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Table 3 Intra- and intersample genetic variability of the HVR1 and outside the HVR1 over time in the two groups of patients

From: Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a

Region Patient Group Samples aIntrasample variability Samples bIntersample variability
    Ks Ka Ka/Ks gd   Ks Ka Ka/Ks gd
  SVR E 0.0195 ± 0.0141 0.0308 ± 0.0130 0.998 0.0283 ± 0.0095      
   B 0.0236 ± 0.0175 0.0225 ± 0.0115* 0.850 † 0.0233 ± 0.0091 B-B 0.0236 ± 0.0175 0.0225 ± 0.0115* 0.850 0.0233 ± 0.0091
   W1 0.0277 ± 0.0152 0.0302 ± 0.0100 1.067 ‡ 0.0302 ± 0.0087 B-W1 0.0293 ± 0.0160 0.0305 ± 0.0110 1.041 0.0305 ± 0.0095
   W2 0.0050 ± 0.0025 0.0375 ± 0.0155 2.700 0.0280 ± 0.0125 B-W2 0.0070 ± 0.0045 0.0370 ± 0.0205 7.300 0.0285 ± 0.0125
   W3/W4 0.0000 ± 0.0000 0.0135 ± 0.0075 NA 0.0095 ± 0.0045 B-W3/4 0.0015 ± 0.0015 0.0150 ± 0.0085 9.333 0.0110 ± 0.0055
HVR1            
  NR E 0.0292 ± 0.0185 0.0585 ± 0.0207 1.860 0.0492 ± 0.0145      
   B 0.0345 ± 0.0192 0.0802 ± 0.0227* 2.427 † 0.0667 ± 0.0185 B-B 0.0345 ± 0.0192 0.0802 ± 0.0227* 2.427 0.0667 ± 0.0185
   W1 0.0172 ± 0.0115 0.0507 ± 0.0175 2.033 ‡ 0.0412 ± 0.0135 B-W1 0.0218 ± 0.0125 0.0538 ± 0.0178 2.332 0.0432 ± 0.0130
   W2/4 0.0205 ± 0.0175 0.0320 ± 0.0135 1.574 0.0290 ± 0.0115 B-W2/4 0.0200 ± 0.0100 0.0325 ± 0.0135 1.648 0.0295 ± 0.0120
   L 0.0160 ± 0.0033 0.008 ± 0.0036 0.285 0.0106 ± 0.0043 B-L 0.0153 ± 0.008 0.0133 ± 0.0057 0.873 0.0137 ± 0.0047
Outside            
  SVR E 0.0106 ± 0.005 0.0023 ± 0.0015 0.216 0.0045 ± 0.0016      
   B 0.0130 ± 0.0061 0.0036 ± 0.0020 0.277 0.0061 ± 0.0023 B-B 0.0130 ± 0.0061 0.0036 ± 0.0020 0.277 0.0061 ± 0.0023
   W1 0.0052 ± 0.0022 0.0017 ± 0.0015 0.327 0.0027 ± 0.0012 B-W1 0.0050 ± 0.0020 0.0018 ± 0.0018 0.360 0.0025 ± 0.0013
   W2 0.0035 ± 0.0025 0.0025 ± 0.0015 0.714 0.0025 ± 0.0020 B-W2 0.0035 ± 0.0025 0.0025 ± 0.0020 0.714 0.0025 ± 0.0020
   W3/W4 0.0015 ± 0.0015 0.0010 ± 0.0010 0.667 0.0010 ± 0.0010 B-W3/4 0.0015 ± 0.0015 0.0010 ± 0.0010 0.667 0.0010 ± 0.0010
  NR E 0.0612 ± 0.0205 0.0042 ± 0.0025 0.068 0.0180 ± 0.0052      
   B 0.0280 ± 0.0115 0.0017 ± 0.0012 0.061 0.0085 ± 0.0032 B-B 0.0280 ± 0.0115 0.0017 ± 0.0012 0.061 0.0085 ± 0.0032
   W1 0.0132 ± 0.0085 0.0005 ± 0.0005 0.038 0.0040 ± 0.0022 B-W1 0.0148 ± 0.0090 0.0008 ± 0.0008 0.054 0.0043 ± 0.0025
   W2/4 0.0100 ± 0.0060 0.0015 ± 0.0010 0.150 0.0047 ± 0.0026 B-W2/4 0.0095 ± 0.0060 0.0015 ± 0.0010 0.158 0.0035 ± 0.0020
   L 0.0133 ± 0.0060 0.0006 ± 0.0006 0.045 0.0030 ± 0.0020 B-L 0.0140 ± 0.0057 0.0010 ± 0.0010 0.071 0.0043 ± 0.0020
  1. a The average number of nucleotide substitutions per nonsynonymous site and per synonymous site for all pairwise comparisons within each sampling point. b The average number of nucleotide substitutions per nonsynonymous site and per synonymous site for all pairwise comparisons for consensus of baseline for baseline sample (B-B) and follow-up samples (B-W1-2-3/4 and B-L). Ka/Ks indicate the ratio of nonsynonymous to synonymous nucleotide substitutions. All data represent mean ± SEM. The statistical significance of comparisons among individual samples or between the two groups of patients were analysed with non parametric Mann-Whitney U test.*, P = 0.05 for comparison between the two groups of patient. †, P = 0.01 for comparison between the two groups of patient. ‡, P = 0.05 for comparison between the two groups of patient.
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