{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T07:47:27Z","timestamp":1790668047122,"version":"4.1.0"},"reference-count":95,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T00:00:00Z","timestamp":1741305600000},"content-version":"vor","delay-in-days":65,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004191","name":"Novo Nordisk","doi-asserted-by":"publisher","award":["NNF19OC0056326"],"award-info":[{"award-number":["NNF19OC0056326"]}],"id":[{"id":"10.13039\/501100004191","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004191","name":"Novo Nordisk","doi-asserted-by":"publisher","award":["NNF19OC0056326"],"award-info":[{"award-number":["NNF19OC0056326"]}],"id":[{"id":"10.13039\/501100004191","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Transmission of influenza A viruses (IAVs) between pigs and humans can trigger pandemics but more often cease as isolated infections without further spread in the new host species population. In Denmark, a major pig-producing country, the first two detections of human infections with swine-like IAVs were reported in 2021. These zoonotic IAVs were reassortants of the H1N1 pandemic 2009 lineage (\u201cH1N1pdm09,\u201d H1 lineage 1A, clade 1A.3.3.2) introduced to swine farms in Denmark through humans approximately 11\u2009years prior. However, predicting the likelihood and outcome of such IAV spillovers is challenging without a better understanding of the viral determinants. This study traced the evolution of H1N1pdm09 from 207 sequenced genomes as the virus propagated across Danish swine farms over a decade. H1N1pdm09 diverged into several genetically distinct viral populations, largely prompted by reassortments with neuraminidase (NA) segments from other enzootic IAV lineages. The genomic segments encoding the viral envelope glycoproteins, hemagglutinin (HA) and NA, evolved at the fastest rates, while the M and NS genomic segments were among the lowest evolutionary rates. The two zoonotic IAVs emerged from separate viral populations and shared the highest number of amino acid mutations in the PB2 and HA proteins. Acquisition of additional predicted glycosylation sites on the HA proteins of the zoonotic IAVs may have facilitated infection of the human patients. Ultimately, the analysis provides a foundation from which to further explore viral genetic indicators of host adaptation and zoonotic risk.<\/jats:p>","DOI":"10.1093\/ve\/veaf014","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T13:14:36Z","timestamp":1741353276000},"source":"Crossref","is-referenced-by-count":6,"title":["Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-8158-4017","authenticated-orcid":false,"given":"Sophie","family":"George","sequence":"first","affiliation":[{"name":"Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C 1870,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pia","family":"Ryt-Hansen","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C 1870,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9650-8965","authenticated-orcid":false,"given":"Anders Gorm","family":"Pedersen","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark , Kgs. Lyngby, Hovedstaden 2800,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2459-8583","authenticated-orcid":false,"given":"Klara M","family":"Anker","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark , Kgs. Lyngby, Hovedstaden 2800,","place":["Denmark"]},{"name":"Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut , Copenhagen S, Hovedstaden 2300,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob N","family":"Nissen","sequence":"additional","affiliation":[{"name":"Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut , Copenhagen S, Hovedstaden 2300,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesper S","family":"Krog","sequence":"additional","affiliation":[{"name":"Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut , Copenhagen S, Hovedstaden 2300,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7557-8876","authenticated-orcid":false,"given":"Charlotte K","family":"Hjulsager","sequence":"additional","affiliation":[{"name":"Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut , Copenhagen S, Hovedstaden 2300,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2352-5726","authenticated-orcid":false,"given":"Ramona","family":"Trebbien","sequence":"additional","affiliation":[{"name":"Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut , Copenhagen S, Hovedstaden 2300,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars E","family":"Larsen","sequence":"additional","affiliation":[{"name":"Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C 1870,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,3,7]]},"reference":[{"key":"2025071112131425400_R1","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1128\/jvi.02681-13","article-title":"Impact of potential permissive neuraminidase mutations on viral fitness of the H275Y oseltamivir-resistant influenza A(H1N1)Pdm09 virus in vitro, in mice and in ferrets","volume":"88","author":"Abed","year":"2014","journal-title":"J