Primers used for GS Junior ultradeep sequencing of RT.

<p>Primers used for GS Junior ultradeep sequencing of RT.</p

Comparison of Sanger and UDPS sequencing results for RT codons 65 and 70; same isolates as in Table 3.

<p>Sanger Y: presence of mutation; N: absence of mutation. UDPS: Frequency of mutations observed in samples.</p

RT bulk sequences of 27 subtype C HIV-1 isolates failing on first line.

<p>DRMs are noted according to ANRS.</p

Primers used for Gag, Nef and Pol amplification.

<p>Primers used for Gag, Nef and Pol amplification.</p

Phylogenetic trees of UDPS sequences (Pol RT2) at baseline and at ART success.

<p>Patients D, B and F according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069029#pone-0069029-t001" target="_blank">Table 1</a>.</p

Potential CTL reactivity against viral (RNA) and/or archived proviral DNA epitopes according to HLA I alleles.

<p>After characterization of HLA alleles, we investigated the CTL epitopes that should be recognized by the patients and have determined the affinity through the MHC IC 50 values. The reference epitopes are from the HXB2 reference. Whether identical or variant, the epitopes were noted in the circulating virus at baseline (RNA) and/or the archived proviral DNA at therapeutic success.</p

Potential CTL reactivity against archived viral epitopes according to HLA I alleles: cross-reactivity to Lipo 5 peptides.

<p>Lipo 5 peptides are located in the viral genome and were designed from the HXB2 reference; according to the HLA alleles, we investigated the predicted reactivity against the corresponding epitopes or variants of these epitopes in archived proviral DNA. The MHC IC 50 values provide an estimation of the cross-reactivity between the epitope and the variant. For example, patient G with allele HLA-A*03:01 has archived a variant epitope that is poorly recognized. It is highly doubtful that the corresponding lipopeptide Gag 17–35 HXB2 vaccine lipopeptide will be useful for cross-stimulation.</p

List of drug resistance mutations (DRM) detected at baseline (BL) and virological failure (VF) by Sanger sequencing (SS) and UDS for patients failing a PI-based regimen (n = 15).

<p><i>Italic</i>: mutations only detected by UDS/Normal: mutations detected by both UDS and SS</p><p><b>Bold</b>: Major protease mutations</p><p><u>Underlined</u>: mutations associated to prescribed treatment</p><p>GSS, Genotypic Sensitivity Score; ART, antiretroviral treatment; ZDV, zidovudine; DDI, didanosine; D4T, stavudine; 3TC, lamivudine; FTC: Emtricitabine; ABC, abacavir; TDF, tenofovir; NFV, nelfinavir; LPV/r, boosted lopinavir; ATZ/r, boosted atazanavir, FPV/r, boosted fosamprenavir</p

Patient ACT 95387.

<p>Patient ACT 95387.</p

Primers used for amplicon generation.

<p>Note that forward and reverse primers are linked to primer A and B (454 Life Sciences; Roche) respectively and contain the TCAG key. To distinguish each sample in the multiplexed UDPS, nine unique sequence tags (MID1 to 9, according Roche's protocol) were inserted between the adaptor A or B and the gene specific primer.</p>1<p>RT1: primers under patent process</p>2<p>Primers from Mitzuya's paper <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086771#pone.0086771-Mitsuya1" target="_blank">[29]</a></p