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Original Articles

Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis

, ORCID Icon, , &
Pages 1-8 | Received 04 Apr 2018, Accepted 20 Sep 2018, Published online: 21 Nov 2018

References

  • BuiCMChughtaiAAAdamDCMacIntyreCRAn overview of the epidemiology and emergence of influenza A infection in humans over timeArch. Public Health20177510.1186/s13690-017-0182-z
  • ImaiMasakiWatanabeTokikoKisoMakiNakajimaNorikoYamayoshiSeiyaIwatsuki-HorimotoKiyokoHattaMasatoYamadaShinyaItoMutsumiSakai-TagawaYukoShirakuraMasayukiTakashitaEmiFujisakiSeiichiroMcBrideRyanThompsonAndrew J.TakahashiKentaMaemuraTadashiMitakeHiromichiChibaShihoZhongGongxunFanShufangOishiKoheiYasuharaAtsuhiroTakadaKosukeNakaoTomomiFukuyamaSatoshiYamashitaMakotoLopesTiago J.S.NeumannGabrieleOdagiriTakatoWatanabeShinjiShuYuelongPaulsonJames C.HasegawaHidekiKawaokaYoshihiroA Highly Pathogenic Avian H7N9 Influenza Virus Isolated from A Human Is Lethal in Some Ferrets Infected via Respiratory DropletsCell Host & Microbe2017225 615-626.e810.1016/j.chom.2017.09.008
  • BuiCA systematic review of the comparative epidemiology of avian and human influenza A H5N1 and H7N9—lessons and unanswered questionsTransbound. Emerg. Dis.201663602 62010.1111/tbed.12327
  • ClaesF.KuznetsovD.LiechtiR.Von DobschuetzS.Dinh TruongB.GleizesA.ConversaD.ColonnaA.DemaioE.RamazzottoS.LarfaouiF.PintoJ.Le MercierP.XenariosI.DauphinG.The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza virusesDatabase201420140bau008bau00810.1093/database/bau008
  • BethmontAQuantified degree of poultry exposure differs for human cases of avian influenza H5N1 and H7N9Epidemiol. Infect.20161442633264010.1017/S0950268816001035
  • BuiC.RahmanB.HeywoodA. E.MacIntyreC. R.A Meta-Analysis of the Prevalence of Influenza A H5N1 and H7N9 Infection in BirdsTransboundary and Emerging Diseases201664396797710.1111/tbed.12466
  • BuiCMGardnerLMacIntyreRSarkarSInfluenza A H5N1 and H7N9 in China: a spatial risk analysisPLoS ONE201712e017498010.1371/journal.pone.0174980
  • LuLLeigh BrownAJLycettSJQuantifying predictors for the spatial diffusion of avian influenza virus in ChinaBMC Evol. Biol.2017171610.1186/s12862-016-0845-3
  • ShiJIsolation and characterization of H7N9 viruses from live poultry markets—implication of the source of current H7N9 infection in humansChin. Sci. Bull.2013581857186310.1007/s11434-013-5873-4
  • Avise, J. C. Phylogeography: The History and Formation of Species (Harvard University Press, Cambridge, MA, 2000).
  • FariaNRSuchardMARambautALemeyPToward a quantitative understanding of viral phylogeographyCurr. Opin. Virol.2011142342910.1016/j.coviro.2011.10.003
  • LamTTDissemination, divergence and establishment of H7N9 influenza viruses in ChinaNature201552210210510.1038/nature14348
  • ScotchMPhylogeography of influenza A H5N1 clade 2.2. 1.1 in EgyptBMC Genom.20131410.1186/1471-2164-14-871
  • TianHAvian influenza H5N1 viral and bird migration networks in AsiaProc. Natl. Acad. Sci. USA201511217217710.1073/pnas.1405216112
  • LemeyPRambautADrummondAJSuchardMABayesian phylogeography finds its rootsPLoS Comput. Biol.20095e100052010.1371/journal.pcbi.1000520
  • LamTTPhylodynamics of H5N1 avian influenza virus in IndonesiaMol. Ecol.2012213062307710.1111/j.1365-294X.2012.05577.x
  • AlkhamisMAMooreBRPerezAMPhylodynamics of H5N1 highly pathogenic avian influenza in Europe, 2005−2010: potential for molecular surveillance of new outbreaksViruses201573310332810.3390/v7062773
  • Lu, J. et al. Molecular evolution, diversity and adaptation of H7N9 influenza A viruses in China. bioRxiv, 10.1101/155218 (2017).
  • WangDTwo outbreak sources of influenza A (H7N9) viruses have been established in ChinaJ. Virol.2016905561557310.1128/JVI.03173-15
  • LamTTThe genesis and source of the H7N9 influenza viruses causing human infections in ChinaNature201350224124410.1038/nature12515
  • HerrickKHuettmannFLindgrenMA global model of avian influenza prediction in wild birds: the importance of northern regionsVet. Res.2013444210.1186/1297-9716-44-42
  • LemeyPUnifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2PLoS Pathog.201410e100393210.1371/journal.ppat.1003932
  • YpmaRJFUnravelling transmission trees of infectious diseases by combining genetic and epidemiological dataProc. Biol. Sci.201227944445010.1098/rspb.2011.0913
  • NelsonMIGlobal migration of influenza A viruses in swineNat. Commun.2015610.1038/ncomms7696
  • BeardRMageeDSuchardMALemeyPScotchMGeneralized linear models for identifying predictors of the evolutionary diffusion of virusesAMIA Jt Summits Transl. Sci. Proc.2014201423284333690
  • TrovaoNSSuchardMABaeleGGilbertMLemeyPBayesian inference reveals host-specific contributions to the epidemic expansion of influenza A H5N1Mol. Biol. Evol.201532326432754831561
  • JinYPhylogeography of Avian influenza A H9N2 in ChinaBMC Genom.20141510.1186/1471-2164-15-1110
  • AdhikariDChettriABarikSKModelling the ecology and distribution of highly pathogenic avian influenza (H5N1) in the Indian subcontinentCurr. Sci.2009977378
