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

Primers used for Gag, Nef and Pol amplification.

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

Patient ACT 95387.

<p>Patient ACT 95387.</p

Patient HTM 399.

<p>Patient HTM 399.</p

Patients' characteristics.

<p>Legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100452#pone-0100452-t002" target="_blank">Table 2</a> to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100452#pone-0100452-t007" target="_blank">7B</a>: The CTL epitopes that should be recognized according to the HLA alleles are defined using the HXB2 reference. The observed corresponding epitopes in the different samples are described either for RNA or DNA. The dates are the dates of sampling.</p><p>« Id » indicates that the epitope observed is identical to the HxB2 reference. The numbers in parenthesis are the theorical MHC IC₅₀ (nM) according to simulation of affinity between the epitopes and the HLA alleles. The numbers in parenthesis and italic represent percentages of RT variants determined by UDPS.</p

Patient GOL041.

<p>Patient GOL041.</p

Patient ACT 87524.

<p>Patient ACT 87524.</p