Analysis of near full-length genome sequences of HIV type 1 BF intersubtype recombinant viruses from Brazil reveals their independent origins and their lack of relationship to CRF12_BF.

We analyze the recombinant structures and phylogenetic relationships of nine near full-length genome sequences of HIV-1 BF intersubtype recombinant viruses from Brazil, eight of them newly derived. These were obtained by PCR amplification from peripheral blood mononuclear cells (PBMCs) DNA or PBMCs culture supernantant RNA. The recombinants exhibited unique mosaic structures, except two viruses with a single near coincident breakpoint. Comparison with CRF12_BF revealed only two coincident breakpoints in two recombinants. Phylogenetic analyses failed to support a common ancestry of Brazilian recombinants or their relationship to CRF12_BF, which widely circulates in Argentina. Intersubtype breakpoint distribution along the genome was uneven, with the highest mean frequency in the polymerase domain of reverse transcriptase, and the lowest in env. These results indicate that HIV-1 BF recombinants from Brazil have independent origins and are unrelated to CRF12_BF, and that intersubtype breakpoints are frequent in pol segments analyzed for drug resistance detection.

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

[2]  Terence Rhodes,et al.  High Rates of Human Immunodeficiency Virus Type 1 Recombination: Near-Random Segregation of Markers One Kilobase Apart in One Round of Viral Replication , 2003, Journal of Virology.

[3]  A. Jetzt,et al.  High Rate of Recombination throughout the Human Immunodeficiency Virus Type 1 Genome , 2000, Journal of Virology.

[4]  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.

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

[6]  D. Pieniążek,et al.  Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil. , 1999, Emerging infectious diseases.

[7]  A. Samri,et al.  A patient with HIV-1 superinfection. , 2002, The New England journal of medicine.

[8]  L. Stuyver,et al.  Sequence Diversity of the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 from Untreated Brazilian Individuals , 1999, Antimicrobial Agents and Chemotherapy.

[9]  D. Pieniążek,et al.  HIV-1 subtypes among blood donors from Rio de Janeiro, Brazil. , 1999, Journal of acquired immune deficiency syndromes and human retrovirology : official publication of the International Retrovirology Association.

[10]  D. Pieniążek,et al.  The HIV Epidemic in the Amazon Basin Is Driven by Prototypic and Recombinant HIV‐1 Subtypes B and F , 2000, Journal of acquired immune deficiency syndromes.

[11]  M. Thomson,et al.  Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. , 2002, The Journal of general virology.

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

[13]  J. Mcnicholl,et al.  Intersubtype Human Immunodeficiency Virus Type 1 Superinfection following Seroconversion to Primary Infection in Two Injection Drug Users , 2002, Journal of Virology.

[14]  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 .

[15]  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.

[16]  P. Sharp,et al.  A Comprehensive Panel of Near-Full-Length Clones and Reference Sequences for Non-Subtype B Isolates of Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.

[17]  Martin Vingron,et al.  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing , 2002, Bioinform..

[18]  M. Thomson,et al.  Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. , 2002, The Lancet. Infectious diseases.

[19]  N. Walker,et al.  Status of the HIV/AIDS epidemic and methods to monitor it in the Latin America and Caribbean region , 2002, AIDS.

[20]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[21]  M. Morgado,et al.  High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions. , 2002, AIDS research and human retroviruses.