Searching for Virus Phylotypes. Bioinformatics, 29 (5): 561-570 (2013).

Publication Latest Publications

Title: Searching for Virus Phylotypes
Authors: surname=de OliveiraChevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O.
Journal: Bioinformatics,29 (5):561-570 (2013)

Journal Impact Factor (I.F.): 5.468
Number of citations (Google Scholar): 10

Abstract

Motivation: Very large phylogenies are being built today in order to study virus evolution, trace the origin of epidemics, establish the mode of transmission, and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.

Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in very low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is very large, containing more than 3,000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones.

Availability: This method and companion tools are implemented in an interactive Web interface (www.phylotype.org), which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of very large data sets.

Download: Full text paper

Citation: surname=de OliveiraChevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O. Searching for Virus Phylotypes Bioinformatics,29 (5):561-570 (2013).

Printed and Online Media Coverage

Pirate Science

Searching for Virus Phylotypes

Pirate Science - 2013-01-22

Viral phylogenies have wide use: studying evolution, tracing the origin of epidemics, establishing dominant mode of transmission, identifying the apparition of drug resistance, even tracking individual body compartments.



Impact of point-of-care Xpert MTB/RIF on tuberculosis treatment initiation: a cluster randomised trial
Journal: Am J Respir Crit Care Med (2017)

Hyperbilirubinemia in atazanavir-treated human immunodeficiency virus-infected patients: the impact of the UGT1A1*28 allele
Journal: Pharmacogenomics and Personalized Medicine (2017)

Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa
Journal: Journal of Antimicrobial Chemotherapy (2017)
All publications...


KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

Page design updated 2013. Many of the pages were previously hosted at bioafrica.net.