Table 1.: Overview of Genotypic and Phenotypic Testing of Artificial Mixed Samples at Various Viral Loads

Sample Characteristics Clonal Genotypeb Ed Phenotypee
VL (log IU/ml) # cp in 7x RT-PCRa X4 present (%) # Clones Analyzed R5 X4 Discordantc X4 Measured (%)
5 17500 2.5 93 91 2 0 2.2 93
5 17500 2.5 92 90 2 0 2.2 92
5 17500 2.5 93 93 0 0 0.0 93
5 17500 2.5 94 94 0 0 0.0 94 R5
5 17500 2.5 95 91 4 0 4.2 95 D/M
5 17500 2.5 93 91 2 0 2.2 93 D/M
5 17500 1 95 95 0 0 0.0 95
5 17500 1 94 94 0 0 0.0 94
5 17500 1 94 93 1 0 1.1 94 D/M
4 1750 20 92 82 10 0 10.9 90
4 1750 20 93 88 5 0 5.4 91
4 1750 20 92 85 7 0 7.6 90
4 1750 20 95 87 8 0 8.4 92 D/M
4 1750 20 91 78 13 0 14.3 89 D/M
4 1750 20 94 92 2 0 2.1 92 D/M
4 1750 8 94 86 8 0 8.5 92
4 1750 8 95 92 3 0 3.2 92
4 1750 8 92 85 7 0 7.6 90
4 1750 8 94 92 2 0 2.1 92
4 1750 8 92 89 3 0 3.3 90 D/M
4 1750 8 92 84 8 0 8.7 90 D/M
3 175 20 95 95 0 0 0.0 73
3 175 20 89 89 0 0 0.0 70
3 175 20 90 86 4 0 4.4 71 R5
3 175 20 94 93 1 0 1.1 73 D/M
3 175 20 93 49 44 0 47.3 72 D/M

a Number of viral copies entered in procedure.
b Tropism was inferred from the generated restriction pattern.
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.