{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:10:52Z","timestamp":1792714252388,"version":"4.5.0"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T00:00:00Z","timestamp":1635206400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T00:00:00Z","timestamp":1635206400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["75N93021C00016"],"award-info":[{"award-number":["75N93021C00016"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["75N93021C00016"],"award-info":[{"award-number":["75N93021C00016"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["75N93021C00016"],"award-info":[{"award-number":["75N93021C00016"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HHSN272201400006C"],"award-info":[{"award-number":["HHSN272201400006C"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["T11-712\/19-N"],"award-info":[{"award-number":["T11-712\/19-N"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-021-00976-y","type":"journal-article","created":{"date-parts":[[2021,10,26]],"date-time":"2021-10-26T12:06:29Z","timestamp":1635249989000},"page":"1455-1465","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs"],"prefix":"10.1038","volume":"6","author":[{"given":"Wen","family":"Su","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhodri","family":"Harfoot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4349-9211","authenticated-orcid":false,"given":"Yvonne C. F.","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"DeBeauchamp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Udayan","family":"Joseph","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayanthi","family":"Jayakumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeri-Carol","family":"Crumpton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trushar","family":"Jeevan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Rubrum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Franks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe Noriel Q.","family":"Pascua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Kackos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Ji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huyen Trang","family":"Bui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9980-2112","authenticated-orcid":false,"given":"Jeremy C.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Kercher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Krauss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Pleschka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael C. W.","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert G.","family":"Webster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chung-Yi","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristien","family":"Van Reeth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8217-5995","authenticated-orcid":false,"given":"Malik","family":"Peiris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4397-7132","authenticated-orcid":false,"given":"Richard J.","family":"Webby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5031-468X","authenticated-orcid":false,"given":"Gavin J. D.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2493-3609","authenticated-orcid":false,"given":"Hui-Ling","family":"Yen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,26]]},"reference":[{"key":"976_CR1","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1126\/science.1122818","volume":"312","author":"T Kuiken","year":"2006","unstructured":"Kuiken, T. et al. Host species barriers to influenza virus infections. Science 312, 394\u2013397 (2006).","journal-title":"Science"},{"key":"976_CR2","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1128\/MMBR.00004-08","volume":"72","author":"CR Parrish","year":"2008","unstructured":"Parrish, C. R. et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol. Mol. Biol. Rev. 72, 457\u2013470 (2008).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"976_CR3","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/j.chom.2010.05.009","volume":"7","author":"JK Taubenberger","year":"2010","unstructured":"Taubenberger, J. K. & Kash, J. C. Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7, 440\u2013451 (2010).","journal-title":"Cell Host Microbe"},{"key":"976_CR4","doi-asserted-by":"publisher","first-page":"e18491","DOI":"10.7554\/eLife.18491","volume":"5","author":"M Lipsitch","year":"2016","unstructured":"Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. Elife 5, e18491 (2016).","journal-title":"Elife"},{"key":"976_CR5","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41579-018-0115-z","volume":"17","author":"JS Long","year":"2019","unstructured":"Long, J. S., Mistry, B., Haslam, S. M. & Barclay, W. S. Host and viral determinants of influenza A virus species specificity. Nat. Rev. Microbiol. 