title: Identification and genetic characterization of unique HIV-1 A1/C recombinant strain in South Africa.
abstract: HIV isolates from South Africa are predominantly subtype C. Sporadic isolation of non-C strains has been reported mainly in cosmopolitan cities. HIV isolate j51 was recovered from a rural South African heterosexual female aged 51 years. Near full length amplification of the genome was attempted using PCR with primers targeting overlapping segments of the HIV genome. Analysis of 5593 bp (gag to vpu) at a bootstrap value greater than 70% found that all but the vpu gene was HIV-1 subtype A1. The vpu gene was assigned HIV-1 subtype C. The recombination breaking point was estimated at position 6035+/- 15 bp with reference to the beginning of the HXB2 reference strain. Isolate j51 revealed a unique genome constellation to previously reported recombinant strains with parental A/C backbones from South Africa though a common recombination with subtype C within the vpu gene. Identification of recombinant strains supports continued surveillance of HIV genetic diversity.
authors.affiliation: HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo (Medunsa Campus) and National Health Laboratory Service , Pretoria, South Africa .
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Musyoki
authors.forename: Johnny N
authors.initials: JN
authors.lastname: Rakgole
authors.forename: Gloria
authors.initials: G
authors.lastname: Selabe
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Mphahlele
mesh_terms: D016000:Cluster Analysis; D005260:Female; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013019:South Africa