Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa☆

Identification and Genetic Characterization of Unique HIV-1 A1/C Recombinant Strain in South Africa

“…5). Comparison with other isolates reported to have an HIV-1 subtype A/C backbone from South Africa 16,18,19 revealed that the study isolate was a unique virus. Nonetheless, all the South African A/C isolates revealed a common recombination with HIV-1 subtype C within the vpu gene (Fig.…”

“…Since then, there has been continued identification of non-subtype C strains mainly in studies on HIV drug resistance. 8,[16][17][18] Monitoring the genetic diversity of circulating HIV strains has been encouraged to generate information on patient management and even vaccine strategies. 3 Recently, Palm et al 11 demonstrated increased risk of AIDS and AIDS-related death in individuals infected with recombinant strain HIV-1 A3/CRF02_AG.…”

“…Previously reported HIV-1 stains with subtypes A and C backbone were downloaded from GenBank and their genome constellations were compared to the isolate in this study. The downloaded sequences were from isolates 98ZADU178, 19 TV239, 16 and 8519. 18 Initial phylogenetic assessment of partial pol (PR-RT) gene sequences isolated from patients at DGMAH indicated the patient sample (isolate j51) as HIV-1 subtype A (Fig.…”

“…To date, isolation of HIV-1 recombinant and or non-subtype C strains has mainly been reported in cosmopolitan urban cities. 8,16 In investigating the importance of HIV-1 subtype differences in drug resistance, Lessells et al 10 concluded that although there is no compelling evidence that the HIV-1 subtype needs to be considered in choosing ART regimens for first-line or second-line therapy, subtype differences may play a role in assessing the response to treatment and surveillance for the transmission of resistance.…”

“…2,4,5,18 However, there have been rare reports of pure HIV-1 non-C and recombinant strains. 8,[16][17][18] In drug resistance analysis of the sequences in an HIV genetic diversity study, the isolate from patient j51 was reported to have no drug resistance-associated mutations, but was classified as HIV-1 subtype A1 on both the PR and RT regions. The recombination event was estimated to have occurred around sequence position 6035 -15 bp with reference to the beginning of the HIV HBX2 strain (Fig.…”