Table 2.: Overview of Genotypic and Phenotypic Testing of 38 HIV-1 Infected Patient Samples at Various Viral Loads

Sample Characteristics Clonal Genotypeb Ed Phenotypee
Sample ID VL (log IU/ml) # cp in 7x RT-PCRa # Clones Analyzed R5 X4 Discordantc X4 Measured (%)
1 5.86 126,776 84 0 2 82 2.4 84 R5
2 5.36 40,250 76 0 2 74 2.6 76 R5
3 6.58 665,331 86 0 0 86 0.0 86 R5
4 6.04 192,500 81 54 0 27 0.0 81 R5
5 5.53 59,500 87 86 0 1 0.0 87 R5
6 5.26 31,500 78 78 0 0 0.0 78 R5
7 5.03 18,614 62 11 0 51 0.0 62 R5
8 5.02 18,200 38 37 0 1 0.0 38 R5
9 4.93 14,893 41 11 0 30 0.0 41 R5
10 4.59 6,825 43 20 0 23 0.0 43 R5
11 4.57 6,550 45 45 0 0 0.0 45 R5
12 4.34 3,798 40 38 0 2 0.0 40 R5
13 4.13 2,341 82 81 0 1 0.0 81 R5
14 3.97 1,624 84 3 0 81 0.0 82 R5
15 3.90 1,379 38 38 0 0 0.0 37 R5
16 3.86 1,279 86 0 0 86 0.0 83 R5
17 3.83 1,183 87 0 0 87 0.0 84 R5
18 3.81 1,129 84 0 0 84 0.0 81 R5
19 3.31 361 88 0 0 88 0.0 78 R5
20 3.29 343 44 0 0 44 0.0 41 R5
21 2.71 90 62 0 0 62 0.0 45 R5
22 2.48 53 81 79 0 2 0.0 42 R5
23 2.47 52 47 0 0 47 0.0 31 R5
24 2.14 24 87 0 0 87 0.0 24 R5
25 6.23 297,500 71 2 7 62 9.9 71 D/M
26 6.15 245,000 71 0 5 66 7.0 71 D/M
27 6.11 227,500 76 1 7 68 9.2 76 D/M
28 5.90 140,000 76 0 10 66 13.2 76 D/M
29 5.83 118,315 83 0 12 71 14.5 83 D/M
30 5.82 115,621 85 0 23 62 27.1 85 D/M
31 5.41 44,982 86 0 11 75 12.8 86 D/M
32 5.20 28,000 76 0 3 73 3.9 76 D/M
33 5.18 26,250 84 0 1 83 1.2 84 D/M
34 4.91 14,225 86 0 10 76 11.6 86 D/M
35 4.43 4,710 76 12 64 0 84.2 75 D/M
36 2.92 146 87 30 57 0 65.5 66 D/M
37 2.66 79 23 20 0 3 0.0 20 D/M
38 2.19 27 86 0 84 2 97.7 26 D/M

a Number of viral copies entered in procedure.
b Tropism determination by clonal genotyping. Prediction was performed on the clonal V3 loop sequences using the PSSM and SVM on-line available software
c Number of discordant clones between PSSM and SVM; all clones were predicted to be R5-tropic in PSSM, but either dual-tropic, X4-tropic or undetermined in SVM.
d E value obtained from the formula E = D(1-((D-1)/D)n) representing the expected number of independent clones, n = number of analyzed clones; D = number of input RNA copies. Numbers in bold italics indicate conditions where the amount of clones analyzed was greater than the expected number of individual amplifiable genomes present, suggesting resampling conditions.
e Population based phenotypic results obtained on same amplicon used for clonal analysis; D/M: dual tropic or mixed tropic virus population.