Shannon Entropy across the HIV-1 clade B proteome.

<p>All full length clade B protein sequences in the LANL HIV Sequence Database were aligned and assessed for Shannon entropy of each amino acid position. The red bars indicate entropy at each codon, and the heavy black lines plot mean entropy for the nine amino acids starting at each position. The shaded regions indicate relatively conserved regions that were examined further. Note that the numbering of the conserved regions (based on HXB2 position) does not necessarily match amino acid positions in the graphs (due to insertions in some sequences relative to HXB2).</p

Recognition of conserved regions by CTL responses in persons with chronic HIV-1 infection.

<p>A panel of 54 persons (from the Los Angeles area) with chronic HIV-1 infection and not receiving antiretroviral treatment was screened for HIV-1-specific CTL responses by IFN-γ ELISpot assays using overlapping peptides spanning each protein. Gag-specific responses were screened using peptides based on clade B consensus and strain DU422 sequences. Env-specific responses were screened using peptides based on clade B consensus or strain MN sequences. Nef-specific responses were screened using peptides based on clade B consensus sequence. The presence or absence of detectable viremia is indicated in the second column; these individuals were biased towards slow progressors due to recruitment selection for being untreated. Recognized peptides that fall entirely within each conserved region are indicated by NIH AIDS Reagent Repository catalog number. The minimal number of epitopes recognized by each person is listed in the last column (assuming that consecutive overlapping peptides contain a single epitope).</p

Shannon entropy in the conserved region cNef.

<p>For HIV-1 Nef amino acids 106–148, Shannon entropies of individual codons (red bars) and average entropies of stretches of 9 codons (black lines) are plotted for clades A1–D. The shaded columns indicate positions where the consensus sequences differ between clades. For each of those positions, the consensus amino acid and most common variant (in parentheses) are indicated.</p

Known and potential epitopes in the conserved regions.

<p>For each region, HLA types for which there are reported and predicted epitopes in the Los Alamos HIV Immunology Database (<a href="http://www.hiv.lanl.gov/content/sequence/ELF/epitope_analyzer.html" target="_blank">http://www.hiv.lanl.gov/content/sequence/ELF/epitope_analyzer.html</a>) are listed. Types in bold font are those in the database that have been reviewed as best defined optimal epitopes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007388#pone.0007388-Frahm1" target="_blank">[42]</a>.</p

Varying consensus sequences and common polymorphisms in cNef.

<p>At each position in cNef (Nef 106–148) where consensus amino acids differ between clades, the frequency of the consensus amino acid and the most common polymorphism(s) within each clade are listed (based on all available whole protein sequences in the LANL HIV Sequence Database).</p

Shannon entropy in the conserved region cEnv.

<p>For HIV-1 Env amino acids 521–606, Shannon entropies of individual codons (red bars) and average entropies of stretches of 9 codons (black lines) are plotted for clades A1–D. The shaded columns indicate positions where the consensus sequences differ between clades. For each of those positions, the consensus amino acid and most common variant (in parentheses) are indicated.</p

Varying consensus sequences and common polymorphisms in cGag-2.

<p>At each position in cGag-2 (Gag 250–335) where consensus amino acids differ between clades, the frequency of the consensus amino acid and the most common polymorphism(s) within each clade are listed (based on all available whole protein sequences in the LANL HIV Sequence Database).</p

Varying consensus sequences and common polymorphisms in cGag-1.

<p>At each position in cGag-1 (Gag 148–214) where consensus amino acids differ between clades, the frequency of the consensus amino acid and the most common polymorphism(s) within each clade are listed (based on all available whole protein sequences in the LANL HIV Sequence Database).</p

Shannon entropy in the conserved region cGag-2.

<p>For HIV-1 Gag amino acids 250–335, Shannon entropies of individual codons (red bars) and average entropies of stretches of 9 codons (black lines) are plotted for clades A1–D. The shaded columns indicate positions where the consensus sequences differ between clades. For each of those positions, the consensus amino acid and most common variant (in parentheses) are indicated.</p

Shannon entropy in the conserved region cGag-1.

<p>For HIV-1 Gag amino acids 148–214, Shannon entropies of individual codons (red bars) and average entropies of stretches of 9 codons (black lines) are plotted for clades A1–D. The shaded columns indicate positions where the consensus sequences differ between clades. For each of those positions, the consensus amino acid and most common variant (in parentheses) are indicated.</p