17, 67\u201381 (2019).","journal-title":"Nat. Rev. Microbiol."},{"key":"976_CR6","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1038\/nature08182","volume":"459","author":"GJ Smith","year":"2009","unstructured":"Smith, G. J. et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459, 1122\u20131125 (2009).","journal-title":"Nature"},{"key":"976_CR7","first-page":"75","volume":"59","author":"M Pensaert","year":"1981","unstructured":"Pensaert, M., Ottis, K., Vandeputte, J., Kaplan, M. M. & Bachmann, P. A. Evidence for the natural transmission of influenza A virus from wild ducts to swine and its potential importance for man. Bull. World Health Organ. 59, 75\u201378 (1981).","journal-title":"Bull. World Health Organ."},{"key":"976_CR8","first-page":"133","volume":"370","author":"IH Brown","year":"2013","unstructured":"Brown, I. H. History and epidemiology of swine influenza in Europe. Curr. Top. Microbiol. Immunol. 370, 133\u2013146 (2013).","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"976_CR9","doi-asserted-by":"publisher","first-page":"2372","DOI":"10.1099\/vir.0.068569-0","volume":"95","author":"A Krumbholz","year":"2014","unstructured":"Krumbholz, A. et al. Origin of the European avian-like swine influenza viruses. J. Gen. Virol. 95, 2372\u20132376 (2014).","journal-title":"J. Gen. Virol."},{"key":"976_CR10","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1111\/eva.12536","volume":"11","author":"U Joseph","year":"2018","unstructured":"Joseph, U., Vijaykrishna, D., Smith, G. J. D. & Su, Y. C. F. Adaptive evolution during the establishment of European avian-like H1N1 influenza A virus in swine. Evol. Appl. 11, 534\u2013546 (2018).","journal-title":"Evol. Appl."},{"key":"976_CR11","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/nature10004","volume":"473","author":"D Vijaykrishna","year":"2011","unstructured":"Vijaykrishna, D. et al. Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473, 519\u2013522 (2011).","journal-title":"Nature"},{"key":"976_CR12","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1073\/pnas.1522643113","volume":"113","author":"H Yang","year":"2016","unstructured":"Yang, H. et al. Prevalence, genetics, and transmissibility in ferrets of Eurasian avian-like H1N1 swine influenza viruses. Proc. Natl Acad. Sci. USA 113, 392\u2013397 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"976_CR13","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1016\/j.chom.2020.07.006","volume":"28","author":"D Henritzi","year":"2020","unstructured":"Henritzi, D. et al. Surveillance of European domestic pig populations identifies an emerging reservoir of potentially zoonotic swine influenza A viruses. Cell Host Microbe 28, 614\u2013627 (2020).","journal-title":"Cell Host Microbe"},{"key":"976_CR14","doi-asserted-by":"publisher","first-page":"e00997-18","DOI":"10.1128\/JVI.00997-18","volume":"93","author":"D Dornfeld","year":"2019","unstructured":"Dornfeld, D., Petric, P. P., Hassan, E., Zell, R. & Schwemmle, M. Eurasian avian-like swine influenza A viruses escape human MxA restriction through distinct mutations in their nucleoprotein. J. Virol. 93, e00997-18 (2019).","journal-title":"J. Virol."},{"key":"976_CR15","doi-asserted-by":"publisher","first-page":"17204","DOI":"10.1073\/pnas.1921186117","volume":"117","author":"H Sun","year":"2020","unstructured":"Sun, H. et al. Prevalent Eurasian avian-like H1N1 swine influenza virus with 2009 pandemic viral genes facilitating human infection. Proc. Natl Acad. Sci. USA 117, 17204\u201317210 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"976_CR16","doi-asserted-by":"publisher","first-page":"1714","DOI":"10.1126\/science.1086185","volume":"301","author":"JW Thornton","year":"2003","unstructured":"Thornton, J. W., Need, E. & Crews, D. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301, 1714\u20131717 (2003).","journal-title":"Science"},{"key":"976_CR17","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1073\/pnas.1012457108","volume":"108","author":"MF Ducatez","year":"2011","unstructured":"Ducatez, M. F. et al. Feasibility of reconstructed ancestral H5N1 influenza viruses for cross-clade protective vaccine development. Proc. Natl Acad. Sci. USA 108, 349\u2013354 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"976_CR18","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1016\/0042-6822(83)90150-2","volume":"127","author":"GN Rogers","year":"1983","unstructured":"Rogers, G. N. & Paulson, J. C. Receptor determinants of human and animal influenza virus isolates: differences in receptor specificity of the H3 hemagglutinin based on species of origin. Virology 127, 361\u2013373 (1983).","journal-title":"Virology"},{"key":"976_CR19","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1128\/JVI.02332-15","volume":"90","author":"J Baumann","year":"2016","unstructured":"Baumann, J., Kouassi, N. M., Foni, E., Klenk, H. D. & Matrosovich, M. H1N1 swine influenza viruses differ from avian precursors by a higher pH optimum of membrane fusion. J. Virol. 