Virol"},{"key":"2025071112131425400_R2","doi-asserted-by":"publisher","first-page":"e01206","DOI":"10.1128\/JVI.01206-18","article-title":"Functional evolution of the 2009 pandemic H1N1 influenza virus NS1 and PA in humans","volume":"92","author":"Aitor","year":"2018","journal-title":"J Virol"},{"key":"2025071112131425400_R3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31147-0","article-title":"Influenza a virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks","volume":"13","author":"Amato","year":"2022","journal-title":"Nat Commun"},{"key":"2025071112131425400_R4","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.3201\/eid2812.220935","article-title":"Severe human case of zoonotic infection with swine-origin influenza A virus, Denmark, 2021","volume":"28","author":"Andersen","year":"2022","journal-title":"Emerg Infect Dis"},{"key":"2025071112131425400_R5","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a038737","article-title":"Swine influenza A viruses and the tangled relationship with humans","volume":"11","author":"Anderson","year":"2021","journal-title":"Cold Spring Harbor Perspect Med"},{"key":"2025071112131425400_R6","doi-asserted-by":"publisher","first-page":"e00275","DOI":"10.1128\/mSphere.00275-16","article-title":"A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from Swine influenza A viruses","volume":"1","author":"Anderson","year":"2016","journal-title":"MSphere"},{"key":"2025071112131425400_R7","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-31397-3","article-title":"Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates","volume":"8","author":"Arai","year":"2018","journal-title":"Sci Rep"},{"key":"2025071112131425400_R8","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1126\/science.1228172","article-title":"The structure of native influenza virion ribonucleoproteins","volume":"338","author":"Arranz","year":"2012","journal-title":"Science"},{"key":"2025071112131425400_R9","doi-asserted-by":"publisher","DOI":"10.3390\/v12091013","article-title":"Infection dynamics of swine influenza virus in a Danish pig herd reveals recurrent infections with different variants of the H1N2 Swine influenza A virus subtype","volume":"12","author":"Bhatta","year":"2020","journal-title":"Viruses"},{"key":"2025071112131425400_R10","doi-asserted-by":"publisher","first-page":"W214","DOI":"10.1093\/nar\/gki385","article-title":"GlyProt: in silico glycosylation of proteins","volume":"33","author":"Bohne-Lang","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2025071112131425400_R11","doi-asserted-by":"publisher","first-page":"28411","DOI":"10.1074\/jbc.R110.117531","article-title":"Influenza A virus polymerase: structural insights into replication and host adaptation mechanisms","volume":"285","author":"Boivin","year":"2010","journal-title":"J Biol Chem"},{"key":"2025071112131425400_R12","doi-asserted-by":"publisher","first-page":"e01930","DOI":"10.1128\/JVI.01930-19","article-title":"A single amino acid at position 431 of the PB2 protein determines the virulence of H1N1 Swine influenza viruses in mice","volume":"94","author":"Chengzhi","year":"2020","journal-title":"J Virol"},{"key":"2025071112131425400_R13","doi-asserted-by":"publisher","first-page":"e00721","DOI":"10.1128\/JVI.00721-17","article-title":"Functional evolution of influenza virus ns1 protein in currently circulating human 2009 pandemic H1N1 viruses","volume":"91","author":"Clark","year":"2017","journal-title":"J Virol"},{"key":"2025071112131425400_R14","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1016\/S1473-3099(12)70121-4","article-title":"Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study","volume":"12","author":"Dawood","year":"2012","journal-title":"Lancet Infect Dis"},{"key":"2025071112131425400_R15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29402-5","article-title":"Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination","volume":"13","author":"Dhanasekaran","year":"2022","journal-title":"Nat Commun"},{"key":"2025071112131425400_R16","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1099\/jgv.0.000500","article-title":"A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on M7GTP ligand binding","volume":"97","author":"Dipali","year":"2016","journal-title":"J Gen Virol"},{"key":"2025071112131425400_R17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34611-z","article-title":"Influenza A virus reassortment in mammals gives rise to genetically distinct within-host subpopulations","volume":"13","author":"Ganti","year":"2022","journal-title":"Nat Commun"},{"key":"2025071112131425400_R18","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00945-20","article-title":"Human monoclonal antibody derived from transchromosomic cattle neutralizes multiple H1 clades of influenza A virus by recognizing a novel conformational epitope in the hemagglutinin head domain","volume":"94","author":"Gao","year":"2020","journal-title":"J Virol"},{"key":"2025071112131425400_R19","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1126\/science.1176225","article-title":"Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans","volume":"325","author":"Garten","year":"2009","journal-title":"Science"},{"key":"2025071112131425400_R20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-33529-w","article-title":"Structural