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.
|Titolo:||A novel methodology for large-scale phylogeny partition|
|Parole Chiave:||immunodeficiency-virus type-1; drug-resistance; HIV-infection; transmission networks; antiretroviral therapy; heterosexual couple; population-dynamics; viral load; individuals; prevalence|
|Settore Scientifico Disciplinare:||Settore MED/17 - Malattie Infettive|
Settore MED/07 - Microbiologia e Microbiologia Clinica
|Data di pubblicazione:||24-mag-2011|
|Digital Object Identifier (DOI):||10.1038/ncomms1325|
|Appare nelle tipologie:||01 - Articolo su periodico|