HIV type 1 V3 domain serotyping and genotyping in Gauteng, Mpumalanga, KwaZulu-Natal, and Western Cape Provinces of South Africa

More than 20.8 million people are living with HIV/AIDS in sub-Saharan Afric a, with southern Africa the worst affected area and accounting for one of t he fastest growing AIDS epidemics worldwide. Samples from 81 patients, incl uding 25 from KwaZulu-Natal, 26 from Gauteng, 5 from Mpumalanga, and 25 fro m Western Cape Province, were serotyped using a competitive V3 peptide enzy me immunoassay (cPEIA), Viral RNA was also isolated from serum and the V3 r egion amplified by reverse transcriptase polymerase chain reaction (RT-PCR) to obtain a 240-bp product for direct sequencing of 29 samples. CLUSTAL W was used to make multiple sequence alignments. Distance calculation, tree c onstruction methods, and bootstrap analysis were done using TREECON, Subtyp e C-like V3 loop sequences predominate in ail provinces tested in South Afr ica. Discordant sero- and genotype results were observed in one patient onl y. The correlation between sero- and genotyping was 96% (24 of 25) in KwaZu lu-Natal and 100% in Gauteng and Mpumalanga. In Western Cape Province 18% o f patients were identified as sero/genotype B and 82% as sero/genotype C. O ur data show that results of the second-generation V3 cPEIA correlated well with V3 sequencing and would be a rapid and affordable screening test to m onitor the explosive southern African HIV-1 epidemic.