A novel methodology for large-scale phylogeny partition.

Journal article

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: Prosperi, M; Ciccozzi, M; Fanti, I; Saladini, F; Pecorari, M

• Journal: Nature communications
• Volume: 2
• Issue: 1
• Pages: 321
• Publication date: 2011-01-01
• DOI: 10.1038/ncomms1325
• EISSN: 2041-1723
• Language: English
• Keywords: Gene Products, pol; Female; ARCA collaborative group; Algorithms; Classification; Male; HIV-1; HIV Infections; Humans; Phylogeny