Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection 英文参考文献.docVIP

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Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection 英文参考文献.doc

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Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection 英文参考文献

SimpleEpidemiologicalDynamicsExplainPhylogenetic ClusteringofHIVfromPatientswithRecentInfection ErikM.Volz1*,JamesS.Koopman1,MelissaJ.Ward2,AndrewLeighBrown2,SimonD.W.Frost3 1DepartmentofEpidemiology,UniversityofMichigan,AnnArbor,Michigan,UnitedStatesofAmerica,2InstituteofEvolutionaryBiology,SchoolofBiologicalSciences, UniversityofEdinburgh,Edinburgh,UnitedKingdom,3DepartmentofVeterinaryMedicine,UniversityofCambridge,Cambridge,UnitedKingdom Abstract Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. SeveralstudieshavedemonstratedthepresenceofclustersofhighlyrelatedHIV-1sequences,particularlyamongrecently HIV-infectedindividuals,whichhavebeenusedtoargueforahightransmissionrateduringacuteinfection.Usingalarge setofHIV-1subtypeBpolsequencescollectedfrommenwhohavesexwithmen,wedemonstratethatvirusfromrecent infectionstendtobephylogeneticallyclusteredatagreaterratethanvirusfrompatientswithchronicinfection(‘excess clustering’)andalsotendtoclusterwithotherrecentHIVinfectionsratherthanchronic,establishedinfections(‘excessco- clustering’),consistentwithpreviousreports.Todeterminetherolethatahigherinfectivityduringacuteinfectionmayplay inexcessclusteringandco-clustering,wedevelopedasimplemodelofHIVinfectionthatincorporatesanearlyperiodof intensifiedtransmission,andexplicitlyconsidersthedynamicsofphylogeneticclustersalongsidethedynamicsofacuteand chronic infected cases. We explored the potential for clustering statistics to be used for inference of acute stage transmission rates and found that no single statistic explains very much variance in parameters controlling acute stage transmission rates.We demonstratethat high transmissionrates during theacute stageis not themaincause ofexcess clustering of virus from patients with early/acute infection compared to chronic infection, which may simply reflect the shorter time since transmission in acute infection. Higher transmission during acute infection can res