Identification of a replication-competent pathogenic human immunodeficiency virus type 1 with a duplication in the TCF-1α region but lacking NF-κB binding sites

Multiple human immunodeficiency virus type 1 (HIV-1) sequences with deletions of NF-κB binding sites at both the 5' and 3' long terminal repeats (LTRs) were identified in serial samples collected from an infected individual. The effect of this deletion on the level of transcription was studied by transient transfection of an LTR-driven luciferase reporter gene and by infection with a full-length recombinant HIV-1 containing a luciferase reporter (HIV(HXBlue)). Detectable levels of gene expression were found in both systems, in the presence or absence of the viral transactivator Tat. Interestingly, a duplication of a putative TCF-1α motif was found in place of the NF-κB elements in these viruses. Higher transcriptional activity was observed with HXBLTR (NF-κB intact) than with the patient's LTR (NF-κB deleted), suggesting that the NF-κB binding sites may promote optimal levels of viral gene transcription. The ability of these viruses with NF-κB deleted to replicate and cause substantial decline in CD4 cell counts demonstrates that the NF-κB binding sites are not absolutely required for vital replication or pathogenicity in vivo. These results are consistent with the notion that the HIV-1 LTR possesses functional redundancy which allows it to interact with multiple transcription factors, thereby ensuring viral replication in a variety of cell types.