://openalex.org/keywords/cross-immunity","display_name":"cross-immunity","score":0.7760000228881836},{"id":"https://openalex.org/keywords/traveling-pulses","display_name":"traveling pulses","score":0.5059999823570251},{"id":"https://openalex.org/keywords/prevalence","display_name":"prevalence","score":0.47999998927116394},{"id":"https://openalex.org/keywords/antigenic-variation","display_name":"antigenic variation","score":0.621999979019165},{"id":"https://openalex.org/keywords/virulence","display_name":"virulence","score":0.6110000014305115},{"id":"https://openalex.org/keywords/host-lifespan","display_name":"host lifespan","score":0.7490000128746033},{"id":"https://openalex.org/keywords/immune-evasion","display_name":"immune evasion","score":0.878000020980835}],"concepts":[{"id":"https://openalex.org/C191942190","wikidata":"https://www.wikidata.org/wiki/Q4774739","display_name":"Antigenic variation","level":3,"score":0.8777999877929688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7461000084877014},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.629800021648407},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6122000217437744},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.6050999760627747},{"id":"https://openalex.org/C7842527","wikidata":"https://www.wikidata.org/wiki/Q575258","display_name":"Antigenic drift","level":4,"score":0.592199981212616},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5490000247955322},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5178999900817871},{"id":"https://openalex.org/C86282344","wikidata":"https://www.wikidata.org/wiki/Q575314","display_name":"Antigenic shift","level":5,"score":0.47429999709129333},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.448199987411499},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44020000100135803},{"id":"https://openalex.org/C2779341262","wikidata":"https://www.wikidata.org/wiki/Q182581","display_name":"Immunity","level":3,"score":0.4368000030517578},{"id":"https://openalex.org/C1627819","wikidata":"https://www.wikidata.org/wiki/Q2572354","display_name":"Epidemic model","level":3,"score":0.4350000023841858},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4000999927520752},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3971000015735626},{"id":"https://openalex.org/C52103748","wikidata":"https://www.wikidata.org/wiki/Q2624927","display_name":"Susceptible individual","level":3,"score":0.3497999906539917},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.32760000228881836},{"id":"https://openalex.org/C2781254715","wikidata":"https://www.wikidata.org/wiki/Q28454687","display_name":"Infection rate","level":2,"score":0.3046000003814697},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.295199990272522},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.29249998927116394},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2863999903202057},{"id":"https://openalex.org/C106192422","wikidata":"https://www.wikidata.org/wiki/Q736798","display_name":"Herd immunity","level":3,"score":0.26759999990463257},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.263700008392334},{"id":"https://openalex.org/C3018558359","wikidata":"https://www.wikidata.org/wiki/Q1660157","display_name":"Immune escape","level":3,"score":0.257999986410141},{"id":"https://openalex.org/C22070199","wikidata":"https://www.wikidata.org/wiki/Q192995","display_name":"Vaccination","level":2,"score":0.25519999861717224}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2609.30515","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.30515","pdf_url":"https://arxiv.org/pdf/2609.30515","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"doi:10.48550/arxiv.2609.30515","doi":"https://doi.org/10.48550/arxiv.2609.30515","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2609.30515","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2609.30515","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.30515","pdf_url":"https://arxiv.org/pdf/2609.30515","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[{"score":0.5683000087738037,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214610062.pdf","grobid_xml":"https://content.openalex.org/works/W7214610062.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1979158913","https://openalex.org/W2005034971","https://openalex.org/W2020891730","https://openalex.org/W2021562946","https://openalex.org/W2030332043","https://openalex.org/W2047647995","https://openalex.org/W2070521125","https://openalex.org/W2147683309","https://openalex.org/W2157547565","https://openalex.org/W2158189516","https://openalex.org/W2158892874","https://openalex.org/W2169437869","https://openalex.org/W3003257820","https://openalex.org/W3010900810"],"related_works":["https://openalex.org/W4403544790","https://openalex.org/W2892082830","https://openalex.org/W2080731247","https://openalex.org/W2316606359","https://openalex.org/W2123596119","https://openalex.org/W4414769050","https://openalex.org/W2100213887","https://openalex.org/W3098841843","https://openalex.org/W3131781247","https://openalex.org/W4200573720"],"abstract_inverted_index":{"Influenza":[0],"A":[1],"persists":[2],"by":[3,35,84],"continually":[4],"changing":[5],"the":[6,27,36,38,61,67,70,93,109,117,124,157,170],"antigens":[7],"that":[8,29,51],"its":[9],"host":[10,154,171],"population":[11],"recognizes.":[12],"How":[13],"fast":[14],"it":[15,21,59],"evolves":[16],"and":[17,56,73,100,120],"how":[18],"many":[19],"hosts":[20,75,162],"infects":[22],"are":[23,76],"not":[24],"independent,":[25],"because":[26],"immunity":[28],"selects":[30],"new":[31],"variants":[32],"is":[33,89,163,174],"produced":[34],"infections":[37],"pathogen":[39],"has":[40],"already":[41],"caused.":[42],"We":[43],"analyze":[44],"a":[45,79,90,97],"model":[46,71],"of":[47,111,126,160],"Andreasen":[48],"et.\\":[49],"al.\\":[50],"captures":[52],"this":[53],"eco-evolutionary":[54],"feedback,":[55],"we":[57,115],"extend":[58],"to":[60],"case":[62],"where":[63],"infection":[64],"may":[65],"kill":[66],"host.":[68],"In":[69,108],"infected":[72,94,161],"recovered":[74],"distributions":[77],"over":[78],"one-dimensional":[80],"antigenic":[81,103,113,127,136,143],"space":[82,104],"coupled":[83],"cross-immunity.":[85],"The":[86],"endemic":[87],"state":[88],"traveling":[91],"pulse:":[92],"distribution":[95],"keeps":[96],"fixed":[98],"shape":[99],"advances":[101],"through":[102],"at":[105,165],"constant":[106],"speed.":[107],"limit":[110],"weak":[112],"mutation":[114],"construct":[116],"pulse":[118],"asymptotically":[119],"find":[121],"that:":[122],"(i)":[123],"speed":[125],"evolution":[128],"decreases":[129],"as":[130],"prevalence":[131],"rises,":[132],"(ii)":[133],"less":[134],"standing":[135],"variation":[137],"accompanies":[138],"either":[139],"faster":[140],"or":[141,153],"slower":[142],"evolution,":[144],"depending":[145],"on":[146],"whether":[147],"pathogens":[148],"differ":[149],"in":[150],"immune":[151],"evasion":[152],"lifespan":[155],"(iii)":[156],"total":[158],"number":[159],"largest":[164],"an":[166],"intermediate":[167],"virulence":[168],"when":[169],"birth":[172],"rate":[173],"sufficiently":[175],"low.":[176]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-09-29T00:00:00"}