90, 1569\u20131577 (2016).","journal-title":"J. Virol."},{"key":"976_CR20","doi-asserted-by":"publisher","first-page":"e1006276","DOI":"10.1371\/journal.ppat.1006276","volume":"13","author":"M Russier","year":"2017","unstructured":"Russier, M. et al. H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. PLoS Pathog. 13, e1006276 (2017).","journal-title":"PLoS Pathog."},{"key":"976_CR21","doi-asserted-by":"publisher","first-page":"4188","DOI":"10.1128\/jvi.70.6.4188-4192.1996","volume":"70","author":"S Pleschka","year":"1996","unstructured":"Pleschka, S. et al. A plasmid-based reverse genetics system for influenza A virus. J. Virol. 70, 4188\u20134192 (1996).","journal-title":"J. Virol."},{"key":"976_CR22","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1084\/jem.20051938","volume":"203","author":"R Salomon","year":"2006","unstructured":"Salomon, R. et al. The polymerase complex genes contribute to the high virulence of the human H5N1 influenza virus isolate A\/Vietnam\/1203\/04. J. Exp. Med. 203, 689\u2013697 (2006).","journal-title":"J. Exp. Med."},{"key":"976_CR23","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/nrg1324","volume":"5","author":"JW Thornton","year":"2004","unstructured":"Thornton, J. W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nat. Rev. Genet. 5, 366\u2013375 (2004).","journal-title":"Nat. Rev. Genet."},{"key":"976_CR24","doi-asserted-by":"publisher","first-page":"3043","DOI":"10.1016\/j.vaccine.2011.01.100","volume":"29","author":"BM Giles","year":"2011","unstructured":"Giles, B. M. & Ross, T. M. A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets. Vaccine 29, 3043\u20133054 (2011).","journal-title":"Vaccine"},{"key":"976_CR25","doi-asserted-by":"publisher","first-page":"a038695","DOI":"10.1101\/cshperspect.a038695","volume":"10","author":"JK Taubenberger","year":"2020","unstructured":"Taubenberger, J. K. & Morens, D. M. The 1918 influenza pandemic and its legacy. Cold Spring Harb. Perspect. Med. 10, a038695 (2020).","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"976_CR26","doi-asserted-by":"publisher","first-page":"12462","DOI":"10.1128\/JVI.78.22.12462-12470.2004","volume":"78","author":"AH Reid","year":"2004","unstructured":"Reid, A. H., Fanning, T. G., Janczewski, T. A., Lourens, R. M. & Taubenberger, J. K. Novel origin of the 1918 pandemic influenza virus nucleoprotein gene. J. Virol. 78, 12462\u201312470 (2004).","journal-title":"J. Virol."},{"key":"976_CR27","doi-asserted-by":"publisher","first-page":"e11","DOI":"10.1371\/journal.ppat.0040011","volume":"4","author":"G Gabriel","year":"2008","unstructured":"Gabriel, G., Herwig, A. & Klenk, H. D. Interaction of polymerase subunit PB2 and NP with importin \u03b11 is a determinant of host range of influenza A virus. PLoS Pathog. 4, e11 (2008).","journal-title":"PLoS Pathog."},{"key":"976_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1158","volume":"2","author":"G Gabriel","year":"2011","unstructured":"Gabriel, G. et al. Differential use of importin-\u03b1 isoforms governs cell tropism and host adaptation of influenza virus. Nat. Commun. 2, 156 (2011).","journal-title":"Nat. Commun."},{"key":"976_CR29","doi-asserted-by":"publisher","first-page":"8133","DOI":"10.1128\/JVI.00712-11","volume":"85","author":"P Zimmermann","year":"2011","unstructured":"Zimmermann, P., M\u00e4nz, B., Haller, O., Schwemmle, M. & Kochs, G. The viral nucleoprotein determines Mx sensitivity of influenza A viruses. J. Virol. 85, 8133\u20138140 (2011).","journal-title":"J. Virol."},{"key":"976_CR30","doi-asserted-by":"publisher","first-page":"e1003279","DOI":"10.1371\/journal.ppat.1003279","volume":"9","author":"B M\u00e4nz","year":"2013","unstructured":"M\u00e4nz, B. et al. Pandemic influenza A viruses escape from restriction by human MxA through adaptive mutations in the nucleoprotein. PLoS Pathog. 9, e1003279 (2013).","journal-title":"PLoS Pathog."},{"key":"976_CR31","doi-asserted-by":"publisher","first-page":"e1006288","DOI":"10.1371\/journal.ppat.1006288","volume":"13","author":"O Ashenberg","year":"2017","unstructured":"Ashenberg, O., Padmakumar, J., Doud, M. B. & Bloom, J. D. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. PLoS Pathog. 