characterisation of hemagglutinin from seven influenza A H1N1 strains reveal diversity in the C05 antibody recognition site","volume":"13","author":"Ghafoori","year":"2023","journal-title":"Sci Rep"},{"key":"2025071112131425400_R21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008109","article-title":"Childhood immune imprinting to influenza A shapes birth year-specific risk during seasonal H1N1 and H3N2 epidemics","volume":"15","author":"Gostic","year":"2019","journal-title":"PLoS Pathogens"},{"key":"2025071112131425400_R22","doi-asserted-by":"publisher","DOI":"10.3390\/v15091959","article-title":"Fitness determinants of influenza A viruses","volume":"15","author":"Griffin","year":"2023","journal-title":"Viruses"},{"key":"2025071112131425400_R23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36389-0","article-title":"The ubiquitination landscape of the influenza A virus polymerase","volume":"14","author":"G\u00fcnl","year":"2023","journal-title":"Nat Commun"},{"key":"2025071112131425400_R24","first-page":"310","article-title":"Prediction of glycosylation across the human proteome and the correlation to protein function","volume":"7","author":"Gupta","year":"2002","journal-title":"Pac Symp Biocomput"},{"key":"2025071112131425400_R25","doi-asserted-by":"publisher","first-page":"6909","DOI":"10.1128\/JVI.00081-10","article-title":"Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein","volume":"84","author":"Hale","year":"2010","journal-title":"J Virol"},{"key":"2025071112131425400_R26","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1038\/s41579-023-00945-8","article-title":"Co-evolution of immunity and seasonal influenza viruses","volume":"21","author":"Han","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"2025071112131425400_R27","doi-asserted-by":"publisher","first-page":"7131","DOI":"10.1128\/JVI.00954-16","article-title":"Critical role of the PA-X C-terminal domain of influenza A Virus in its subcellular localization and shutoff activity","volume":"90","author":"Hayashi","year":"2016","journal-title":"J Virol"},{"key":"2025071112131425400_R28","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1016\/j.chom.2020.07.006","article-title":"Surveillance of European domestic pig populations identifies an emerging reservoir of potentially zoonotic swine influenza A viruses","volume":"28","author":"Henritzi","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2025071112131425400_R29","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.coviro.2014.07.007","article-title":"Challenges of selecting seasonal influenza vaccine strains for humans with diverse pre-exposure histories","volume":"8","author":"Hensley","year":"2014","journal-title":"Curr Opin Virol"},{"key":"2025071112131425400_R30","doi-asserted-by":"publisher","first-page":"8607","DOI":"10.1128\/JVI.00159-10","article-title":"Adaptation of pandemic H1N1 influenza viruses in mice","volume":"84","author":"Ilyushina","year":"2010","journal-title":"J Virol"},{"key":"2025071112131425400_R31","doi-asserted-by":"publisher","first-page":"2169","DOI":"10.4049\/jimmunol.1202433","article-title":"Addition of glycosylation to influenza A virus hemagglutinin modulates antibody-mediated recognition of H1N1 2009 pandemic viruses","volume":"190","author":"Job","year":"2013","journal-title":"J Immunol"},{"key":"2025071112131425400_R32","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1243567","article-title":"Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil","volume":"14","author":"Junqueira","year":"2023","journal-title":"Front Microbiol"},{"key":"2025071112131425400_R33","doi-asserted-by":"publisher","first-page":"10807","DOI":"10.1128\/jvi.74.22.10807-10810.2000","article-title":"Molecular correlates of influenza A H5N1 virus pathogenesis in mice","volume":"74","author":"Katz","year":"2000","journal-title":"J Virol"},{"key":"2025071112131425400_R34","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Kazutaka","year":"2013","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011341","article-title":"Pandemic (H1N1) 2009 influenza community transmission was established in one Australian state when the virus was first identified in North America","volume":"5","author":"Kelly","year":"2010","journal-title":"PLoS One"},{"key":"2025071112131425400_R36","doi-asserted-by":"publisher","first-page":"3035","DOI":"10.1007\/s00705-018-3962-z","article-title":"Evolution and dynamics of the pandemic H1N1 influenza hemagglutinin protein from 2009 to 2017","volume":"163","author":"Khatib","year":"2018","journal-title":"Arch Virol"},{"key":"2025071112131425400_R37","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28706-1","article-title":"The influenza virus hemagglutinin head evolves faster than the stalk domain","volume":"8","author":"Kirkpatrick","year":"2018","journal-title":"Sci Rep"},{"key":"2025071112131425400_R38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41572-018-0002-y","article-title":"Influenza","volume":"4","author":"Krammer","year":"2018","journal-title":"Nat