Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method.

The increased complexity of HIV-1 genetic heterogeneity raises the issue for reliable classification and analysis of these sequences. Until now, bootscanning analysis has been the main method used for the analysis of potential HIV-1 intersubtype recombinants. We show evidence that in some cases of complex recombinants, where three or more segments with discordant phylogenetic signal may exist in protease (PR) and partial reverse transcriptase (RT) region, Bayesian scanning provides a clearer picture than bootscanning plots about the boundaries of potential recombination. Thus, a recently developed Bayesian scanning tool can facilitate the analysis and classification of HIV-1 mosaic sequences.

[1]  K. Lole,et al.  Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination , 1999, Journal of Virology.

[2]  D. Winkler,et al.  Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences. , 2002, Molecular phylogenetics and evolution.

[3]  Jonathan P. Bollback,et al.  Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.

[4]  M. Salminen,et al.  HIV‐1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad , 1998, AIDS.

[5]  J. Margolick,et al.  High rates of transmission of subtype E human immunodeficiency virus type 1 among heterosexual couples in Northern Thailand: role of sexually transmitted diseases and immune compromise. , 1999, The Journal of infectious diseases.

[6]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[7]  M. Thomson,et al.  Widespread circulation of a B/F intersubtype recombinant form among HIV-1-infected individuals in Buenos Aires, Argentina. , 2000, AIDS.

[8]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[9]  Joseph Felsenstein,et al.  DISTANCE METHODS FOR INFERRING PHYLOGENIES: A JUSTIFICATION , 1984, Evolution; international journal of organic evolution.

[10]  D. Burke,et al.  Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. , 1995, AIDS research and human retroviruses.

[11]  M. Thomson,et al.  Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure. , 2002 .

[12]  J. Carr,et al.  Diverse BF recombinants have spread widely since the introduction of HIV-1 into South America , 2001, AIDS.

[13]  M. Suchard,et al.  Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1. , 2003, Molecular biology and evolution.

[14]  V. Lukashov,et al.  Simultaneous introduction of HIV type 1 subtype A and B viruses into injecting drug users in southern Ukraine at the beginning of the epidemic in the former Soviet Union. , 2002, AIDS research and human retroviruses.

[15]  M. Peeters,et al.  Most env and gag subtype A HIV-1 viruses circulating in West and West Central Africa are similar to the prototype AG recombinant virus IBNG. , 2000 .

[16]  A. Vandamme,et al.  In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: determination of hot spots and correlation with sequence similarity. , 2003, The Journal of general virology.

[17]  Anne-Mieke Vandamme,et al.  Prevalence and origin of HIV-1 group M subtypes among patients attending a Belgian hospital in 1999. , 2002, Virus research.

[18]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[19]  Victoria A Johnson,et al.  Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA Panel. , 2003, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[20]  Masatoshi Nei,et al.  Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  B. Korber,et al.  HIV sequence compendium 2002 , 2002 .

[22]  D. Gotte,et al.  Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand , 1996, Journal of virology.

[23]  M. Peeters,et al.  High genetic diversity of HIV-1 strains in Chad, West Central Africa. , 2003, Journal of acquired immune deficiency syndromes.

[24]  Nick Goldman,et al.  Statistical tests of models of DNA substitution , 1993, Journal of Molecular Evolution.

[25]  R. Parreira,et al.  Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon, Portugal. , 2003, AIDS research and human retroviruses.

[26]  W. Doolittle,et al.  Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. , 2003, Molecular biology and evolution.

[27]  D. Gotte,et al.  The AG recombinant IbNG and novel strains of group M HIV-1 are common in Cameroon. , 2001, Virology.

[28]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .