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.
The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.
Thomson
Michael M
MM
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Delgado
Elena
E
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Herrero
Isabel
I
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Villahermosa
María Luisa
ML
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Vázquez-de Parga
Elena
E
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Cuevas
María Teresa
MT
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Carmona
Rocío
R
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Medrano
Leandro
L
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Pérez-Álvarez
Lucía
L
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Cuevas
Laureano
L
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
Nájera
Rafael
R
Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1.
D001118:Argentina; D001483:Base Sequence; D004279:DNA, Viral; D005260:Female; D015683:Gene Products, gag / Q000235:genetics / Q000502:physiology; D015694:Gene Products, rev / Q000235:genetics / Q000502:physiology; D014644:Genetic Variation; D016679:Genome, Viral; D015488:HIV Antigens / Q000235:genetics / Q000502:physiology; D015700:HIV Envelope Protein gp41 / Q000235:genetics / Q000502:physiology; D015658:HIV Infections / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics / Q000502:physiology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009030:Mosaicism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011995:Recombination, Genetic; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics / Q000502:physiology; D054301:gag Gene Products, Human Immunodeficiency Virus; D054321:rev Gene Products, Human Immunodeficiency Virus; D000086082:Viroporin Proteins
D004279:DNA, Viral; D015683:Gene Products, gag; D015694:Gene Products, rev; D015488:HIV Antigens; D015700:HIV Envelope Protein gp41; D054303:HIV Reverse Transcriptase; D054298:Human Immunodeficiency Virus Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; D054321:rev Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins