14th International AIDS Conference Barcelona, Spain - July 7-12, 2002

Int Conf AIDS 2002 Jul 7-12; 14:(abstract no. A10032)

Dowling W, Harris ME, Hoelscher M, Murphy D, Elson L, Robb ML, Birx DL, McCutchan FE, Carr JK
Walter Reed Army Institute of Research, Rockville, United States

BACKGROUND: It is currently estimated that 30% of HIV-1 strains circulating in East Africa are unique inter-subtype recombinants combining subtypes A, C, and D in a variety of ways. Crossover points in inter-subtype recombinant strains have typically been mapped by Bootscan and Distance Scan with a sliding window of 300 bases, imposing a practical detection limit for the distance between crossover points. It is not known whether more closely spaced crossover points are present, but undetected, hampering a complete analysis of the frequency of recombination across the genome. It is also possible that some HIV-1 strains characterized as non-recombinant have undetected close-spaced crossovers.

METHODS: A new computer application for the fine mapping of HIV-1 subtype in recombinant strains whose parental subtypes have already been determined has been developed and applied to full-genome sequences of HIV-1 strains from East Africa. The frequency, spacing, and genome location of crossover points between different subtypes has been analyzed.

RESULTS: HIV-1 inter-subtype recombinant strains were commonly found to contain previously undetected, closely spaced crossover points, especially in the envelope gene. Undetected regions of a second subtype were very rare in "pure" subtypes.

CONCLUSIONS: Current methods of analysis provide a clear and accurate distinction between recombinant and non-recombinant strains, but, within recombinant strains, the application of additional analysis approaches, as described here, is required to more fully document their structure. The extreme mosaicism of envelope is of interest, possibly reflecting biological or immunological selection.

020707
A10032

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