Full-Length Genome Analysis of HIV-1 Subtype C Utilizing CXCR4 and Intersubtype Recombinants Isolated in South Africa

Abstract

The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use CCR5 as a coreceptor for infection. We describe full-length genome sequences of two CXCR4-utilizing HIV-1 subtype C viruses and two intersubtype recombinants from South Africa. Three of the viruses (99ZACM4, 99ZACM9, and 99ZASW7) were isolated in 1999 from AIDS patients in Johannesburg, and a fourth virus (98ZADu178) was isolated in Durban in 1998 from an asymptomatic female sex worker. Isolates 99ZASW7 and 99ZACM9 from Johannesburg were subtype C throughout the genome, 99ZASW7 used the CXCR4 coreceptor, and 99ZACM9 used both CCR5 and CXCR4. Isolate 98ZADu178 from Durban was a novel recombinant between subsubtype A2 and subtype C. The third isolate from Johannesburg, 99ZACM4, was a complex, novel recombinant with multiple breakpoints and contained segments of subtypes A, C, D, G, and K. These results establish the presence of intersubtype recombinants in South Africa, indicating that ongoing surveillance for other subtypes and recombinants is necessary.

Phylogenetic Characterization of Six Full-Length HIV-1 Subtype C Molecular Clones from Three Patients: Identification of Rare Subtype C Strains Containing Two NF-κB Motifs in the Long Terminal Repeat

“…2A), a molecular feature uncommon for subtype C with a small number of such variants reported previously. 11 Importantly, as was observed previously, the C-jB motif (5¢ GGGGCG TTCC 3¢), which is unique for subtype C, was retained in these two clones suggesting its critical function in subtype C.…”

The CCR5 and CXCR4 Coreceptors Are Both Used by Human Immunodeficiency Virus Type 1 Primary Isolates from Subtype C

“…Thirteen isolates were also subtyped in gag by HMA and shown to belong to subtype C (data not shown), suggesting that these isolates were unlikely to be intersubtype recombinants, although this cannot be ex- cluded. Two viruses, CM9 and SW7, have been confirmed as being subtype C throughout its genome (37). Coreceptor usage of HIV-1 subtype C isolates in transfected cell lines.…”

Laboratory Evaluation of the Liat HIV Quant (IQuum) Whole-Blood and Plasma HIV-1 Viral Load Assays for Point-of-Care Testing in South Africa

“…Overall, the Liat HIV Quant whole-blood and plasma assays show good precision and accuracy compared to existing technologies, such as the Roche CAP/CTMv2 and Abbott RealTime HIV-1. This was evident on the frozen plasma verification panel and fresh clinical specimens and also shows that the Liat HIV Quant whole-blood and plasma assays are well suited to HIV subtype C specimens representative of the South African HIV-infected population (although no sequencing was performed) (26). Overall, the agreement of the Liat HIV Quant assays are aligned more with that of Roche CAP/CTMv2 than that of Abbott RealTime HIV-1.…”