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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.

Original publication




Journal article


J Gen Virol

Publication Date





2715 - 2722


Evolution, Molecular, Genome, Viral, HIV Envelope Protein gp41, HIV Reverse Transcriptase, HIV-1, Humans, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, Sequence Alignment, Viral Proteins