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Emerging Microbes & Infections Volume 7, 2018 - Issue 1
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Original Articles

Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses

Lei WenDepartment of MicrobiologyThe University of Hong KongHong KongChina
,
Hin ChuDepartment of MicrobiologyThe University of Hong KongHong KongChina;State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina;Research Centre of Infection and ImmunologyThe University of Hong KongHong KongChina
,
Bosco Ho-Yin WongState Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina
,
Dong WangDepartment of MicrobiologyThe University of Hong KongHong KongChina
,
Cun LiDepartment of MicrobiologyThe University of Hong KongHong KongChina
,
Xiaoyu ZhaoDepartment of MicrobiologyThe University of Hong KongHong KongChina
,
Man-Chun ChiuDepartment of MicrobiologyThe University of Hong KongHong KongChinaORCID Iconhttp://orcid.org/0000-0001-9503-6396
ORCID Icon,
Shuofeng YuanDepartment of MicrobiologyThe University of Hong KongHong KongChinaORCID Iconhttp://orcid.org/0000-0001-7996-1119
ORCID Icon,
Yanhui FanDepartment of BiochemistryThe University of Hong KongHong KongChinaORCID Iconhttp://orcid.org/0000-0001-9677-3777
ORCID Icon,
Honglin ChenDepartment of MicrobiologyThe University of Hong KongHong KongChina;State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina;Research Centre of Infection and ImmunologyThe University of Hong KongHong KongChina;Carol Yu Centre for InfectionThe University of Hong KongHong KongChinaORCID Iconhttp://orcid.org/0000-0001-5108-8338
ORCID Icon,
Jie ZhouDepartment of MicrobiologyThe University of Hong KongHong KongChina;State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina;Research Centre of Infection and ImmunologyThe University of Hong KongHong KongChinaCorrespondence[email protected]
&
Kwok-Yung YuenDepartment of MicrobiologyThe University of Hong KongHong KongChina;State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina;Research Centre of Infection and ImmunologyThe University of Hong KongHong KongChina;Carol Yu Centre for InfectionThe University of Hong KongHong KongChina
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Pages 1-12 | Received 22 Dec 2017, Accepted 18 Feb 2018, Published online: 29 Mar 2018

