<br><div> <head profile="http://www.w3.org/1999/xhtml/vocab"> <!--[if IE]><![endif]--> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <link rel="dns-prefetch" href="//scholar.google.com"/> <link rel="dns-prefetch" href="//pnas-movie.glencoesoftware.com"/> <link rel="dns-prefetch" href="//www.google.com"/> <link rel="dns-prefetch" href="//www.google-analytics.com"/> <link rel="dns-prefetch" href="//stats.g.doubleclick.net"/> <meta name="viewport" content="initial-scale=1, maximum-scale=1, width=device-width, user-scalable=yes"/> <link rel="shortcut icon" href="https://www.pnas.org/sites/default/files/images/favicon.ico" type="image/vnd.microsoft.icon"/> <link rel="canonical" href="https://www.pnas.org/content/early/2020/08/31/2013267117"/> <meta name="Generator" content="Drupal 7 (http://drupal.org)"/> <link rel="alternate" type="application/pdf" title="Full Text (PDF)" href="http://www.pnas.org/content/early/2020/08/31/2013267117.full.pdf"/> <link rel="alternate" type="text/plain" title="Full Text (Plain)" href="http://www.pnas.org/content/early/2020/08/31/2013267117.full.txt"/> <link rel="alternate" type="application/vnd.ms-powerpoint" title="Powerpoint" href="http://www.pnas.org/content/early/2020/08/31/2013267117.ppt"/> <meta name="citation_funding_source" content="citation_funder_id=501100005063;citation_grant_number=81822040;"/> <meta name="citation_funding_source" content="citation_grant_number=JCYJ20150402111430617; JCYJ2015029151932602;"/> <meta name="citation_funding_source" content="citation_grant_number=201161;"/> <meta name="citation_funding_source" content="citation_grant_number=20150733Q45;"/> <meta name="citation_funding_source" content="citation_grant_number=81621091;"/> <meta name="type" content="article"/> <meta name="category" content="research-article"/> <meta name="HW.identifier" content="/pnas/early/2020/08/31/2013267117.atom"/> <meta name="HW.pisa" content="pnas;2013267117v1"/> <meta name="DC.Format" content="text/html"/> <meta name="DC.Language" content="en"/> <meta name="DC.Title" content="Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation"/> <meta name="DC.Identifier" content="10.1073/pnas.2013267117"/> <meta name="DC.Date" content="2020-09-01"/> <meta name="DC.Publisher" content="National Academy of Sciences"/> <meta name="DC.Rights" content="Copyright © 2020 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND)."/> <meta name="DC.AccessRights" content="open-access"/> <meta name="DC.Description" content="Deep-sequencing of viral genomes based on original specimens from H7N9-infected patients and the surrounding poultry/environment has provided the first in-depth data on virus adaptation at the interface between poultry and humans. In contrast to the consistent dominance of 627E in poultry-derived H7N9, diverse but longitudinally changing ratios of the mammalian signature substitution PB2-E627K from patient specimens indicate a dynamic viral adaptation during infection, termed “genetic tuning” of avian influenza viruses in new hosts. Furthermore, the correlation between rapid host adaptation of H7N9 PB2-627 and the disease severity in patients is brought to light. Of note, under a one-health vision, our study provides direct big data evidence that “genetic tuning” of PB2-E627K is associated with H7N9 pathogenicity during human infection. Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed “genetic tuning,” actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection. All study data are included in the main text and [ SI Appendix ][1]. [1]: https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2013267117/-/DCSupplemental"/> <meta name="DC.Contributor" content="William J. Liu"/> <meta name="DC.Contributor" content="Jun Li"/> <meta name="DC.Contributor" content="Rongrong Zou"/> <meta name="DC.Contributor" content="Jingcao Pan"/> <meta name="DC.Contributor" content="Tao Jin"/> <meta name="DC.Contributor" content="Liqiang Li"/> <meta name="DC.Contributor" content="Peipei Liu"/> <meta name="DC.Contributor" content="Yingze Zhao"/> <meta name="DC.Contributor" content="Xinfen Yu"/> <meta name="DC.Contributor" content="Haoqiu Wang"/> <meta name="DC.Contributor" content="Guang Liu"/> <meta name="DC.Contributor" content="Hui Jiang"/> <meta name="DC.Contributor" content="Yuhai Bi"/> <meta name="DC.Contributor" content="Lei Liu"/> <meta name="DC.Contributor" content="Kwok-Yung Yuen"/> <meta name="DC.Contributor" content="Yingxia Liu"/> <meta name="DC.Contributor" content="George F. Gao"/> <meta name="article:published_time" content="2020-09-01"/> <meta name="article:section" content="Biological Sciences"/> <meta name="citation_title" content="Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation"/> <meta name="citation_abstract" lang="en" content="<p>Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed “genetic tuning,” actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection.</p>"/> <meta name="citation_abstract" lang="en" scheme="executive-summary" content="<h3>Significance</h3> <p>Deep-sequencing of viral genomes based on original specimens from H7N9-infected patients and the surrounding poultry/environment has provided the first in-depth data on virus adaptation at the interface between poultry and humans. In contrast to the consistent dominance of 627E in poultry-derived H7N9, diverse but longitudinally changing ratios of the mammalian signature substitution PB2-E627K from patient specimens indicate a dynamic viral adaptation during infection, termed “genetic tuning” of avian influenza viruses in new hosts. Furthermore, the correlation between rapid host adaptation of H7N9 PB2-627 and the disease severity in patients is brought to light. Of note, under a one-health vision, our study provides direct big data evidence that “genetic tuning” of PB2-E627K is associated with H7N9 pathogenicity during human infection.</p>"/> <meta name="citation_journal_title" content="Proceedings of the National Academy of Sciences"/> <meta name="citation_publisher" content="National Academy of Sciences"/> <meta name="citation_publication_date" content="2020/09/01"/> <meta name="citation_mjid" content="pnas;2013267117v1"/> <meta name="citation_id" content="2013267117v1"/> <meta name="citation_public_url" content="https://www.pnas.org/content/early/2020/08/31/2013267117"/> <meta name="citation_abstract_html_url" content="https://www.pnas.org/content/early/2020/08/31/2013267117.abstract"/> <meta name="citation_full_html_url" content="https://www.pnas.org/content/early/2020/08/31/2013267117.full"/> <meta name="citation_pdf_url" content="https://www.pnas.org/content/pnas/early/2020/08/31/2013267117.full.pdf"/> <meta name="citation_issn" content="0027-8424"/> <meta name="citation_issn" content="1091-6490"/> <meta name="citation_journal_abbrev" content="PNAS"/> <meta name="citation_doi" content="10.1073/pnas.2013267117"/> <meta name="citation_pmid" content="32873642"/> <meta name="citation_num_pages" content="8"/> <meta name="citation_article_type" content="Research Article"/> <meta name="citation_section" content="Biological Sciences"/> <meta name="citation_access" content="all"/> <meta name="citation_author" content="William J. 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Chen;citation_title=Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: Clinical analysis and characterisation of viral genome;citation_pages=1916-1925;citation_volume=381;citation_year=2013;citation_pmid=23623390;citation_doi=10.1016/S0140-6736(13)60903-4"/> <meta name="citation_reference" content="citation_journal_title=Lancet;citation_author=D. Liu;citation_title=Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: Phylogenetic, structural, and coalescent analyses;citation_pages=1926-1932;citation_volume=381;citation_year=2013;citation_pmid=23643111;citation_doi=10.1016/S0140-6736(13)60938-1"/> <meta name="citation_reference" content="citation_journal_title=Emerg. Infect. Dis.;citation_author=H. Chen;citation_title=Nosocomial co-transmission of avian influenza A(H7N9) and A(H1N1)pdm09 viruses between 2 patients with hematologic disorders;citation_pages=598-607;citation_volume=22;citation_year=2016"/> <meta name="citation_reference" content="citation_journal_title=Emerg. Infect. Dis.;citation_author=C. Quan;citation_title=Avian influenza A viruses among occupationally exposed populations, China, 2014-2016;citation_pages=2215-2225;citation_volume=25;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Emerg. Microbes Infect.;citation_author=W. Shi;citation_title=Co-circulation and persistence of multiple A/H3N2 influenza variants in China;citation_pages=1157-1167;citation_volume=8;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Sci. China Life Sci.;citation_author=C. Quan;citation_title=Genomic characterizations of H4 subtype avian influenza viruses from live poultry markets in Sichuan province of China, 