Research Article
1 March 2001

Multisite Comparison of Reproducibility and Recovery from the Standard and Ultrasensitive Roche AMPLICOR HIV-1 MONITOR Assays

ABSTRACT

Reproducibility and recovery from the standard and ultrasensitive Roche AMPLICOR HIV-1 MONITOR kits were compared in 19 laboratories. The results were generally similar, but the consistently low level of recovery from the ultrasensitive assay in one laboratory points to the need to include external controls in order to track assay performance.
Measurements of human immunodeficiency virus (HIV) type 1 (HIV-1) RNA levels in plasma are widely used to monitor responses to antriretroviral therapy. Widespread interest in the quantification of HIV-1 RNA to the lowest possible levels led to the development of the ultrasensitive Roche AMPLICOR HIV-1 MONITOR assay. In this version of the MONITOR assay, sensitivity is increased over that in the standard MONITOR assay by concentrating the virus particles in plasma through centrifugation prior to RNA extraction (2). However, neither the internal quantitation standard nor the external controls that are supplied with the kit are subjected to this concentration step; thus, there is no control for the effects of this step in the current design of the kit. Comparative data on the performance characteristics of the ultrasensitive and standard MONITOR assays are limited to a few studies in individual laboratories (1, 2). A multisite comparison was, therefore, undertaken to assess the impact of the extra centrifugation step on intra-assay variation, interassay variation, and recovery of HIV-1 RNA.
Data were obtained from the HIV RNA Proficiency Testing Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health-sponsored Virology Quality Assessment Program. Under this program, participating laboratories periodically receive panels of coded samples of HIV-1 from a well-characterized, HIV-1 subtype B concentrate spiked into plasma from healthy subjects, usually at fivefold serial dilutions (3). Data from three different panels that were assayed with the standard kit and three others that were assayed with the ultrasensitive kit were included in the analyses. The panels consisted of 16 to 18 coded samples, with 3 to 6 replicates at each of four to five nominal HIV-1 RNA concentrations. The nominal concentrations in the panels assayed with the standard kit ranged from 500 to 312,500 HIV-1 RNA copies/ml, while those in panels assayed with the ultrasensitive kit ranged from 50 to 31,250 HIV-1 RNA copies/ml. These concentrations spanned most of the linear ranges of the two assays. All assays took place between June 1999 and January 2000. To avoid confounding differences between the two versions of the kit with differences among laboratories, the analysis was limited to data from 19 laboratories in which at least five of the six panels were assayed (8 laboratories, five panels each; 11 laboratories, six panels each).
The intra-assay standard deviation (SD) of log10 HIV-1 RNA concentration for each panel in each laboratory was estimated from the mean square error of a log-log regression of estimated HIV-1 RNA concentration on nominal HIV-1 RNA concentration. The distributions of the SDs for the two versions of the kit were very similar (for the standard kit, 56 SDs [10th percentile, 0.063; median, 0.106, 90th percentile, 0.177]; for the ultrasensitive kit, 50 SDs [10th percentile, 0.058; median, 0.111; 90th percentile, 0.168]). To determine if the SDs from the two assays were correlated, a summary intra-assay SD for each version of the kit in each laboratory was obtained from the mean square error of a log-log regression of estimated HIV-1 RNA concentration on nominal HIV-1 RNA concentration and indicators for the panel. The resulting SDs were positively correlated ( r = 0.53 ; P = 0.02 ). Thus, there was some consistency to the intra-assay SDs across the two versions of the kit within laboratories.
Interassay variation was estimated from the expected mean squares from a regression of log10 estimated HIV-1 RNA concentration on log10 nominal HIV-1 RNA concentration, indicators for laboratory, indicators for panel within a laboratory, and the interaction of laboratory and log10 nominal concentration. The interassay SD for the standard kit was 0.082 log10HIV-1 RNA copies/ml, while the interassay SD for the ultrasensitive kit was 0.096 log10 HIV-1 RNA copies/ml. While these estimates were similar, this analysis could not eliminate the possibility that interassay variation is greater for one version of the kit than the other in a small subset of laboratories. Therefore, a second assessment of interassay variation within each laboratory was obtained by calculating median log10 recovery for each panel in each laboratory and finding the range of medians for each kit in each laboratory. The distributions of the ranges for the two kits were very similar (Table 1). Furthermore, the ranges for the two versions of the kit were not correlated ( r = 0.20 ; P = 0.40 ). There was, therefore, little if any tendency for high or low interassay variation with one version to predict high or low interassay variation with the other.
Table 1.
Table 1. Descriptive statistics for the range of median log10 recovery across panels within 19 laboratories in which both the standard and ultrasensitive HIV-1 MONITOR assays were used
KitRange of median log10 recoveries
MinimumPercentilesMaximum
25th50th (Median)75th
Standard MONITOR0.0280.0680.1290.1900.330
Ultrasensitive MONITOR0.0200.0700.1760.2130.356
Finally, log10 recoveries from the standard and ultrasensitive assays were compared to determine if there were systematic differences in estimated HIV-1 RNA concentrations between the two. Descriptive statistics for the distributions of median log10 recovery among laboratories show little evidence of differences between the two assays (Table2). When data were pooled across panels within kits and laboratories, the differences between median log10 recoveries from the two kits within each laboratory ranged from −0.12 to 0.20 log10 HIV-1 copies/ml (median for the standard assay minus median for the ultrasensitive assay). This range implies that median estimated HIV-1 RNA concentration from the standard MONITOR assay ranged from 76 to 158% of median concentration from the ultrasensitive assay. Differences of 0.20 log10were obtained in two laboratories. In the other 17 laboratories, differences ranged from −0.12 to 0.10 log10 (76 to 126%). While these values indicate that, on average, the recoveries from the two versions of the kit were very similar, recovery from the ultrasensitive assay was substantially lower than recovery from the standard assay in one laboratory. The median log10 recovery for panel 007ruA in this laboratory was only −0.507 (31%). Recovery was <50% for 81% of the samples in the panel. This laboratory accounted for the lowest median recovery for each of the three panels that were tested by the ultrasensitive assay (minimums in Table 2). However, recovery from the standard assay in this laboratory was close to the middle of the range across all laboratories. Panels 007ruB and 007ruC, which are recoded versions of panel 007ruA, were also assayed in this laboratory. Median log10 recoveries were −0.19 (65%) and −0.26 (55%), respectively. Thus, recovery from the ultrasensitive assay at this site has been consistently low.
Table 2.
Table 2. Descriptive statistics for median within-laboratory log10 recovery for three panels of coded samples that were assayed with the standard HIV-1 MONITOR assay and three that were assayed with the ultrasensitive MONITOR assay
KitPanelNo.aMedian log10 recovery
MinimumPercentilesMaximum
25th50th (Median)75th
Standard MONITOR017rA18−0.127−0.0460.0690.1020.242
 018rA19−0.140−0.106−0.0870.0150.317
 019rA19−0.178−0.136−0.0320.0270.171
Ultrasensitive MONITOR005ruA18−0.167−0.0510.0030.0540.326
 006ruA18−0.201−0.061−0.0270.0210.172
 007ruA14−0.507−0.216−0.136−0.0590.158
a
Number of laboratories that participated in each round of testing.
In it unlikely that the low recovery was caused by reduced amplification. The optical densities for the internal quantitation standard were similar to those obtained for this panel in other laboratories (data not shown). This could indicate that the problem involves a sample processing step that takes place before the quantitation standard is added, which would point directly to the centrifugation step that is part of the ultrasensitive assay but not the standard assay. The possibility is still under investigation.
In summary, there is no evidence that the additional concentration step in the ultrasensitive assay alters intra-assay or interassay variation. With the exception of one laboratory, the recoveries were also similar for the two versions of the kit. While the results are encouraging, consistently low levels of recovery at one site are grounds for caution. Neither the internal quantitation standard nor the external controls that are supplied with the kit provided any evidence of a problem. However, given the design of the assay, these resources could not detect problems that take place during the concentration step. Only a control or controls that are processed through the entire assay could detect these problems. Laboratory personnel should consider using such a control to periodically monitor the performance of the ultrasensitive assay.

