Development of a latency model based on HIV-1 subtype C to study how long terminal repeat genetic variation impacts viral persistence and latency reversal

Most people living with HIV (PLWH) reside in sub-Saharan Africa. South Africa is the epicentre where 98% of HIV-1 infections are subtype C. However, partially due to unavailability of non-subtype B latency models, most studies of HIV-1 latency and cure have focused on HIV-1 subtype B (HIV-1B) which predominates Europe and USA. Moreover, the effect of inter- and intra-subtype genetic variation of the viral promoter, long terminal repeat (LTR), from PLWH on latency reversal is unknown. We constructed a retroviral vector expressing green fluorescent protein and HIV-1 subtype C (HIV-1C) consensus Tat protein under the control of either HIV-1C consensus or PLWH-derived transmitted/founder (T/F) LTR, produced respective LTR pseudotyped viruses, infected Jurkat E6 and primary CD4+ T cells in vitro, enriched for latently infected cells, and treated these cells with different latency reversing agents. We show that the HIV-1C LTR exhibited lower reactivation compared to HIV-1B. Furthermore, HIV-1C T/F LTR pseudotyped proviral variants with four NF-kB motifs exhibited lower reactivation compared to those with three NF-kB motifs. Our data indicate that inter- and intra-subtype HIV-1 LTR genetic variation in combination with host variation modulates latency reversal.