A novel methodology for large-scale phylogeny partition

Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data. Supplementary information The online version of this article (doi:10.1038/ncomms1325) contains supplementary material, which is available to authorized users.

[1]  G. Fadda,et al.  Declining Prevalence of HIV-1 Drug Resistance in Treatment-Failing Patients: A Clinical Cohort Study , 2007, Antiviral therapy.

[2]  Bernard Hirschel,et al.  The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection , 2009, AIDS.

[3]  Rebecca R. Gray,et al.  Spatial phylodynamics of HIV-1 epidemic emergence in east Africa , 2009, AIDS.

[4]  D. Pillay,et al.  The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy , 2006, AIDS.

[5]  D. Nickle,et al.  Importance and detection of virus reservoirs and compartments of HIV infection. , 2003, Current opinion in microbiology.

[6]  M. Zazzi,et al.  Three-Class-Resistant Human Immunodeficiency Virus Type 1 Variant in a Drug-Naive Heterosexual Couple , 2008, Journal of Clinical Microbiology.

[7]  R. Tubiana,et al.  Detection of HIV-1 RNA in seminal plasma samples from treated patients with undetectable HIV-1 RNA in blood plasma , 2008, AIDS.

[8]  Ard van Sighem,et al.  Transmission networks of HIV-1 among men having sex with men in the Netherlands , 2010, AIDS.

[9]  D. Pillay,et al.  The effect of intrinsic stochasticity on transmitted HIV drug resistance patterns. , 2010, Journal of theoretical biology.

[10]  Peter M. A. Sloot,et al.  International Journal of Computer Mathematics Stochastic Simulation of Hiv Population Dynamics through Complex Network Modelling Stochastic Simulation of Hiv Population Dynamics through Complex Network Modelling , 2022 .

[11]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[12]  Stéphane Hué,et al.  HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy , 2004, AIDS.

[13]  M. Zazzi,et al.  Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades * , 2010, HIV Medicine.

[14]  Donald Ervin Knuth,et al.  The Art of Computer Programming , 1968 .

[15]  Steven M Goodreau.  Assessing the Effects of Human Mixing Patterns on Human Immunodeficiency Virus-1 Interhost Phylogenetics Through Social Network Simulation , 2006, Genetics.

[16]  Marco Salemi,et al.  Phylodynamics of HIV-1 in Lymphoid and Non-Lymphoid Tissues Reveals a Central Role for the Thymus in Emergence of CXCR4-Using Quasispecies , 2007, PloS one.

[17]  N. Wicker,et al.  Secator: a program for inferring protein subfamilies from phylogenetic trees. , 2001, Molecular biology and evolution.

[18]  S. Frost,et al.  Sexual networks and the transmission of drug-resistant HIV , 2008, Current opinion in infectious diseases.

[19]  David Dunn,et al.  Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom , 2009, PLoS pathogens.

[20]  W. Fitch,et al.  Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS , 2005, Journal of Virology.

[21]  Matthias Egger,et al.  Sexual transmission of HIV according to viral load and antiretroviral therapy: systematic review and meta-analysis , 2009, AIDS.

[22]  David L. Robertson,et al.  CTree: comparison of clusters between phylogenetic trees made easy , 2007, Bioinform..

[23]  M. Zazzi,et al.  Detection of a drug-resistant human immunodeficiency virus variant in a newly infected heterosexual couple. , 2002, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[24]  David Dunn,et al.  Demonstration of Sustained Drug-Resistant Human Immunodeficiency Virus Type 1 Lineages Circulating among Treatment-Naïve Individuals , 2009, Journal of Virology.

[25]  D. Pillay,et al.  Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions. , 2009, The Journal of infectious diseases.

[26]  C. Archibald,et al.  Longitudinal Phylogenetic Surveillance Identifies Distinct Patterns of Cluster Dynamics , 2010, Journal of acquired immune deficiency syndromes.

[27]  Kuo-Bin Li,et al.  ClustalW-MPI: ClustalW analysis using distributed and parallel computing , 2003, Bioinform..

[28]  B. Masquelier,et al.  HIV Type-1 Transmission Dynamics in Recent Seroconverters: Relationship with Transmission of drug Resistance and Viral Diversity , 2008, Antiviral therapy.

[29]  Anne M Johnson,et al.  Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach , 2010, AIDS.

[30]  S. Yerly,et al.  Travel and the spread of HIV-1 genetic variants. , 2003, The Lancet. Infectious diseases.

[31]  A. Rambaut,et al.  Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics , 2008, PLoS medicine.

[32]  Rebecca R. Gray,et al.  Multiple independent lineages of HIV-1 persist in breast milk and plasma , 2011, AIDS.

[33]  Erin N. Bodine,et al.  Evolutionary Dynamics of Complex Networks of HIV Drug-Resistant Strains: The Case of San Francisco , 2010, Science.

[34]  Michel Roger,et al.  Transmission networks of drug resistance acquired in primary/early stage HIV infection , 2008, AIDS.

[35]  Alan S. Perelson,et al.  Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1 , 2009, The Journal of experimental medicine.

[36]  Matthias Cavassini,et al.  Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. , 2010, The Journal of infectious diseases.

[37]  Anne-Mieke Vandamme,et al.  Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. , 2007, AIDS research and human retroviruses.

[38]  Matthew G Law,et al.  Relation between HIV viral load and infectiousness: a model-based analysis , 2008, The Lancet.

[39]  J Desmyter,et al.  Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Klaus Korn,et al.  Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. , 2005, The Journal of infectious diseases.