Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms

Abstract

The critical role of the regulatory elements at the 5′ end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13-17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strainspecific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5ʹ UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5′ end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA-protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection. Human immunodeficiency virus type 1 (HIV-1) is characterized by extensive genetic diversity. HIV-1 group M, which accounts for the majority of infections worldwide, has been subdivided into at least nine genetically distinct subtypes (A-D, F-H, J, and K), a few sub-subtypes (A1-A3, F1, F2), and numerous circulating and unique recombinant forms (CRFs and URFs respectively). HIV-1 diversity is featured by high mutagenesis rates and recombination events occurring during the life cycle of the virus. Nucleotide changes generated from these mechanisms affect the entire viral genome, including its highly structured 5′ end region. Indeed, the HIV-1 genome variability was found to be as much as 23% in the 5′LTR-U3 region, about 10% in the gag/pol genes, and more than 30% in the env gene, with overall differences observed primarily between intra and inter-subtype 1,2. Previous studies have revealed that strain differences may influence transmission, replication, and virulence of HIV-1. It was reported that CRF01_AE has a higher rate of sexual transmission than subtype B 3 , while this rate was higher in subtype A compared to D 4. Subtype A was also shown to have a lower replication rate than subtype C 5 , and a lower rate of disease progression than its related CRFs and subtype D 4. Association of these

Infectious RNA: Human Immunodeficiency Virus (HIV) Biology, Therapeutic Intervention, and the Quest for a Vaccine

“…The U5 element is followed by the primer binding site (PBS), the dimerization initiation signal (DIS), and the major splice-donor site (D1), all not shown in Figure 1. The packaging signal Psi (ψ) mediates the packaging of the viral gRNA [19]. The consecutive gag gene encodes the structural viral core proteins.…”

HIV UTR, LTR, and Epigenetic Immunity

“…The 3D structure, but not the RNA sequence, is conserved across the distinct HIV-1 subtypes such as in C, B and A [ 28 ]. The tertiary motif is correlated to the region in 5′LTR after a reverse transcription for the formation subtypes of HIV [ 28 , 29 , 30 ].…”

“…The HIV enhancer, located in the HIV LTR, has played an indispensable role in determining the viral tropism. In other words, the HIV enhancer has dictated a range of cell types to host the viral RNA expression, therefore the viral tropism and the subtype formation [ 29 , 30 , 45 , 46 , 47 , 48 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ].…”

“…Similar to its cellular counterpart, HIV enhancer is a driver for the cell and tissue specific expressions of HIV RNA, and, therefore, controls the HIV tropism [ 29 , 30 , 45 , 46 , 47 , 48 , 55 , 76 ]. This underlines a molecular mechanism that adds onto the viral tropism, which used to refer an expression of cell surface co-receptors for the entry of R5 or X4 viruses.…”

“…Lastly, the expression and function of ncRNA have been known to be the cell and tissue specific [ 87 , 88 , 89 ]. Taken together, studies have shown that the HIV 3′UTR, its ncRNA, and the cellular ncRNA not only play roles in formation the so-called T tropic, M tropic, R5, X4, and the founder virus or quasispecies of HIV, but also on the host immunity against these HIV strains [ 29 , 30 , 45 , 46 ].…”