Searching for virus phylotypes

被引:24
作者
Chevenet, Francois [1 ,2 ,3 ]
Jung, Matthieu [1 ,4 ]
Peeters, Martine [4 ]
de Oliveira, Tulio [5 ]
Gascuel, Olivier [1 ]
机构
[1] Univ Montpellier 2, CNRS, UMR 5506, Inst Biol Computat,LIRMM, Montpellier, France
[2] Univ Montpellier I, CNRS 5290, IRD 224, MIVEGEC, Montpellier, France
[3] Univ Montpellier 2, CNRS 5290, IRD 224, MIVEGEC, Montpellier, France
[4] Univ Montpellier I, IRD, UMI233, TransVIHMI, Montpellier, France
[5] Univ KwaZulu Natal, Africa Ctr Hlth & Populat Studies, Durban, South Africa
基金
英国惠康基金;
关键词
SUBTYPE C EPIDEMIC; HIV-1; PHYLOGENIES; PHYLOGEOGRAPHY; IDENTIFICATION; DISPERSAL;
D O I
10.1093/bioinformatics/btt010
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Large phylogenies are being built today 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 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 large, containing > 3000 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.
引用
收藏
页码:561 / 570
页数:10
相关论文
共 31 条
[1]   Identification of a genetic subcluster of HIV type 1 subtype C (C′) widespread in Ethiopia [J].
Abebe, A ;
Pollakis, G ;
Fontanet, AL ;
Fisseha, B ;
Tegbaru, B ;
Kliphuis, A ;
Tesfaye, G ;
Negassa, H ;
Cornelissen, M ;
Goudsmit, J ;
De Wit, TFR .
AIDS RESEARCH AND HUMAN RETROVIRUSES, 2000, 16 (17) :1909-1914
[2]   SIMMAP: Stochastic character mapping of discrete traits on phylogenies [J].
Bollback, JP .
BMC BIOINFORMATICS, 2006, 7 (1)
[3]   High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America [J].
Collaco Veras, Nazle Mendonca ;
Gray, Rebecca R. ;
de Macedo Brigido, Luis Fernando ;
Rodrigues, Rosangela ;
Salemi, Marco .
JOURNAL OF GENERAL VIROLOGY, 2011, 92 :1698-1709
[4]   The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom [J].
de Oliveira, Tulio ;
Pillay, Deenan ;
Gifford, Robert J. .
PLOS ONE, 2010, 5 (02)
[5]   Bayesian Phylogenetics with BEAUti and the BEAST 1.7 [J].
Drummond, Alexei J. ;
Suchard, Marc A. ;
Xie, Dong ;
Rambaut, Andrew .
MOLECULAR BIOLOGY AND EVOLUTION, 2012, 29 (08) :1969-1973
[6]   CONSERVATION EVALUATION AND PHYLOGENETIC DIVERSITY [J].
FAITH, DP .
BIOLOGICAL CONSERVATION, 1992, 61 (01) :1-10
[7]   Unifying the epidemiological and evolutionary dynamics of pathogens [J].
Grenfell, BT ;
Pybus, OG ;
Gog, JR ;
Wood, JLN ;
Daly, JM ;
Mumford, JA ;
Holmes, EC .
SCIENCE, 2004, 303 (5656) :327-332
[8]   New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 [J].
Guindon, Stephane ;
Dufayard, Jean-Francois ;
Lefort, Vincent ;
Anisimova, Maria ;
Hordijk, Wim ;
Gascuel, Olivier .
SYSTEMATIC BIOLOGY, 2010, 59 (03) :307-321
[9]   Global trends in molecular epidemiology of HIV-1 during 2000-2007 [J].
Hemelaar, Joris ;
Gouws, Eleanor ;
Ghys, Peter D. ;
Osmanov, Saladin .
AIDS, 2011, 25 (05) :679-689
[10]   Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups [J].
Húe, S ;
Pillay, D ;
Clewley, JP ;
Pybus, OG .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (12) :4425-4429