title: In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: determination of hot spots and correlation with sequence similarity.
abstract: Recombination plays a pivotal role in the evolutionary process of many different virus species, including retroviruses. Analysis of all human immunodeficiency virus type 1 (HIV-1) intersubtype recombinants revealed that they are more complex than described initially. Recombination frequency is higher within certain genomic regions, such as partial reverse transcriptase (RT), vif/vpr, the first exons of tat/rev, vpu and gp41. A direct correlation was observed between recombination frequency and sequence similarity across the HIV-1 genome, indicating that sufficient sequence similarity is required upstream of the recombination breakpoint. This finding suggests that recombination in vivo may occur preferentially during reverse transcription through the strand displacement-assimilation model rather than the copy-choice model.
mesh_terms: D019143:Evolution, Molecular; D016679:Genome, Viral; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D015700:HIV Envelope Protein gp41; D014764:Viral Proteins; D054303:HIV Reverse Transcriptase