2014-2015;citation_pages=1123-1126;citation_volume=61;citation_year=2018"/> <meta name="citation_reference" content="citation_journal_title=Cell Host Microbe;citation_author=Y. Bi;citation_title=Genesis, Evolution and prevalence of H5N6 avian influenza viruses in China;citation_pages=810-821;citation_volume=20;citation_year=2016;citation_doi=10.1016/j.chom.2016.10.022"/> <meta name="citation_reference" content="citation_journal_title=Clin. Infect. Dis.;citation_author=Y. Bi;citation_title=Clinical and immunological characteristics of human infections with H5N6 avian influenza virus;citation_pages=1100-1109;citation_volume=68;citation_year=2019;citation_doi=10.1093/cid/ciy681"/> <meta name="citation_reference" content="citation_journal_title=China CDC Week;citation_author=G. F. Gao;citation_title=China’s outreach to the world: public health goes global;citation_pages=1-2;citation_volume=1;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Biosaf Health;citation_author=G. Wu;citation_title=Laboratory biosafety in China: Past, present, and future;citation_pages=56-58;citation_volume=1;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Sci. Rep.;citation_author=W. Zhu;citation_title=Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models;citation_pages=14170;citation_volume=5;citation_year=2015;citation_pmid=26391278;citation_doi=10.1038/srep14170"/> <meta name="citation_reference" content="citation_journal_title=Sci. Rep.;citation_author=S. Yamayoshi;citation_title=Amino acids substitutions in the PB2 protein of H7N9 influenza A viruses are important for virulence in mammalian hosts;citation_pages=8039;citation_volume=5;citation_year=2015;citation_pmid=25623817;citation_doi=10.1038/srep08039"/> <meta name="citation_reference" content="citation_journal_title=Journal of Virology;citation_journal_abbrev=J. Virol.;citation_author=E. K. Subbarao;citation_author=W. London;citation_author=B. R. Murphy;citation_title=A single amino acid in the PB2 gene of influenza A virus is a determinant of host range.;citation_pages=1761-1764;citation_volume=67;citation_year=1993;citation_issue=4;citation_pmid=8445709;citation_doi=10.1128/JVI.67.4.1761-1764.1993"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=Y. Bi;citation_title=Assessment of the internal genes of influenza A (H7N9) virus contributing to high pathogenicity in mice;citation_volume=89;citation_year=2015;citation_pmid=25320305;citation_doi=10.1128/JVI.02390-14"/> <meta name="citation_reference" content="citation_journal_title=Journal of General Virology;citation_journal_abbrev=J. Gen. Virol.;citation_author=N. Naffakh;citation_author=P. Massin;citation_author=N. Escriou;citation_author=B. Crescenzo-Chaigne;citation_author=S. van der Werf;citation_title=Genetic analysis of the compatibility between polymerase proteins from human and avian strains of influenza A viruses;citation_pages=1283-1291;citation_volume=81;citation_year=2000;citation_issue=5;citation_pmid=10769071;citation_doi=10.1099/0022-1317-81-5-1283"/> <meta name="citation_reference" content="citation_journal_title=Science;citation_journal_abbrev=Science;citation_author=M. Hatta;citation_author=P. Gao;citation_author=P. Halfmann;citation_author=Y. Kawaoka;citation_title=Molecular Basis for High Virulence of Hong Kong H5N1 Influenza A Viruses;citation_pages=1840-1842;citation_volume=293;citation_year=2001;citation_issue=5536;citation_pmid=11546875;citation_doi=10.1126/science.1062882"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=C. K. Mok;citation_title=Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts;citation_volume=88;citation_year=2014;citation_pmid=24403592;citation_doi=10.1128/JVI.02740-13"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=Q. Liu;citation_title=Analysis of recombinant H7N9 wild-type and mutant viruses in pigs shows that the Q226L mutation in HA is important for transmission;citation_volume=88;citation_year=2014;citation_pmid=24807722;citation_doi=10.1128/JVI.00894-14"/> <meta name="citation_reference" content="citation_journal_title=Infect. Genet. Evol.;citation_author=K. Mei;citation_title=Deep sequencing reveals the viral adaptation process of environment-derived H10N8 in mice;citation_pages=8-13;citation_volume=37;citation_year=2016"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=J. Y. Min;citation_title=Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus;citation_volume=87;citation_year=2013;citation_pmid=23864613;citation_doi=10.1128/JVI.01016-13"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=M. Jonges;citation_title=Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing;citation_volume=88;citation_year=2014;citation_pmid=24257603;citation_doi=10.1128/JVI.02044-13"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=Q. M. Le;citation_author=Y. Sakai-Tagawa;citation_author=M. Ozawa;citation_author=M. Ito;citation_author=Y. Kawaoka;citation_title=Selection of H5N1 influenza virus PB2 during replication in humans;citation_volume=83;citation_year=2009;citation_pmid=19264775;citation_doi=10.1128/JVI.00063-09"/> <meta name="citation_reference" content="citation_journal_title=J. Infect. Dis.;citation_author=L. Xu;citation_title=Novel avian-origin human influenza A(H7N9) can be transmitted between ferrets via respiratory droplets;citation_volume=209;citation_year=2014;citation_pmid=23990570;citation_doi=10.1093/infdis/jit474"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=G. S. Luk;citation_title=Transmission of H7N9 influenza viruses with a polymorphism at PB2 residue 627 in chickens and ferrets;citation_volume=89;citation_year=2015;citation_pmid=26202239;citation_doi=10.1128/JVI.01444-15"/> <meta name="citation_reference" content="citation_journal_abbrev=PLoS Pathog;citation_author=J. Steel;citation_author=A. C. Lowen;citation_author=S. Mubareka;citation_author=P. Palese;citation_title=Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N.;citation_pages=e1000252-e1000252;citation_volume=5;citation_year=2009;citation_issue=1;citation_pmid=19119420;citation_doi=10.1371/journal.ppat.1000252"/> <meta name="citation_reference" content="citation_journal_title=Infect. Genet. Evol.;citation_author=X. Ding;citation_author=J. Luo;citation_author=L. Quan;citation_author=A. Wu;citation_author=T. Jiang;citation_title=Evolutionary genotypes of influenza A (H7N9) viruses over five epidemic waves in China;citation_pages=269-276;citation_volume=55;citation_year=2017"/> <meta name="citation_reference" content="citation_journal_title=Trends Microbiol.;citation_author=S. Su;citation_title=Epidemiology, evolution, and pathogenesis of H7N9 influenza viruses in five epidemic waves since 2013 in China;citation_pages=713-728;citation_volume=25;citation_year=2017;citation_doi=10.1016/j.tim.2017.06.008"/> <meta name="citation_reference" content="citation_journal_title=Biosafety Heal.;citation_author=L. Yang;citation_title=Mutations associated with egg adaptation of influenza A(H1N1)pdm09 virus in laboratory-based surveillance in China, 2009–2016;citation_pages=41-45;citation_volume=1;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=J. Kirui;citation_author=M. D. Bucci;citation_author=D. S. Poole;citation_author=A. Mehle;citation_title=Conserved features of the PB2 627 domain impact influenza virus polymerase function and replication;citation_volume=88;citation_year=2014;citation_pmid=24623411;citation_doi=10.1128/JVI.00508-14"/> <meta name="citation_reference" content="citation_journal_title=Journal of Virology;citation_journal_abbrev=J. Virol.;citation_author=P. Massin;citation_author=S. van der Werf;citation_author=N. Naffakh;citation_title=Residue 627 of PB2 Is a Determinant of Cold Sensitivity in RNA Replication of Avian Influenza Viruses;citation_pages=5398-5404;citation_volume=75;citation_year=2001;citation_issue=11;citation_pmid=11333924;citation_doi=10.1128/JVI.75.11.5398-5404.2001"/> <meta name="citation_reference" content="citation_journal_title=J. Biol. Chem.;citation_author=S. Aggarwal;citation_author=S. Dewhurst;citation_author=T. Takimoto;citation_author=B. Kim;citation_title=Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex;citation_volume=286;citation_year=2011;citation_pmid=21816827;citation_doi=10.1074/jbc.M111.262048"/> <meta name="citation_reference" content="citation_journal_title=Nature structural & molecular biology;citation_journal_abbrev=Nat Struct Mol Biol;citation_author=F. Tarendeau;citation_title=Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit.;citation_pages=229-233;citation_volume=14;citation_year=2007;citation_issue=3;citation_pmid=17310249;citation_doi=10.1038/nsmb1212"/> <meta name="citation_reference" content="citation_journal_title=J. Biol. Chem.;citation_author=S. Boivin;citation_author=D. J. Hart;citation_title=Interaction of the influenza A virus polymerase PB2 C-terminal region with importin alpha isoforms provides insights