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. Author manuscript; available in PMC: 2010 Aug 11.
Published in final edited form as: Virus Res. 2007 Jun 29;130(1-2):285–291. doi: 10.1016/j.virusres.2007.05.016

Table 3.

Mean genetic estimates of HCV quasispecies in the HVR-1 and NS3 regions. The number clones sequenced for each HCV region is indicated before the estimates. dN/dS ratios suggestive of positive immune pressure are bolded. (1) All HIV(+) vs. HIV(−); Mann-Whitney U test. (2) Comparison between HIV(+) CD4<200, HIV(+)>200, and HIV(−); Kruskal-Wallis test.

Patient Group
HIV(+)
Sample CD4<200 (cells/mm3) CD4>200 (cells/mm3) All HIV(+) HIV(−) P value
HVR-1 (1) (2)
 No. clones T0 5.67 0.88 5.67 1.45 5.67 0.76 9.00 5.00 1.000 0.989
T1 5.33 0.67 8.00 3.51 6.67 1.71 9.67 4.18 0.381 0.431
  Sn T0 0.5830 0.6220 0.6026 0.8330 0.548 0.304
T1 0.1680 0.4461 0.3067 0.8230 0.95 0.126
ΔSn (btw.) −0.4160 −0.1760 −0.2959 −0.0090 0.714 0.733
  d (nt) T0 0.1225 0.0263 0.0744 0.0067 0.167 0.288
T1 0.1332 0.0493 0.0912 0.0812 0.548 0.739
Between 0.0180 0.0130 0.0152 0.1482 0.381 0.491
  d (aa) T0 0.2019 0.0676 0.1347 0.0068 0.381 0.651
T1 0.2646 0.0881 0.1764 0.1972 0.262 0.413
Between 0.2461 0.0365 0.1407 0.3024 0.714 0.587
  dN/dS T0 0.5702 1.4373 0.9170 1.2584 0.857 0.915
T1 0.8493 0.7904 0.8297 1.9837 0.200 0.304
Between −5.6136 3.1432 −1.2350 2.3371 1.00 0.213
NS3
 No. clones T0 10.67 0.33 11.00 0.58 10.83 0.31 10.00 0.58 0.216 0.99
T1 11.67 0.88 10.67 0.33 11.17 0.48 16.00 3.46 0.291 0.476
  Sn T0 0.5200 0.8420 0.6812 0.6000 0.905 0.179
T1 0.5760 0.5590 0.5675 0.6400 0.548 0.714
ΔSn (btw.) 0.0560 −0.2830 −0.1138 0.0410 0.348 0.061
  d-nt T0 0.0044 0.0147 0.0096 0.0133 0.381 0.193
T1 0.0051 0.0147 0.0096 0.0091 0.262 0.066
Between 0.0034 0.0063 0.0048 0.0040 0.714 0.488
  d-aa T0 0.0041 0.0107 0.0074 0.0097 0.381 0.193
T1 0.0057 0.0114 0.0086 0.0089 0.905 0.252
Between 0 0.00065 0.0032 0.0021 0.714 0.039
  dN/dS T0 0.2949 0.1972 0.2461 0.1623 0.905 0.957
T1 0.2832 0.4144 0.3488 0.2254 0.381 0.561
Between 0.0911 0.3401 0.2156 0.3855 0.548 0.298

NOTE: Change in HCV sequence complexity (ΔSn) was calculated as ΔSn = Sn(T1)−Sn(T0). Genetic distances and substitution frequencies were determined both in every given sample (within-sample) and between samples of the same patient at the two different time points (net distance between samples, defined as the net change in intrasubject distances between baseline and follow-up groups of HCV clones dA=(dXY−(dX−dY)/2), were dXY is the average distance between groups of clones from baseline (X) and follow-up samples (Y), and dX and dY are the mean within-group distances).