Abstract
The LCx human immunodeficiency virus (HIV) RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan assays for HIV type 1 (HIV-1) were compared for their abilities to quantitate HIV-1 RNA in plasma. High degrees of correlation and agreement were observed between the assays. Differences in HIV-1 RNA levels according to HIV-1 subtypes did not reach statistical significance.
Measurement of human immunodeficiency virus (HIV) type 1 (HIV-1) RNA levels in plasma is a major tool for the management of HIV-1-infected patients. Several commercial assays based on viral nucleic acid amplification have been developed over the course of the past decade. These different assays have been progressively improved by (i) lowering the lower limit of HIV-1 RNA detection and quantitation (6, 7, 9, 13), (ii) adapting primers and a probe for recognition of the different HIV-1 subtypes and circulating recombinant forms (CRFs) (5, 8, 12, 15-17), and (iii) developing automated methods (2, 11). More recently, commercial assays based on real-time nucleic acid amplification methods have been developed (4, 10). In the present study, we have compared the analytical performances of three assays: the LCx HIV RNA Quantitative assay (Abbott Molecular, Rungis, France), based on end-point PCR; the RealTime HIV assay (Abbott); and the COBAS AmpliPrep-COBAS TaqMan HIV-1 test (Roche Diagnostics, Meylan, France). The last two assays are based on real-time PCR. The Abbott LCx HIV RNA Quantitative and the RealTime HIV assays target the pol integrase region of HIV-1, whereas the COBAS AmpliPrep-COBAS TaqMan HIV-1 test targets the gag p24 region of HIV-1. Using the 1-ml sample preparation protocol, the reported upper limit of quantitation and lower limit of quantitation (LLQ) are 1,000,000 (6.0 log10) RNA copies/ml and 50 (1.7 log10) RNA copies/ml, respectively, for the LCx HIV RNA Quantitative assay, and 10,000,000 (7.0 log10) RNA copies/ml and 40 (1.6 log10) RNA copies/ml, respectively, for both the Abbott RealTime HIV-1 and the COBAS AmpliPrep-COBAS TaqMan HIV-1 test.
Plasma samples were obtained from 91 HIV-1-seropositive patients: 58 of them were infected with HIV-1 subtype B and 30 were infected with non-B subtypes (Table 1). For the remaining three patients, the HIV-1 subtype could not be determined because of an insufficient RNA level or a lack of sample availability.
TABLE 1.
Numbers of plasma samples with HIV-1 RNA levels higher than the lower limit of quantitation as determined by the LCx HIV RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan HIV-1 assays
| Samples | No. (%) of samples
|
Pa | ||
|---|---|---|---|---|
| LCx HIV RNA Quantitative | RealTime HIV | COBAS AmpliPrep-COBAS TaqMan HIV-1 | ||
| All samples (n = 91) | 67 (73.6) | 70 (76.9) | 70 (76.9) | 0.83 |
| Subtype B (n = 58) | 46 (79.3) | 45 (77.6) | 47 (81.0) | 0.90 |
| Non-subtype B (n = 30) | 19 (63.3) | 22 (73.3) | 20 (66.7) | 0.70 |
| Non-subtype B, non-CRF02 (n = 19) | 13 (68.4) | 13 (68.4) | 13 (68.4) | 1.0 |
| CRF02 (n = 11) | 6 (54.5) | 9 (81.8) | 7 (63.6) | 0.38 |
Chi-square test.
Plasma samples were frozen at −80°C before testing. For the LCx HIV RNA Quantitative and the Abbott RealTime HIV assays, automatic RNA extraction was performed on an M1000 apparatus (Abbott) with the 1-ml sample preparation protocol and with elution volumes of 140 μl for the LCx HIV RNA Quantitative assay and 70 μl for the RealTime HIV assay. For the COBAS AmpliPrep-COBAS TaqMan HIV-1 test, extraction was done on an AmpliPrep apparatus (Roche Diagnostics) with 0.85 ml of plasma and an elution volume of 75 μl. The three assays were then performed by following the manufacturer's instructions and by using a 50-μl eluate volume. For calculations, the value of the LLQ was assigned to samples with HIV RNA levels below the LLQ.