13, e1006288 (2017).","journal-title":"PLoS Pathog."},{"key":"976_CR32","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312\u20131313 (2014).","journal-title":"Bioinformatics"},{"key":"976_CR33","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nature10724","volume":"481","author":"GC Finnigan","year":"2012","unstructured":"Finnigan, G. C., Hanson-Smith, V., Stevens, T. H. & Thornton, J. W. Evolution of increased complexity in a molecular machine. Nature 481, 360\u2013364 (2012).","journal-title":"Nature"},{"key":"976_CR34","unstructured":"Tamuri, A. U. Treesub: annotating ancestral substitution on a tree. Github https:\/\/github.com\/tamuri\/treesub (2013)."},{"key":"976_CR35","doi-asserted-by":"publisher","first-page":"e139","DOI":"10.1093\/nar\/gkn646","volume":"36","author":"J Stech","year":"2008","unstructured":"Stech, J. et al. Rapid and reliable universal cloning of influenza A virus genes by target-primed plasmid amplification. Nucleic Acids Res. 36, e139 (2008).","journal-title":"Nucleic Acids Res."},{"key":"976_CR36","doi-asserted-by":"publisher","first-page":"6108","DOI":"10.1073\/pnas.100133697","volume":"97","author":"E Hoffmann","year":"2000","unstructured":"Hoffmann, E., Neumann, G., Kawaoka, Y., Hobom, G. & Webster, R. G. A DNA transfection system for generation of influenza A virus from eight plasmids. Proc. Natl Acad. Sci. USA 97, 6108\u20136113 (2000).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"976_CR37","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1006\/viro.1999.0140","volume":"267","author":"E Hoffmann","year":"2000","unstructured":"Hoffmann, E., Neumann, G., Hobom, G., Webster, R. G. & Kawaoka, Y. \u2018Ambisense\u2019 approach for the generation of influenza A virus: vRNA and mRNA synthesis from one template. Virology 267, 310\u2013317 (2000).","journal-title":"Virology"},{"key":"976_CR38","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1128\/JVI.01633-12","volume":"87","author":"O Moncorge","year":"2013","unstructured":"Moncorge, O. et al. Investigation of influenza virus polymerase activity in pig cells. J. Virol. 87, 384\u2013394 (2013).","journal-title":"J. Virol."},{"key":"976_CR39","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1126\/science.1239844","volume":"341","author":"H Zhu","year":"2013","unstructured":"Zhu, H. et al. Infectivity, transmission, and pathology of human-isolated H7N9 influenza virus in ferrets and pigs. Science 341, 183\u2013186 (2013).","journal-title":"Science"},{"key":"976_CR40","doi-asserted-by":"publisher","first-page":"e55358","DOI":"10.1371\/journal.pone.0055358","volume":"8","author":"H Nishiura","year":"2013","unstructured":"Nishiura, H., Yen, H. L. & Cowling, B. J. Sample size considerations for one-to-one animal transmission studies of the influenza A viruses. PLoS ONE 8, e55358 (2013).","journal-title":"PLoS ONE"},{"key":"976_CR41","first-page":"493","volume":"27","author":"LJ Reed","year":"1938","unstructured":"Reed, L. J. & Muench, H. A simple method of estimating fifty percent endpoints. Am. J. Hyg. 27, 493\u2013497 (1938).","journal-title":"Am. J. Hyg."},{"key":"976_CR42","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059\u20133066 (2002).","journal-title":"Nucleic Acids Res."},{"key":"976_CR43","doi-asserted-by":"crossref","unstructured":"Miller, M. A., Pfeiffer, W. & Schwartz, T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In 2010 Gateway Computing Environments Workshop (GCE) 1\u20138 (IEEE, 2010).","DOI":"10.1109\/GCE.2010.5676129"},{"key":"976_CR44","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5096-9","volume":"19","author":"S Bruinsma","year":"2018","unstructured":"Bruinsma, S. et al. Bead-linked transposomes enable a normalization-free workflow for NGS library preparation. BMC Genomics 19, 722 (2018).","journal-title":"BMC Genomics"},{"key":"976_CR45","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00976-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00976-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00976-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T17:55:03Z","timestamp":1733939703000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00976-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,26]]},"references-count":45,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["976"],"URL":"https:\/\/doi.org\/10.1038\/s41564-021-00976-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-436907\/v1","asserted-by":"object"}]},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,26]]},"assertion":[{"value":"18 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 September 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}