AEGiS-12IAC: Full-length sequencing of 4 east African HIV-1 reveals 2 recombinants and a geographic subcluster within subtype A.

12th International AIDS Conference

Geneva, Switzerland - June 28-July 3, 1998

Full-length sequencing of 4 east African HIV-1 reveals 2 recombinants and a geographic subcluster within subtype A.

Int Conf AIDS 1998 Jun 28-Jul 3; 12:19 (abstract no. 11186)

Carr JK, Salminen MO, Albert J, Birx D, McCutchan FE
Henry M. Jackson Foundation, Rockville, MD, USA.

BACKGROUND: The genetic diversity of HIV-1 in Africa has been studied in detail with partial sequencing of the genome. Subtype A, probably the most abundant subtype in Africa, has recombined extensively with other subtypes and is difficult to understand using partial sequencing. It is now more feasible to do full-length genomic sequencing and this was done for four new subtype A genomes from East Africa.

METHODS: Four individuals from East Africa were identified as seropositive in Sweden and their virus expanded using co-cultivation with PHA-stimulated donor PBMCs. Proviral DNA was extracted from infected cells and a 9 kb fragment containing the majority of the genome was amplified and directly sequenced.

RESULTS: All four of the viruses had been classified as subtype A based on sequencing of a small part of the envelope gene, but full-length sequencing revealed two (50%) to be recombinant. One, from Kenya, was an A/D recombinant, with the entire genome subtype A except for one kb of pol, which was subtype D. The second, from Ethiopia, was a complex recombinant between subtype A and subtype C, with multiple breakpoints. The two non-recombinant subtype A viruses were from Somalia and Tanzania. In phylogenetic analysis with reference isolates from all subtypes, the two new viruses form a significant cluster with UG037 from Uganda and Q43 from Kenya and distinct from West African subtype A/G strains.

CONCLUSIONS: Full-length sequencing of four isolates designated as subtype A by partial sequencing revealed two to be recombinant with other subtypes, a higher percentage of recombination than is commonly estimated. New viral sequences from Somalia and Tanzania, which were non-recombinant, join sequences from Kenya and Uganda to form a significant cluster within subtype A. These may represent an East African subtype A.

Keywords: AEGIS, HIV-1, Tanzania, Recombination, Genetic, Variation (Genetics), Kenya, Africa, Uganda, Ethiopia, Somalia, Greece, Sweden, genetics, ICA12
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