HIV-1 RNA levels fell within the dynamic ranges of the three assays for 62 (68.1%) samples, whereas it was lower than the LLQ of the three assays for 14 (15.4%) samples and was lower than the LLQ of one or two of the three assays for the remaining 15 (16.5%) samples. Overall, the LCx HIV RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan HIV-1 assays allowed quantitation of HIV-1 RNA in 67 (73.6%), 70 (76.9%), and 70 (76.9%) of the samples, respectively. HIV-1 RNA was detected at a level lower than the LLQ in eight, four, and nine additional samples by the LCx HIV RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan HIV-1 assays, respectively. Thus, the number of samples positive for HIV-1 RNA were 75 (82.4%) with the LCx HIV RNA Quantitative assay, 74 (81.3%) with the RealTime HIV assay, and 79 (86.8%) with the COBAS AmpliPrep-COBAS TaqMan HIV-1 assay (P = 0.57).
As shown in Table 1, a significant difference in the number of samples with HIV-1 RNA levels higher than the LLQ was not observed between the assays. CRF02_AG HIV-1 RNA could be detected at a level lower than the LLQ in two, one, and three additional samples by the LCx HIV RNA Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan HIV-1 assays, respectively. Thus, the number of samples positive for CRF02_AG HIV-1 RNA were 8 (72.7%) with the LCx HIV RNA Quantitative assay, 10 (90.9%) with the RealTime HIV assay, and 10 (90.9%) with the COBAS AmpliPrep-COBAS TaqMan HIV-1 assay (P = 0.58).
As shown in Table 2, the HIV-1 RNA levels measured by the RealTime HIV assay in samples from subtype B-infected patients were lower than those obtained by either the LCx HIV RNA quantitative assay or the COBAS AmpliPrep-COBAS TaqMan HIV-1 test. Conversely, the HIV-1 RNA levels measured with the RealTime HIV assay in samples from patients infected with CRF02_AG HIV-1 strains were higher than those obtained with the two other assays, but these differences were not statistically significant.
TABLE 2.
Quantitation of HIV-1 RNA level in plasma samples by the LCx HIV Quantitative, RealTime HIV, and COBAS AmpliPrep-COBAS TaqMan HIV-1 assays
| Sample | Median (interquartile range) HIV-1 RNA level (log10 copies/ml)
|
Pa | ||
|---|---|---|---|---|
| LCx HIV RNA Quantitative | RealTime HIV | COBAS AmpliPrep-COBAS TaqMan HIV-1 | ||
| All samples (n = 91)b | 2.96 (1.70-4.27) | 2.93 (1.65-4.02) | 3.05 (1.67-4.39) | 0.24 |
| Subtype B (n = 58) | 3.12 (1.84-4.56) | 2.85 (1.66-4.17) | 3.23 (2.01-4.54) | 0.15 |
| Subtype non B (n = 30) | 2.70 (1.70-3.78) | 3.11 (1.60-3.89) | 3.00 (1.60-3.98) | 0.96 |
| Subtype non-B non-CRF02 (n = 19) | 3.30 (1.70-3.85) | 3.47 (1.60-3.89) | 3.53 (1.60-4.09) | 0.78 |
| CRF02 (n = 11) | 2.01 (1.70-3.50) | 2.67 (1.93-4.05) | 2.37 (1.60-3.71) | 0.76 |
| Subset of samples with RNA levels falling within the dynamic ranges of the three assays | ||||
| All samples (n = 62) | 3.81 (2.95-4.63) | 3.74 (2.77-4.24) | 3.93 (2.95-4.63) | 0.28 |
| Subtype B (n = 42) | 4.17 (2.93-4.70) | 3.66 (2.61-4.29) | 4.14 (2.89-4.75) | 0.12 |
| Non-subtype B (n = 18) | 3.55 (2.99-4.04) | 3.83 (3.47-4.12) | 3.82 (3.11-4.28) | 0.61 |
| Non-subtype B, non-CRF02 (n = 12) | 3.68 (3.33-4.09) | 3.83 (3.52-4.07) | 3.93 (3.56-4.33) | 0.63 |
| CRF02 (n = 6) | 3.23 (2.44-3.98) | 3.87 (3.11-4.14) | 3.33 (2.64-4.25) | 0.71 |
Kruskal-Wallis test.
