Article Figures & Data
Figures
- FIG. 1.
Sequence logo diagram (http://weblogo.berkeley.edu ) showing amino acids 227 through 340 of the HCV NS5B protein from 26 genotype 1a consensus sequences. Numbers shown below the sequence represent the amino acid position in the complete HCV polyprotein. For polymorphic sites (i.e., those with more than one letter shown per position), the height of each letter represents the relative proportion of each amino acid at that position.
Tables
- TABLE 1.
Codons under positive or negative selection pressure among 29 HCV-seropositive women with genotype 1 based on the FEL and REL methods
Patient no. Codon no. based on FEL witha: Codon no. based on REL witha: Positive selection Negative selection Positive selection Negative selection 62 None None None 2785, 2788 90 None None None None 106 None None None None 116 None 2771 None None 119 None None None None 124 None None None None 135 None 2733 , 2769 None 2718, 2722, 2733, 2737, 2764, 2769 , 2790, 2792, 2813, 2817 149 None None None None 184 None None None None 186 None None None None 199 None None None None 211 None 2761 None 2719, 2743, 2750, 2754, 2761, 2769 , 2776, 2781, 2786, 2795, 2798, 2810, 2815 217 None None None None 220 None None 2818 None 230 None 2715 None None 249 None None None None 269 None None 2807 None 282 None None None None 285 None 2747 None 2742, 2747 , 2780 , 2784 287 None None None None 304 None 2717, 2738 None None 340 None 2809 None None 383 None None None 2708, 2817 , 2818 389 None None None None 392 None None None 2712, 2715, 2766, 2797, 2800 , 2804, 2805, 2811, 2816 394 None 2733 None None 504 None 2728, 2747 , 2761, 2769 None 2728, 2747 , 2756, 2769 , 2775, 2780 , 2800 514 None None None None 520 None None None None ↵ a Codons under positive or negative selection pressure among 29 HCV-seropositive women with genotype 1. Shown are codons with a significance of P ≤0.05 (FEL method) or posterior probability of ≥0.99 (REL method). Codons detected in more than one individual are underlined.
- TABLE 2.
Correlation of NS5B intrapatient diversity with clinical variables among 29 HCV-infected women
Comparison Spearman correlation coefficient P valuea NS5B genetic distance vs HCV RNA 0.286 NS NS5B entropy vs HCV RNA 0.163 NS NS5B dN − dS vs HCV RNA −0.492 0.007 NS5B genetic distance vs CD4 cell count −0.033 NS NS5B entropy vs CD4 cell count 0.186 NS NS5B dN − dS vs CD4 cell count 0.387 0.056 NS5B genetic distance vs ALT −0.222 NS NS5B entropy vs ALT −0.002 NS NS5B dN − dS vs ALT 0.199 NS NS5B genetic distance vs AST −0.178 NS NS5B entropy vs AST −0.144 NS NS5B dN − dS vs AST 0.165 NS NS5B genetic distance vs HIV viral load 0.122 NS NS5B entropy vs HIV viral load −0.079 NS NS5B dN − dS vs HIV viral load −0.142 NS ↵ a P values of <0.10 are shown. NS, not significant.