  • Zeng, D. Z. Building Engines for Growth and Competitiveness in China (The World Bank, Geneva, 2010).
  • BahlJEcosystem interactions underlie the spread of Avian influenza A viruses with pandemic potentialPLoS Pathog.201612e100562010.1371/journal.ppat.1005620
  • TakekawaJYMovements of wild ruddy shelducks in the Central Asian Flyway and their spatial relationship to outbreaks of highly pathogenic avian influenza H5N1Viruses201352129215210.3390/v5092129
  • GaidetNPotential spread of highly pathogenic avian influenza H5N1 by wildfowl: dispersal ranges and rates determined from large-scale satellite telemetryJ. Appl. Ecol.2010471147115710.1111/j.1365-2664.2010.01845.x
  • TakekawaJYMigration of waterfowl in the East Asian flyway and spatial relationship to HPAI H5N1 outbreaksAvian Dis.20105446647610.1637/8914-043009-Reg.1
  • TakekawaJYVictims and vectors: highly pathogenic avian influenza H5N1 and the ecology of wild birdsAvian Biol. Res.20103517310.3184/175815510X12737339356701
  • Bingsheng, K. & Yijun, H. Poultry sector in China: structural changes during the past decade and future trends. Paper presented at Poultry in the 21st Century: Avian Influenza and Beyond. Food and Agricultural Organization, Bangkok, 5−7 November (2007).
  • SuSEpidemiology, evolution, and pathogenesis of H7N9 influenza viruses in five epidemic waves since 2013 in ChinaTrends Microbiol.20172571372810.1016/j.tim.2017.06.008
  • ChengWComparison of the three waves of avian influenza A(H7N9) virus circulation since live poultry markets were permanently closed in the main urban areas in Zhejiang Province, July 2014−June 2017Influenza Other Respir. Virus.20181225926610.1111/irv.12532
  • FamulareMHuHExtracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in NigeriaInt. Health2015713013810.1093/inthealth/ihv012
  • MageeDScotchMSuchardMABayesian phylogeography of influenza A/H3N2 for the 2014−15 season in the United States using three frameworks of ancestral state reconstructionPLoS Comput. Biol.201713e100538910.1371/journal.pcbi.1005389
  • NelsonMIThe evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, NicaraguaVirology2014462-463819010.1016/j.virol.2014.05.025
  • TianHSpatial, temporal and genetic dynamics of highly pathogenic avian influenza A (H5N1) virus in ChinaBmc Infect. Dis.20151510.1186/s12879-015-0770-x
  • ElbeSBuckland-MerrettGData, disease and diplomacy: GISAID’s innovative contribution to global healthGlob. Chall.20171334610.1002/gch2.1018
  • DrummondAJSuchardMAXieDRambautABayesian phylogenetics with BEAUti and the BEAST 1.7Mol. Biol. Evol.2012291969197310.1093/molbev/mss075
  • ChenJFirst genome report and analysis of chicken H7N9 influenza viruses with poly-basic amino acids insertion in the hemagglutinin cleavage siteSci. Rep.2017710.1038/s41598-017-10605-6
  • LiuWOccurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in ChinaJ. Virol.201488133441335110.1128/JVI.01777-14
  • FusaroAEvolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria from 2006 to 2008J. Virol.2010843239324710.1128/JVI.02385-09
  • LamTTEvolutionary and transmission dynamics of reassortant H5N1 influenza virus in IndonesiaPLoS Pathog.20084e100013010.1371/journal.ppat.1000130
  • LiXGlobal and local persistence of influenza A(H5N1) virusEmerg. Infect. Dis.2014201287129510.3201/eid2008.130910
  • VijaykrishnaDEvolutionary dynamics and emergence of panzootic H5N1 influenza virusesPLoS Pathog.20084e100016110.1371/journal.ppat.1000161
  • LeeDHHighly pathogenic Avian influenza viruses and generation of novel reassortants, United States, 2014−2015Emerg. Infect. Dis.2016221283128510.3201/eid2207.160048
  • ShapiroBRambautADrummondAJChoosing appropriate substitution models for the phylogenetic analysis of protein-coding sequencesMol. Biol. Evol.2006237910.1093/molbev/msj021
  • DrummondAJHoSYPhillipsMJRambautARelaxed phylogenetics and dating with confidencePLoS Biol.20064e8810.1371/journal.pbio.0040088
  • WangYTowards a better understanding of the novel avian-origin H7N9 influenza A virus in ChinaSci. Rep.2013310.1038/srep02318
  • CuiLDynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virusNat. Commun.2014510.1038/ncomms4142
  • BaeleGImproving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertaintyMol. Biol. Evol.2012292157216710.1093/molbev/mss084
  • BaeleGLiWLDrummondAJSuchardMALemeyPAccurate model selection of relaxed molecular clocks in bayesian phylogeneticsMol. Biol. Evol.20133023924310.1093/molbev/mss243
  • YuGggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated dataMethods Ecol. Evol.20178283610.1111/2041-210X.12628
  • BielejecFSpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processesMol. Biol. Evol.2016332167216910.1093/molbev/msw082
  • FariaNRSuchardMARambautAStreickerDGLemeyPSimultaneously reconstructing viral cross-species transmission history and identifying the underlying constraintsPhilos. Trans. R. Soc. Lond. B Biol. Sci.20133682012019610.1098/rstb.2012.0196
  • LemeyPThe seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testingarXiv201212105877