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LTR GENETIC DIVERSITY AMONG HIV-2 ARV-NAÏVE PATIENTS IN THE ANRS CO5 HIV-2 COHORT
Quentin Le Hingrat1, Benoit Visseaux1, Mélanie Bertine1, Fideline Collin2, Florence Damond1, Olivier Schwartz3, Sophie Matheron1, Diane Descamps1, Charlotte Charpentier1
1Bichat Hosp, Paris, France,2INSERM, Bordeaux, France,3Inst Pasteur, Paris, France
Long terminal repeat regions (LTR) include binding sites of transcription factors (TF) and are essential to HIV DNA transcription. The aim of this study was to assess associations between HIV-2 LTR genetic diversity and reservoir size.
All plasma samples of HIV-2 ARV-naïve patients included in the French ANRS HIV-2 Cohort collected with PBMC during the year 2015 were assessed. LTR sequencing was performed using Sanger technology. HIV-2 total DNA quantification was performed using a real-time PCR assay with a limit of quantification (LOQ) of 6 c/PCR. The LTR transcriptional activity was assessed using a luciferase assay on HEK293T cells transfected by LTR-luciferase plasmids.
Among the 99 samples tested, LTR sequencing was successful in 65 (66%) including 27 HIV-2 group A and 38 group B, among them 8 had plasma viral load >40 c/mL. Demographic and immuno-virological characteristics were similar between group A and group B-infected patients. HIV-2 DNA was above the LOQ in 24 patients (37%) with a median of 2.04 log10c/106PBMC and was detectable below the LOQ in 39 patients (60%). The proportion of patients with a reservoir above the LOQ was significantly higher in group A than in group B (67% and 16%, respectively; p <0.001). Genetic distances showed the highest variability in the U3 region of the LTR. Variability was significantly higher in group B than in group A sequences (p<0.001). No specific LTR mutation could be associated with the size of reservoir. However, 4 group B sequences (11%) showed a deletion in the first binding site of Sp1 TF. Interestingly, transcriptional activity of this Sp1-deleted LTR is 2-fold less than that of the group A or B references. Binding sites of the following TF: PuB2, peri-κb and NFκB were conserved among group A and group B sequences. On the contrary, the region between the PuB1 and pets TF described in group A sequences was not observed in group B sequences. Furthermore, bioinformatics analysis identified two new potential binding sites of TF: IRF in group A sequences and C/EBP in group B sequences.
In this first large analysis on HIV-2 LTR sequences we observed a high genetic variability in the U3 region of the LTR in which is located TF binding sites. The highest genetic variability and also the lack of some TF binding sites observed in group B sequences might be an explanation to the lowest proportion of patients with a reservoir above the LOQ observed in this group.