Proteasome, TAP and MHC score of CTL epitopes.

<p>Wild type epitope scores are matched with the corresponding divergent epitope score (Prot. score = proteasome score).</p>a<p>Epitopes for which amino acid divergence induces improved MHC binding.</p>b<p>Epitopes for which amino acid divergence decreases MHC binding.</p

Drug resistance mutation (DRM) in RT sequences according to the international list of surveillance drug-resistance mutations (SDRMs) updated in 2009 [26].

<p>NVP = nevirapine, EFV = efavirenz, TDF = tenofovir, 3TC = lamivudine, ETV = etravirine.</p

Percentage of homology between CRF01_AE Vietnamese consensus sequences of RT, Prot and Gag aligned with the consensus CRF01_AE or B strain.

<p>Percentage of homology between CRF01_AE Vietnamese consensus sequences of RT, Prot and Gag aligned with the consensus CRF01_AE or B strain.</p

Comparison of Gag (A) and RT (B) Vietnamese consensus sequences with HxB2 strains.

<p>Optimal CTL epitopes are highlighted by boxes. HLA restriction is indicated on the corresponding epitopes. Amino acid substitutions are indicated in bold. Shaded vertical bars separate blocks of 10 amino acids.</p

Comparisons of proteasome, TAP and MHC scores between wild-type (B sub-type) and divergent epitopes (CRF01_AE sequences).

<p>All scores are logarithmic values, high values corresponding to highly predicted efficiency.</p

HLA allele frequencies in the Vietnamese Mekong Delta population (n = 116) compared to Kinh Vietnamese (dashed bars), Chinese (grey bars) and European (white bars) populations.

<p>The 6 most representative HLA alleles of the Mekong Delta population are represented.</p

Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in low- and middle-income countries of south and southeast Asia.

<p>The <i>x</i>-axes represent the number of years since ARV scale-up for each isolate. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of years since ARV scale-up in generalized linear mixed model regression.</p

Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in Europe (and Israel).

<p>The <i>x</i>-axes represent the calendar year of the sample. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of sample year in generalized linear mixed model regression.</p