The Long terminal repeat (LTR) sequence of Subtype C and CRF01_AE recombinants in China.

HIV-1 provirus is flanked by one LTR at each terminal. The 5' LTR plays important roles in HIV-1 life cycle, especially, it determines HIV-1 transcription. However, there are 810 5' LTR entries exist in the HIV-1 sequence database, accounting for only 0.085% (810/949484). Here, we collected plasma samples from HIV-1-infected patients in Shenzhen province and got 219 5' LTR sequences. In addition, we found recombination in the LTR region. The recombinant (LS13145, LS11614, LS14862, LS14863) possess an insertion of CRF01_AE segment at HXB2 482-630bp (149bp) in the skeleton of 5' LTR of subtype C. At the same time, our study found that the occurrence of recombination caused changes in many TFBSs. As the increasing investigation on 5' LTRs diversity and characterization, we will get a deeper understanding of HIV-1 transmission, evolution, and the basic mechanism of transcriptional regulation.