Rev Dis Prim"},{"key":"2025071112131425400_R39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002443","article-title":"Eurasian-origin gene segments contribute to the transmissibility, aerosol release, and morphology of the 2009 pandemic H1N1 influenza virus","volume":"7","author":"Lakdawala","year":"2011","journal-title":"PLoS Pathogens"},{"key":"2025071112131425400_R40","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/978-1-4939-7366-8_4","volume-title":"Protein Engineering: Methods and Protocols","author":"Land","year":"2018"},{"key":"2025071112131425400_R41","article-title":"\u00c5rsstatistikker for Grisek\u00f8d","author":"Landbrug & F\u00f8devarer","year":".."},{"key":"2025071112131425400_R42","doi-asserted-by":"publisher","DOI":"10.3390\/v10090475","article-title":"Host shutoff in influenza A virus: many means to an end","volume":"10","author":"Levene","year":"2018","journal-title":"Viruses"},{"key":"2025071112131425400_R43","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41579-018-0115-z","article-title":"Host and viral determinants of influenza A virus species specificity","volume":"17","author":"Long","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2025071112131425400_R44","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1111143","article-title":"Vaccination against swine influenza in pigs causes different drift evolutionary patterns upon swine influenza virus experimental infection and reduces the likelihood of genomic reassortments","volume":"13","author":"L\u00f3pez-Vali\u00f1as","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"2025071112131425400_R45","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003279","article-title":"Pandemic influenza A viruses escape from restriction by human MxA through adaptive mutations in the nucleoprotein","volume":"9","author":"M\u00e4nz","year":"2013","journal-title":"PLoS Pathogens"},{"key":"2025071112131425400_R46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011476","article-title":"Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential","volume":"19","author":"Markin","year":"2023","journal-title":"PLoS Pathogens"},{"key":"2025071112131425400_R47","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.16777","article-title":"Origins of the 2009 H1N1 influenza pandemic in swine in Mexico","volume":"5","author":"Mena","year":"2016","journal-title":"eLife"},{"key":"2025071112131425400_R48","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2203919119","article-title":"A Eurasian avian-like H1N1 swine influenza reassortant virus became pathogenic and highly transmissible due to mutations in its PA gene","volume":"119","author":"Meng","year":"2022","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112131425400_R49","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a038489","article-title":"The ecology and evolution of influenza viruses","volume":"10","author":"Michelle","year":"2020","journal-title":"Cold Spring Harbor Perspect Med"},{"key":"2025071112131425400_R50","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R51","doi-asserted-by":"publisher","first-page":"e10","DOI":"10.1097\/CCM.0b013e3181ceb25b","article-title":"The 1918 influenza pandemic: lessons for 2009 and the future","volume":"38","author":"Morens","year":"2010","journal-title":"Crit Care Med"},{"key":"2025071112131425400_R52","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002764","article-title":"Detecting individual sites subject to episodic diversifying selection","volume":"8","author":"Murrell","year":"2012","journal-title":"PLoS Genet"},{"key":"2025071112131425400_R53","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1086\/512813","article-title":"Cases of swine influenza in humans: a review of the literature","volume":"44","author":"Myers","year":"2007","journal-title":"Clinl Infect Dis"},{"key":"2025071112131425400_R54","doi-asserted-by":"publisher","first-page":"3202","DOI":"10.3201\/eid2712.211361","article-title":"Reassortant influenza A(H1N1)Pdm09 virus in elderly woman, Denmark, January 2021","volume":"27","author":"Nissen","year":"2021","journal-title":"Emerg Infect Dis"},{"key":"2025071112131425400_R55","doi-asserted-by":"publisher","DOI":"10.3390\/genes12060809","article-title":"Origin, evolution and stability of overlapping genes in viruses: a systematic review","volume":"12","author":"Pavesi","year":"2021","journal-title":"Genes"},{"key":"2025071112131425400_R56","doi-asserted-by":"publisher","first-page":"e00213","DOI":"10.1128\/jvi.00213-23","article-title":"Mammalian ANP32A and ANP32B proteins drive differential polymerase adaptations in avian influenza virus","volume":"97","author":"Peacock","year":"2023","journal-title":"J Virol"},{"key":"2025071112131425400_R57","doi-asserted-by":"publisher","first-page":"2573","DOI":"10.1073\/pnas.1200039109","article-title":"Hemagglutinin stalk antibodies elicited by the 2009 pandemic influenza virus as a mechanism for the extinction of seasonal H1N1 