The Long Terminal Repeat Sequence of Subtype C and CRF01_AE Recombinants in China

HIV-1 provirus is flanked by one long terminal repeat (LTR) at each terminal. The 5 & PRIME; LTR plays important roles in HIV-1 life cycle, especially, it determines HIV-1 transcription. However, there are 810 5 & PRIME; LTR entries exist in the HIV-1 sequence database, accounting for only 0.085% (810/949,484). In this study, we collected plasma samples from HIV-1-infected patients in Shenzhen province and got 219 5 & PRIME; LTR sequences. In addition, we found recombination in the LTR region. The recombinants (LS13145, LS11614, LS14862, and LS14863) possess an insertion of CRF01_AE segment at HXB2 482-630 bp (149 bp) in the skeleton of 5 & PRIME; LTR of subtype C. At the same time, our study found that the occurrence of recombination caused changes in many transcription factor binding sites. As the increasing investigation on 5 & PRIME; LTRs diversity and characterization, we will get a deeper understanding of HIV-1 transmission, evolution, and the basic mechanism of transcriptional regulation.