6533b835fe1ef96bd129feb7
RESEARCH PRODUCT
A novel methodology for large-scale phylogeny partition
Mattia C. F. ProsperiMassimo CiccozziIuri FantiFrancesco SaladiniMonica PecorariVanni BorghiSimona Di GiambenedettoBianca BruzzoneAmedeo CapettiAngela VivarelliStefano RusconiRe Maria CarlaMaria Rita GismondoLaura SighinolfiRebecca R. GrayMarco SalemiMaurizio ZazziAndrea De LucaA GiacomettiL ButiniS MenzoD TacconiG CorbelliS ZanussiL MonnoG PunziF MaggioloA CallegaroL CalzaMc ReR PristeràP TurconiA MandasS TiniA ZoncadaE PaoliniG AmadioL SighinolfiG ZuccatiM MorfiniR ManettiP CorsiL GalliM Di PietroF BartalesiG ColaoA TostiA Di BiagioM SettiB BruzzoneG PencoM TrezziA OraniR PardelliM De GennaroA ChioderaA ScalziniL PalvariniP AlmiG TodaroP CicconiS RusconiMr GismondoMr GismondoV MicheliMl BiondiN GianottiA CapettiP MeravigliaE BoeriC MussiniM PecorariA SoriaL VecchiM SantirocchiD BrustiaP RavaniniF Dal BelloN RomanoS MancusoC CalzettiR MaseratiG FiliceF BaldantiD FrancisciG ParrutiE PolilliD SacchiniC MartinelliR ConsoliniL VatteroniA VivarelliD DionisioA NerliL LenziG MagnaniP OrtolaniM AndreoniG PalamaraC FimianiL PalmisanoA De LucaG FaddaVincenzo VulloOmbretta TurrizianiM MontanoG CenderelloA GonnelliM PalumboV GhisettiS BonoraP Delle FoglieC RossiP GrossiE SeminariF PolettiV MondinoM MalenaE. Lattuadasubject
Genetics and Molecular Biology (all)MalepolTheoretical computer scienceInferenceGene Products polGeneral Physics and AstronomyHIV InfectionsBiologyNetwork topologySettore MED/17 - MALATTIE INFETTIVEBiochemistryArticleGeneral Biochemistry Genetics and Molecular Biology03 medical and health sciencesPhysics and Astronomy (all)0302 clinical medicineSearch algorithmphylogenetic analysis; virus transmissionGene ProductsHumansHIV Infection030212 general & internal medicinePhylogeny030304 developmental biologyAlgorithms; Classification; Female; Gene Products pol; HIV Infections; HIV-1; Humans; Male; Phylogeny; Biochemistry Genetics and Molecular Biology (all); Chemistry (all); Physics and Astronomy (all)Genetics0303 health sciencesBiochemistry Genetics and Molecular Biology (all)MultidisciplinaryPhylogenetic treeNode (networking)phylogenetic analysisChemistry (all)HIVGeneral Chemistryvirus transmissionClassificationPartition (database)AlgorithmIdentification (information)Transmission (telecommunications)HIV-1FemaleMETHODOLOGYAlgorithmsHumandescription
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics. © 2011 Macmillan Publishers Limited. All rights reserved.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2011-05-24 | Nature Communications |