AEGiS-13IAC: Frequent inter-subtype recombination detected in complete HIV-1 RNA sequences from highly exposed Kenyan women.

13th International AIDS Conference

Durban, South Africa - July 9-July 14, 2000

Frequent inter-subtype recombination detected in complete HIV-1 RNA sequences from highly exposed Kenyan women.

Int Conf AIDS 2000 Jul 9-14; 13:(abstract no. MoOrA168)

Burger H, Weiser B, Plummer F, Fang G, Rowland-Jones S, Chen C-H, Anzala A, Bwayo J, Oyugi J
H. Burger, Wadsworth Center, Wadsworth Center, New York State Dept. of Health, 120 New Scotland Avenue, Albany, NY 12208, United States, Tel.: +1518-486-4323, Fax: +1518-473-4110, E-mail: burger@wadsworth.org

BACKGROUND: In sub-Saharan Africa, where the HIV-1 epidemic has had a major impact, several HIV-1 clades often co-exist within communities. To design vaccines and understand pathogenesis, it is necessary to address viral diversity, evolution, and recombination in vivo, as well as to map the full range of immunologic determinants encoded by the complete viral genome of replicating viruses.

METHODS: Because HIV-1 RNA in plasma represents replicating virus, we obtained full-length HIV-1 RNA genomic sequences from plasma. To focus on a cohort with an increased chance of harboring inter-subtype recombinants, we chose 10 women from the Nairobi, Kenya female sex worker cohort who are long-term survivors, having been infected at least 10 years. After isolating viral RNA from plasma, full-length cDNAs were synthesized by reverse transcription and amplified by long PCR. Complete HIV-1 sequences were obtained and clade genotypes determined using computational analysis and the retroviruses genotyping program (National Center for Biotechnology Information, NIH) for the entire viral genome.

RESULTS: The distribution of subtypes in this group was: 5 (50%) completely subtype A, 1 (10%) subtype D, and 4 of the 10 sequences analyzed (40%) were inter-subtype recombinants including 2 A/C, 1 A/D, and 1 D/C. Comparison of the detection of subtypes and recombinants by using full-length sequencing with that obtained by RFLP and HMA showed that RFLP and HMA did not yield as complete a picture of subtypes present as did sequencing.

CONCLUSIONS: Determination of complete viral RNA sequences reveals a high degree of clade diversity and recombination that may be missed by sub-typing methods that focus on fragments of the genome. In addition, full-length viral RNA sequencing makes it possible to study the wide range of virus-encoded epitopes, facilitating analysis of virus-host interactions.

Keywords: AEGIS, HIV-1, Base Sequence, Recombination, Genetic, Genome, Viral, RNA, Viral, HIV-1 Reverse Transcriptase, Polymerase Chain Reaction, Disease Outbreaks, Kenya, Africa South of the Sahara, Greece, Human, Female, genetics
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