AEGiS-14IAC: Equivalent detection of HIV-1 subtypes and recombinants in the Rakai district of Uganda by full length sequencing and by a multi-region hybridization assay (MHA).

14th International AIDS Conference

Barcelona, Spain - July 7-12, 2002

Equivalent detection of HIV-1 subtypes and recombinants in the Rakai district of Uganda by full length sequencing and by a multi-region hybridization assay (MHA).

Int Conf AIDS 2002 Jul 7-12; 14:(abstract no. A10029)

Harris M, Wilson G, Kim B, Hoelscher M, Merling R, Serwada D, Sewankambo N, Wabwire F, Phillips J, Meehen M, Lutalo T, Kiwanuka N, Lane J, Gray R, Wawer M, Robb M, Birx D, McCutchan F
Walter Reed Army Institute of Research, Rockville, MD, United States

BACKGROUND: To determine the diversity of HIV-1 in Rakai, Uganda, full length sequencing was conducted because it is the "gold standard" for detection of recombinant HIV-1. A newly developed screening assay, the Multi-region Hybridization Assay (MHAacd) uses real time PCR to detect subtypes A, C, and D, which circulate in East Africa. By screening 5 genome regions, MHAacd can detect recombinant viruses. In this report, results from full length sequencing and the MHAacd are compared.

METHODS: Phylogenetic analysis of near full length HIV-1 sequences was performed on proviral DNA amplified from genomic DNA extracted from one group of seropositive, Rakai volunteers' peripheral blood mononuclear cells. The MHAacd was performed on RNA extracted from the serum of a second group of seropositive, Rakai volunteers. The blood draw periods were the same for both groups.

RESULTS: Forty six near full length sequences were generated. Sequencing data suggested that subtype D represented 54.3%, subtype A 15.2%, and recombinants 30.4% of HIV-1 in Rakai. MHAacd results from viral RNA were not significantly different: 71% subtype D, 5% A, and 23% recombinant. In addition, MHAacd also detected dual infections in several volunteers.

CONCLUSIONS: Subtype D represents the majority of the subtypes in Rakai in both nonrecombinant and recombinant viruses as determined by both methods. Continued surveillance of viruses in the Rakai district can be more rapidly performed by MHAacd than by full genome sequencing in preparation for vaccine trials.

Keywords: AEGIS, HIV-1, Hybridization, Genetic, Uganda, Polymerase Chain Reaction, Africa, genetics

020707
A10029