Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains

<div><p>Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a TATAA motif in U3 promoter region from the majority of HIV-1 strains and a TAAAA motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.</p></div

Variability in the R region of diverse HIV-1 subtypes and CRFs.

<p>N = any base; W = A or T; R = A or G; Y = C or T; K = G or T; M = A or C; S = G or C; D = A, G or T; H = A, C or T; B = C, G or T.</p

Variability in the U3 enhancer and promoter region of diverse HIV-1 subtypes and CRFs.

<p>N = any base; W = A or T; R = A or G; Y = C or T; K = G or T; M = A or C; S = G or C; D = A, G or T; H = A, C or T; B = C, G or T.</p

Specimens description and LTR subtype assignment.

<p>Specimens description and LTR subtype assignment.</p

Primers used for amplification of the 5’end of the HIV-1 genome.

<p>Primers used for amplification of the 5’end of the HIV-1 genome.</p

Variability in the U3 modulatory region of diverse HIV-1 subtypes and CRFs.

<p>N = any base; W = A or T; R = A or G; Y = C or T; K = G or T; M = A or C; S = G or C; D = A, G or T; H = A, C or T; B = C, G or T.</p

Operating characteristics of Point of Care (POC) technologies for CD4+ T-cell enumeration.

<p>Operating characteristics of Point of Care (POC) technologies for CD4+ T-cell enumeration.</p

Methodological quality of included studies.

<p>EQA: external quality assurance, IQC: internal quality control.</p

Operating characteristics of dedicated single platform CD4+ T-cell enumeration systems.

<p>PCA = personal cell analysis, SSC = side scatter.</p><p>Operating characteristics of dedicated single platform CD4+ T-cell enumeration systems.</p

Intra- and inter-assay variation (% CV) for the Apogee Auto 40 and for the MBio SnapCount at thresholds <350 cells/mL and >350 cells/mL.

<p>Intra- and inter-assay variation (% CV) for the Apogee Auto 40 and for the MBio SnapCount at thresholds <350 cells/mL and >350 cells/mL.</p