1887

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 (), /, the first exons of /, and . 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 may occur preferentially during reverse transcription through the strand displacement-assimilation model rather than the copy-choice model.

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2003-10-01
2020-01-20
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Representative analysis of a CRF02 strain of HIV-1 (HDJ264). To investigate the recombination pattern of each sequence, bootscanning plot analysis was performed; all nine pure HIV-1 subtypes (A–D, F–H, J and K) were included. Subtype classification of each region was confirmed by subsequent phylogenetic analysis. To search for any similarity of the unclassified regions with any HIV-1 sequences characterized previously, BLAST searchs were performed using the default settings ( http://www.ncbi.nlm.nih.gov/BLAST/).

Magiorkinis (2003). , , part 10, pp. 2715–2722.

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Graphic representation of the frequency of recombination breakpoints (black) and the extent of sequence similarity (grey) across the HIV-1 genome for a sliding window of 1000 bp if recombination frequency was strongly ruled by evolutionary selection (negative correlation with similarity). A small phase difference might also be observed.

Representative analysis of a CRF02 strain of HIV-1 (HDJ264). To investigate the recombination pattern of each sequence, bootscanning plot analysis was performed; all nine pure HIV-1 subtypes (A–D, F–H, J and K) were included. Subtype classification of each region was confirmed by subsequent phylogenetic analysis. To search for any similarity of the unclassified regions with any HIV-1 sequences characterized previously, BLAST searchs were performed using the default settings ( http://www.ncbi.nlm.nih.gov/BLAST/).

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