into host adaptation and polymerase assembly;citation_volume=286;citation_year=2011;citation_pmid=21216958;citation_doi=10.1074/jbc.M110.182964"/> <meta name="citation_reference" content="citation_journal_title=J. Am. Chem. Soc.;citation_author=E. Delaforge;citation_title=Large-scale conformational dynamics control H5N1 influenza polymerase PB2 binding to importin alpha;citation_pages=15122-15134;citation_volume=137;citation_year=2015"/> <meta name="citation_reference" content="citation_journal_title=MBio;citation_author=E. Bortz;citation_title=Host- and strain-specific regulation of influenza virus polymerase activity by interacting cellular proteins;citation_pages=e00151-11;citation_volume=2;citation_year=2011;citation_pmid=21846828;citation_doi=10.1128/mBio.00151-11"/> <meta name="citation_reference" content="citation_journal_title=Cell Host Microbe;citation_author=M. Weber;citation_title=Influenza virus adaptation PB2-627K modulates nucleocapsid inhibition by the pathogen sensor RIG-I;citation_pages=309-319;citation_volume=17;citation_year=2015;citation_pmid=25704008;citation_doi=10.1016/j.chom.2015.01.005"/> <meta name="citation_reference" content="citation_journal_title=Nature;citation_author=J. S. Long;citation_title=Species difference in ANP32A underlies influenza A virus polymerase host restriction;citation_pages=101-104;citation_volume=529;citation_year=2016;citation_pmid=26738596;citation_doi=10.1038/nature16474"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=J. L. Fornek;citation_title=A single amino acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T-cell activation in mice;citation_volume=83;citation_year=2009;citation_pmid=19692471;citation_doi=10.1128/JVI.00994-09"/> <meta name="citation_reference" content="citation_journal_title=J. Virol.;citation_author=A. Forero;citation_title=The 1918 influenza virus PB2 protein enhances virulence through the disruption of inflammatory and Wnt-mediated signaling in mice;citation_pages=2240-2253;citation_volume=90;citation_year=2015"/> <meta name="citation_reference" content="citation_journal_title=Nat. Commun.;citation_author=A. S. Taft;citation_title=Identification of mammalian-adapting mutations in the polymerase complex of an avian H5N1 influenza virus;citation_pages=7491;citation_volume=6;citation_year=2015;citation_pmid=26082035;citation_doi=10.1038/ncomms8491"/> <meta name="citation_reference" content="citation_journal_title=PLoS Pathog.;citation_author=Y. Arai;citation_title=PB2 mutations arising during H9N2 influenza evolution in the Middle East confer enhanced replication and growth in mammals;citation_pages=e1007919;citation_volume=15;citation_year=2019;citation_doi=10.1371/journal.ppat.1007919"/> <meta name="citation_reference" content="citation_journal_title=Proc. Natl. Acad. Sci. U.S.A.;citation_author=A. Mehle;citation_author=J. A. Doudna;citation_title=Adaptive strategies of the influenza virus polymerase for replication in humans;citation_volume=106;citation_year=2009;citation_pmid=19995968;citation_doi=10.1073/pnas.0911915106"/> <meta name="citation_reference" content="citation_journal_abbrev=PLoS Pathog;citation_author=S. Yamada;citation_title=Biological and structural characterization of a host-adapting amino acid in influenza virus.;citation_pages=e1001034-e1001034;citation_volume=6;citation_year=2010;citation_issue=8;citation_pmid=20700447;citation_doi=10.1371/journal.ppat.1001034"/> <meta name="citation_reference" content="citation_journal_title=Nat. Commun.;citation_author=W. Song;citation_title=The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication;citation_pages=5509;citation_volume=5;citation_year=2014;citation_pmid=25409547;citation_doi=10.1038/ncomms6509"/> <meta name="citation_reference" content="citation_journal_abbrev=Protein Cell;citation_author=W. Zhang;citation_title=Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus.;citation_pages=459-467;citation_volume=1;citation_year=2010;citation_issue=5;citation_pmid=21203961;citation_doi=10.1007/s13238-010-0059-1"/> <meta name="citation_reference" content="citation_journal_title=Virol. J.;citation_author=J. Qin;citation_title=Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice;citation_pages=3;citation_volume=16;citation_year=2019"/> <meta name="citation_reference" content="citation_journal_title=Sci. Rep.;citation_author=H. Katsura;citation_title=Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein;citation_pages=19933;citation_volume=6;citation_year=2016;citation_doi=10.1038/srep19933"/> <meta name="citation_reference" content="citation_journal_title=Archives of virology;citation_journal_abbrev=Arch Virol;citation_author=E. Hoffmann;citation_author=J. Stech;citation_author=Y. Guan;citation_author=R. G. Webster;citation_author=D. R. Perez;citation_title=Universal primer set for the full-length amplification of all influenza A viruses.;citation_pages=2275-2289;citation_volume=146;citation_year=2001;citation_issue=12;citation_pmid=11811679;citation_doi=10.1007/s007050170002"/> <meta name="citation_reference" content="citation_journal_title=Bioinformatics;citation_author=H. Li;citation_author=R. Durbin;citation_title=Fast and accurate short read alignment with Burrows-Wheeler transform;citation_volume=25;citation_year=2009;citation_pmid=19451168;citation_doi=10.1093/bioinformatics/btp324"/> <meta name="citation_reference" content="citation_journal_title=Bioinformatics;citation_author=H. Li;citation_title=The sequence alignment/map format and SAMtools;citation_volume=25;citation_year=2009;citation_pmid=19505943;citation_doi=10.1093/bioinformatics/btp352"/> <meta name="citation_reference" content="citation_journal_title=Genome Res.;citation_author=R. Li;citation_title=De novo assembly of human genomes with massively parallel short read sequencing;citation_volume=20;citation_year=2010;citation_pmid=20019144;citation_doi=10.1101/gr.097261.109"/> <meta name="citation_fulltext_world_readable" content=""/> <meta name="twitter:title" content="Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation"/> <meta name="twitter:card" content="summary_large_image"/> <meta name="twitter:image" content="https://www.pnas.org/sites/default/files/highwire/pnas/117/35.cover-source.jpg"/> <meta name="twitter:description" content="Deep-sequencing of viral genomes based on original specimens from H7N9-infected patients and the surrounding poultry/environment has provided the first in-depth data on virus adaptation at the interface between poultry and humans. In contrast to the consistent dominance of 627E in poultry-derived H7N9, diverse but longitudinally changing ratios of the mammalian signature substitution PB2-E627K from patient specimens indicate a dynamic viral adaptation during infection, termed “genetic tuning” of avian influenza viruses in new hosts. Furthermore, the correlation between rapid host adaptation of H7N9 PB2-627 and the disease severity in patients is brought to light. Of note, under a one-health vision, our study provides direct big data evidence that “genetic tuning” of PB2-E627K is associated with H7N9 pathogenicity during human infection. Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed “genetic tuning,” actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection. All study data are included in the main text and [ SI Appendix ][1]. [1]: https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2013267117/-/DCSupplemental"/> <meta name="og-title" property="og:title" content="Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation"/> <meta name="og-url" property="og:url" content="https://www.pnas.org/content/early/2020/08/31/2013267117"/> <meta name="og-site-name" property="og:site_name" content="PNAS"/> <meta name="og-description" property="og:description" content="Deep-sequencing of viral genomes based on original specimens from H7N9-infected patients and the surrounding poultry/environment has provided the first in-depth data on virus adaptation at the interface between poultry and humans. In contrast to the consistent dominance of 627E in poultry-derived H7N9, diverse but longitudinally changing ratios of the mammalian signature substitution PB2-E627K from patient specimens indicate a dynamic viral adaptation during infection, termed “genetic tuning” of avian influenza viruses in new hosts. Furthermore, the correlation between rapid host adaptation of H7N9 PB2-627 and the disease severity in patients is brought to light. Of note, under a one-health vision, our study provides direct big data evidence that “genetic tuning” of PB2-E627K is associated with H7N9 pathogenicity during human infection. Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed “genetic tuning,” actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection. All study data are included in the main text and [ SI Appendix ][1]. 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