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EnglishUnderstanding 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. | |
| Autore/i: | Prosperi MC; Ciccozzi M, Fanti I; Saladini F; Pecorari M; Borghi V; Di Giambenedetto S; Bruzzone B; Capetti A; Vivarelli A; Rusconi S; RE, MARIA CARLA; Gismondo MR; Sighinolfi L; Gray RR; Salemi M; Zazzi M; De Luca A; ARCA collaborative group | |
| Autore/i Unibo: | ||
| Anno: | 2011 | |
| Rivista: | ||
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1038/ncomms1325 | |
| 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. | |
| Data prodotto definitivo in UGOV: | 2013-06-27 | |
| Appare nelle tipologie: | 1.01 Articolo in rivista |
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