title: A novel methodology for large-scale phylogeny partition.
abstract: 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.
authors: Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy. m.prosperi@epi.ufl.edu
authors: Mattia C F
authors: MC
authors: Prosperi
authors: Massimo
authors: M
authors: Ciccozzi
authors: Iuri
authors: I
authors: Fanti
authors: Francesco
authors: F
authors: Saladini
authors: Monica
authors: M
authors: Pecorari
authors: Vanni
authors: V
authors: Borghi
authors: Simona
authors: S
authors: Di Giambenedetto
authors: Bianca
authors: B
authors: Bruzzone
authors: Amedeo
authors: A
authors: Capetti
authors: Angela
authors: A
authors: Vivarelli
authors: Stefano
authors: S
authors: Rusconi
authors: Maria Carla
authors: MC
authors: Re
authors: Maria Rita
authors: MR
authors: Gismondo
authors: Laura
authors: L
authors: Sighinolfi
authors: Rebecca R
authors: RR
authors: Gray
authors: Marco
authors: M
authors: Salemi
authors: Maurizio
authors: M
authors: Zazzi
authors: Andrea
authors: A
authors: De Luca
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