The value of the LLQ was assigned to samples with HIV-1 RNA levels below the LLQ.
As shown in Fig. 1, a high level of correlation between assays was observed, with Pearson's correlation coefficient (r) values ranging from 0.94 to 0.98. The agreement between methods was analyzed by using Bland-Altman plot analysis (3), and high levels of agreement were observed: 93.4% between the LCx HIV RNA Quantitative and the RealTime HIV assays as well as between the LCx HIV RNA Quantitative and the COBAS AmpliPrep-COBAS TaqMan HIV-1 assays and 94.5% between the RealTime HIV and the COBAS AmpliPrep-COBAS TaqMan HIV-1 assays (Fig. 2).
FIG. 1.
Correlation between the LCx HIV RNA Quantitative and RealTime HIV assays (A), the LCx HIV RNA Quantitative and COBAS Ampliprep-COBAS Taqman HIV-1 assays (B), and the RealTime HIV and COBAS Ampliprep-COBAS Taqman HIV-1 assays (C). The bold line represents the regression line. The equation of the fitted line and the Pearson's correlation coefficient are presented on the plot. Values are expressed as log10 HIV-1 RNA copies per ml.
FIG. 2.
Differences between HIV-1 RNA values obtained by comparing the LCx HIV RNA Quantitative and RealTime HIV assays (A), the LCx HIV RNA Quantitative and COBAS Ampliprep-COBAS Taqman HIV-1 assays (B), and the RealTime HIV and COBAS Ampliprep-COBAS Taqman HIV-1 assays (C) by Bland-Altman analysis by plotting the differences against the mean. The mean difference (bold line) and plus and minus 2 standard deviations (dashed lines) are shown. The means ± 2 standard deviations are 0.14 ± 0.86 (A), −0.07 ± 0.56 (B), and −0.21 ± 0.88 (C). Values are expressed as log10 HIV-1 RNA copies per ml. The numbers of samples ranging within the mean ± 2 standard deviation interval are 85 of 91 (93.4%) in panels A and B and 86 of 91 (94.5%) in panel C.
Taken together these data indicate that the three assays have similar performances for the quantitation of HIV-1 RNA in the samples tested in this study. The Abbott RealTime HIV assay and the COBAS AmpliPrep-COBAS TaqMan HIV-1 assay, both of which are supported by a fully automated extraction and both of which are based on real-time PCR, allow high throughputs (48 to 96 samples) and short turnaround times (nearly 3 h). This could be a major advantage for clinical laboratories.
In several studies, it has been reported that the LCx HIV RNA Quantitative assay is effective for quantitation of HIV-1 RNA in plasma samples from subjects infected with various group M subtypes, including CRF02_AG (15), or with group O viruses (14, 17). However, in one study, it has been reported that the performance of this assay is suboptimal only for the detection and quantification of CRF02_AG HIV-1 RNA (1). In the present study, HIV-1 RNA could be quantitated in 6 of 11 (54.5%) CRF02_AG-infected samples by the LCx HIV RNA Quantitative assay, whereas HIV-1 RNA could be quantitated in 7 (63.6%) and 9 (81.8%) of these samples by the COBAS AmpliPrep-COBAS TaqMan HIV-1 assay and the RealTime HIV assay, respectively. It was also observed that the HIV-1 RNA levels measured by the RealTime HIV assay were higher than those measured by the two other assays in the CRF02_AG-infected samples but were lower than those measured by the other two assays in subtype B-infected samples. These differences, however, did not reach statistical significance. This lack of significance could be due to small sample sizes. Therefore, larger studies are needed to better assess the possible impact of HIV-1 genetic diversity on the HIV-1 RNA levels measured by these assays.
Acknowledgments
We acknowledge Abbott Molecular and Roche Diagnostics for providing test kits.
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