viruses","volume":"109","author":"Pica","year":"2012","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112131425400_R58","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2016.0138","article-title":"High turnover drives prolonged persistence of influenza in managed pig herds","volume":"13","author":"Pitzer","year":"2016","journal-title":"J Royal Soc Interface"},{"key":"2025071112131425400_R59","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: a comparison of methods for detecting amino acid sites under selection","volume":"22","author":"Pond","year":"2005","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R60","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1093\/molbev\/msz197","article-title":"HyPhy 2.5\u2014a customizable platform for evolutionary hypothesis testing using phylogenies","volume":"37","author":"Pond","year":"2020","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R61","doi-asserted-by":"publisher","first-page":"1891","DOI":"10.1093\/molbev\/msl051","article-title":"Automated phylogenetic detection of recombination using a genetic algorithm","volume":"23","author":"Pond","year":"2006","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R62","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1128\/JVI.05699-11","article-title":"Combination of PB2 271A and SR polymorphism at positions 590\/591 is critical for viral replication and virulence of swine influenza virus in cultured cells and in vivo","volume":"86","author":"Qinfang","year":"2012","journal-title":"J Virol"},{"key":"2025071112131425400_R63","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evolut"},{"key":"2025071112131425400_R64","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1073\/pnas.1715471115","article-title":"Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody","volume":"115","author":"Raymond","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112131425400_R65","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/nature05114","article-title":"The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design","volume":"443","author":"Russell","year":"2006","journal-title":"Nature"},{"key":"2025071112131425400_R66","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0224854","article-title":"Acute influenza A virus outbreak in an enzootic infected sow herd: impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination","volume":"14","author":"Ryt-Hansen","year":"2019","journal-title":"PLoS One"},{"key":"2025071112131425400_R67","doi-asserted-by":"publisher","DOI":"10.3390\/v12020248","article-title":"Substantial antigenic drift in the hemagglutinin protein of swine influenza A viruses","volume":"12","author":"Ryt-Hansen","year":"2020","journal-title":"Viruses"},{"key":"2025071112131425400_R68","article-title":"Overv\u00e5gning af influenza a virus i svin Slutrapport 2021","author":"Ryt-Hansen","year":"2022"},{"key":"2025071112131425400_R69","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.60940","article-title":"Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses","volume":"10","author":"Ryt-Hansen","year":"2021","journal-title":"eLife"},{"key":"2025071112131425400_R70","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vex042","article-title":"TreeTime: maximum-likelihood phylodynamic analysis","volume":"4","author":"Sagulenko","year":"2018","journal-title":"Virus Evolut"},{"key":"2025071112131425400_R71","doi-asserted-by":"publisher","DOI":"10.1186\/s40813-021-00196-0","article-title":"Current and prospective control strategies of influenza A virus in swine","volume":"7","author":"Salvesen","year":"2021","journal-title":"Porcine Health Manag"},{"key":"2025071112131425400_R72","doi-asserted-by":"publisher","DOI":"10.1038\/srep15928","article-title":"Adaptation of H9N2 AIV in guinea pigs enables efficient transmission by direct contact and inefficient transmission by respiratory droplets","volume":"5","author":"Sang","year":"2015","journal-title":"Sci Rep"},{"key":"2025071112131425400_R73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1011317","article-title":"Repeatability and timing of tropical influenza epidemics","volume":"19","author":"Servadio","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2025071112131425400_R74","doi-asserted-by":"publisher","DOI":"10.3390\/ijms18081650","article-title":"Evolution of influenza A virus by mutation and re-assortment","volume":"18","author":"Shao","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2025071112131425400_R75","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1093\/molbev\/msv022","article-title":"Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection","volume":"32","author":"Smith","year":"2015","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R76","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/978-1-4939-9074-0_14","volume-title":"Evolutionary Genomics: Statistical and Computational Methods","author":"Spielman","year":"2019"},{"key":"2025071112131425400_R77","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.1038\/emboj.2013.79","article-title":"Precision mapping of the human O-GalNAc glycoproteome through simplecell technology","volume":"32","author":"Steentoft","year":"2013","journal-title":"EMBO