References

  • TaubenbergerJKKashJCInfluenza virus evolution, host adaptation and pandemic formationCell Host Microbe20107 440 45110.1016/j.chom.2010.05.0092892379
  • FodorEA single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAsJ. Virol.2002768989900110.1128/JVI.76.18.8989-9001.2002136441
  • DiasAThe cap-snatching endonuclease of influenza virus polymerase resides in the PA subunitNature200945891491810.1038/nature07745
  • MedinaRAGarcia-SastreAInfluenza A viruses: new research developmentsNat. Rev. Microbiol.2011959060310.1038/nrmicro2613
  • WebsterRGBeanWJGormanOTChambersTMKawaokaYEvolution and ecology of influenza A virusesMicrobiol. Rev.199256152179372859
  • SubbaraoEKLondonWMurphyBRA single amino acid in the PB2 gene of influenza A virus is a determinant of host rangeJ. Virol.19936717611764240216
  • HattaMGrowth of H5N1 influenza A viruses in the upper respiratory tracts of micePLoS Pathog.200731374137910.1371/journal.ppat.0030133
  • SteelJLowenACMubarekaSPalesePTransmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701NPLoS Pathog.20095e100025210.1371/journal.ppat.10002522603332
  • Czudai-MatwichVOtteAMatrosovichMGabrielGKlenkHDPB2 mutations D701N and S714R promote adaptation of an influenza H5N1 virus to a mammalian hostJ. Virol.2014888735874210.1128/JVI.00422-144136279
  • ZhuWDual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian modelsSci. Rep.2015510.1038/srep141704585756
  • MehleADoudnaJAAdaptive strategies of the influenza virus polymerase for replication in humansProc. Natl. Acad. Sci. USA2009106213122131610.1073/pnas.09119151062789757
  • LiuQCombination 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 vivoJ. Virol.2012861233123710.1128/JVI.05699-113255826
  • SongWThe K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replicationNat. Commun.2014510.1038/ncomms65094263149
  • BusseyKAPA residues in the 2009 H1N1 pandemic influenza virus enhance avian influenza virus polymerase activity in mammalian cellsJ. Virol.2011857020702810.1128/JVI.00522-113126589
  • XuCAmino acids 473V and 598P of PB1 from an avian-origin influenza A virus contribute to polymerase activity, especially in mammalian cellsJ. Gen. Virol.20129353154010.1099/vir.0.036434-0
  • DankarSKInfluenza A virus NS1 gene mutations F103L and M106I increase replication and virulenceVirol. J.201181310.1186/1743-422X-8-133032709
  • KryazhimskiySDushoffJBazykinGAPlotkinJBPrevalence of epistasis in the evolution of influenza A surface proteinsPLoS Genet.20117e100130110.1371/journal.pgen.10013013040651
  • FanSNovel residues in avian influenza virus PB2 protein affect virulence in mammalian hostsNat. Commun.2014510.1038/ncomms60215841464
  • FinkelsteinDBPersistent host markers in pandemic and H5N1 influenza virusesJ. Virol.200781102921029910.1128/JVI.00921-072045501
  • ChenGWGenomic signatures of human versus avian influenza A virusesEmerg. Infect. Dis.2006121353136010.3201/eid1209.0602763294750
  • MiottoOComplete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strainsPLoS ONE.20105e902510.1371/journal.pone.00090252815782
  • MiottoOHeinyATTanTWAugustJTBrusicVIdentification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysisBMC Bioinformatics2008910.1186/1471-2105-9-S1-S182259419
  • ElgendyEMIdentification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeonsJ. Gen. Virol.20179861710.1099/jgv.0.000674
  • AshenbergOLaubMTUsing analyses of amino acid coevolution to understand protein structure and functionMethods Enzymol.201352319121210.1016/B978-0-12-394292-0.00009-6
  • MartinLCGloorGBDunnSDWahlLMUsing information theory to search for co-evolving residues in proteinsBioinformatics2005214116412410.1093/bioinformatics/bti671
  • SimonettiFLTeppaEChernomoretzANielsenMMarino BusljeCMISTIC: mutual information server to infer coevolutionNucleic Acids Res.201341W8W1410.1093/nar/gkt4273692073
  • NilssonBEte VelthuisAJWFodorERole of the PB2 627 domain in influenza A virus polymerase functionJ. Virol.201791e02467024165355620
  • KimJHRole of host-specific amino acids in the pathogenicity of avian H5N1 influenza viruses in miceJ. Gen. Virol.2010911284128910.1099/vir.0.018143-02878586
  • PicaNHemagglutinin stalk antibodies elicited by the 2009 pandemic influenza virus as a mechanism for the extinction of seasonal H1N1 virusesProc. Natl. Acad. Sci. USA20121092573257810.1073/pnas.12000391093289326
  • ZhouJA functional variation in CD55 increases the severity of 2009 pandemic H1N1 influenza A virus infectionJ. Infect. Dis.201220649550310.1093/infdis/jis378
  • TamuriAUdos ReisMHayAJGoldsteinRAIdentifying changes in selective constraints: host shifts in influenzaPLoS Comput. Biol.20095e100056410.1371/journal.pcbi.10005642770840
  • WeinreichDMWatsonRAChaoLPerspective: sign epistasis and genetic constraint on evolutionary trajectoriesEvolution20055911651174
  • GongLISuchardMABloomJDStability-mediated epistasis constrains the evolution of an influenza proteineLife20132e0063110.7554/eLife.006313654441
  • MenaIOrigins of the 2009 H1N1 influenza pandemic in swine in MexicoeLife20165e167774957980
  • HungIFEffect of clinical and virological parameters on the level of neutralizing antibody against pandemic influenza A virus H1N1 2009Clin. Infect. Dis.20105127427910.1086/653940
  • EdgarRCMUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Res.2004321792179710.1093/nar/gkh340390337
  • CockPJBiopython: freely available Python tools for computational molecular biology and bioinformaticsBioinformatics2009251422142310.1093/bioinformatics/btp1632682512
  • Ash, R. B. Information Theory. (Dover Publications, 1965).
  • StamatakisARAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesBioinformatics2014301312131310.1093/bioinformatics/btu0333998144
  • RambautALamTTMax CarvalhoLPybusOGExploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)Virus Evol.20162vew00710.1093/ve/vew0074989882
  • GraefKMThe PB2 subunit of the influenza virus RNA polymerase affects virulence by interacting with the mitochondrial antiviral signaling protein and inhibiting expression of beta interferonJ. Virol.2010848433844510.1128/JVI.00879-102919034
  • WangJMouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulencePLoS ONE20127e4075210.1371/journal.pone.00407523393695
  • ZhouBPB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in miceJ. Virol.20118535736510.1128/JVI.01694-10
  • NgaiKLKChanMCWChanPKSReplication and transcription activities of ribonucleoprotein complexes reconstituted from avian H5N1, H1N1pdm09 and H3N2 influenza A virusesPLoS ONE20138e6503810.1371/journal.pone.00650383672204
  • YamajiRIdentification of PB2 mutations responsible for the efficient replication of H5N1 influenza viruses in human lung epithelial cellsJ. Virol.2015893947395610.1128/JVI.03328-144403392
  • MokCKAmino acid residues 253 and 591 of the PB2 protein of avian influenza virus A H9N2 contribute to mammalian pathogenesisJ. Virol.2011859641964510.1128/JVI.00702-113165745
  • ManzoorRPB2 protein of a highly pathogenic avian influenza virus strain A/chicken/Yamaguchi/7/2004 (H5N1) determines its replication potential in pigsJ. Virol.2009831572157810.1128/JVI.01879-08
  • BusseyKABousseTLDesmetEAKimBTakimotoTPB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cellsJ. Virol.2010844395440610.1128/JVI.02642-092863787
  • HayashiTWillsSBusseyKATakimotoTIdentification of influenza A virus PB2 residues involved in enhanced polymerase activity and virus growth in mammalian cells at low temperaturesJ. Virol.2015898042804910.1128/JVI.00901-154505657
  • ChenGWGenomic signatures for avian H7N9 viruses adapting to humansPLoS ONE201611e014843210.1371/journal.pone.01484324742285
  • CauldwellAVMoncorgeOBarclayWSUnstable polymerase-nucleoprotein interaction is not responsible for avian influenza virus polymerase restriction in human cellsJ. Virol.2013871278128410.1128/JVI.02597-123554100
  • XiaoCPB2-588V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza virusesSci. Rep.2016610.1038/srep194744726052
  • ZhaoZPB2-588I enhances 2009 H1N1 pandemic influenza virus virulence by increasing viral replication and exacerbating PB2 inhibition of beta interferon expressionJ. Virol.2014882260226710.1128/JVI.03024-133911566
  • FoegleinAacuteInfluence of PB2 host-range determinants on the intranuclear mobility of the influenza A virus polymeraseJ. Gen. Virol.2011921650166110.1099/vir.0.031492-03167894
  • GabrielGThe viral polymerase mediates adaptation of an avian influenza virus to a mammalian hostProc. Natl. Acad. Sci. USA2005102185901859510.1073/pnas.05074151021317936

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