J"},{"key":"2025071112131425400_R78","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms8952","article-title":"Phylodynamics of H1N1\/2009 influenza reveals the transition from host adaptation to immune-driven selection","volume":"6","author":"Su","year":"2015","journal-title":"Nat Commun"},{"key":"2025071112131425400_R79","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Subha","year":"2017","journal-title":"Nat Methods"},{"key":"2025071112131425400_R80","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003194","article-title":"Environmental predictors of seasonal influenza epidemics across temperate and tropical climates","volume":"9","author":"Tamerius","year":"2013","journal-title":"PLoS Pathogens"},{"key":"2025071112131425400_R81","doi-asserted-by":"publisher","first-page":"13868","DOI":"10.1128\/jvi.01955-13","article-title":"Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions","volume":"87","author":"Vries","year":"2013","journal-title":"J Virol"},{"key":"2025071112131425400_R82","doi-asserted-by":"publisher","first-page":"e00670","DOI":"10.1128\/msystems.00670-23","article-title":"Deep mutational scanning of influenza A virus neuraminidase facilitates the identification of drug resistance mutations in vivo","volume":"8","author":"Wang","year":"2023","journal-title":"MSystems"},{"key":"2025071112131425400_R83","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-017-0471-0","article-title":"Synergistic effect of PB2 283M and 526R contributes to enhanced virulence of H5N8 influenza viruses in mice","volume":"48","author":"Wang","year":"2017","journal-title":"Vet Res"},{"key":"2025071112131425400_R84","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025071112131425400_R85","doi-asserted-by":"publisher","first-page":"9920","DOI":"10.1128\/JVI.00840-15","article-title":"Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013","volume":"89","author":"Watson","year":"2015","journal-title":"J Virol"},{"key":"2025071112131425400_R86","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol Biol Evolut"},{"key":"2025071112131425400_R87","article-title":"Recommendations for Influenza Vaccine Composition","author":"World Health Organization","year":".."},{"key":"2025071112131425400_R88","doi-asserted-by":"publisher","first-page":"9221","DOI":"10.1128\/jvi.00697-12","article-title":"Functional balance of the hemagglutinin and neuraminidase activities accompanies the emergence of the 2009 H1N1 influenza pandemic","volume":"86","author":"Xu","year":"2012","journal-title":"J Virol"},{"key":"2025071112131425400_R89","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1093\/bioinformatics\/13.5.555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"2025071112131425400_R90","doi-asserted-by":"publisher","DOI":"10.1186\/s44149-021-00024-6","article-title":"The epidemiology of swine influenza","volume":"1","author":"Yin","year":"2021","journal-title":"Animal Diseases"},{"key":"2025071112131425400_R91","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/jvi.00868-16","article-title":"An amino acid in the stalk domain of N1 neuraminidase is critical for enzymatic activity","volume":"91","author":"Zanin","year":"2017","journal-title":"J Virol"},{"key":"2025071112131425400_R92","doi-asserted-by":"publisher","first-page":"5935","DOI":"10.1128\/jvi.02537-14","article-title":"Pandemic swine H1N1 influenza viruses with almost undetectable neuraminidase activity are not transmitted via aerosols in ferrets and are inhibited by human mucus but not swine mucus","volume":"89","author":"Zanin","year":"2015","journal-title":"J Virol"},{"key":"2025071112131425400_R93","doi-asserted-by":"publisher","DOI":"10.3390\/v12070762","article-title":"Cocirculation of swine H1N1 influenza A virus lineages in Germany","volume":"12","author":"Zell","year":"2020","journal-title":"Viruses"},{"key":"2025071112131425400_R94","doi-asserted-by":"publisher","first-page":"2260","DOI":"10.1128\/jvi.03024-13","article-title":"PB2-588I enhances 2009 H1N1 pandemic influenza virus virulence by increasing viral replication and exacerbating PB2 inhibition of beta interferon expression","volume":"88","author":"Zhao","year":"2014","journal-title":"J Virol"},{"key":"2025071112131425400_R95","doi-asserted-by":"publisher","first-page":"10309","DOI":"10.1128\/JVI.01109-09","article-title":"Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses","volume":"83","author":"Zhou","year":"2009","journal-title":"J Virol"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaf014\/62340047\/veaf014.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf014\/62340047\/veaf014.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf014\/62340047\/veaf014.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T16:13:26Z","timestamp":1752250406000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaf014\/8063604"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":95,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,3,29]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaf014","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"veaf014"}}