Acknowledgments

This work was supported by NIAID contract NO-AI-85354.
The following institutions and laboratory directors participated in the Virology Quality Assessment Program and contributed data to this analysis: Stanford University Medical Center, D. Katzenstein; University of California at San Diego, S. Spector; San Francisco General Hospital, R. Grant; University of Miami School of Medicine, W. Scott; University of Washington, R. Coombs; University of Medicine and Dentistry of New Jersey-New Jersey Medical School, P. Palumbo; Rush Presbyterian-St. Lukes Medical Center, J. Bremer; University of North Carolina, S. Fiscus; Quest Diagnostics Laboratory, W. Meyer; Cleveland Clinic Foundation, B. Yen-Lieberman; University of Massachusetts Medical Center, J. Sullivan; University of Rochester Medical Center, L. Demeter; University of Alabama at Birmingham, V. Johnson; University of California at Los Angeles School of Medicine, Y. Bryson; Virology Quality Assessment Laboratory at Rush Presbyterian-St. Lukes Medical Center, J. Bremer; Istituto Superiore di Sanita, S. Vella; University of Southern California School of Medicine, A. Kovacs; Johns Hopkins University, B. Jackson; and University of Alabama, G. Aldrovandi.

REFERENCES

1.
Erali M. and Hillyard D. R. Evaluation of the ultrasensitive Roche Amplicor HIV-1 Monitor assay for quantitation of human immunodeficiency virus type I RNA.J. Clin. Microbiol.371999792-795
2.
Sun R., Ku J., Jayakar H., Kuo J. C., Brambilla D., Herman S., Rosenstraus M., and Spadoro J. Ultrasensitive reverse transcription-PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma.J. Clin. Microbiol.3619982964-2969
3.
Yen-Lieberman B., Brambilla D., Jackson B., Bremer J., Coombs R., Cronin M., Herman S., Katzenstein D., Leung S., Lin H.-J., Palumbo P., Rasheed S., Todd J., Vahey M., and Reichelderfer P. Evaluation of a quality assurance program for quantitation of human immunodeficiency virus type 1 RNA in plasma by the AIDS Clinical Trials Group virology laboratories.J. Clin. Microbiol.3419962695-2701

Information & Contributors

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Published In

cover image Journal of Clinical Microbiology
Journal of Clinical Microbiology
Volume 39Number 31 March 2001
Pages: 1121 - 1123
PubMed: 11230438

History

Received: 9 May 2000
Returned for modification: 23 October 2000
Accepted: 15 December 2000
Published online: 1 March 2001

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Authors

Donald J. Brambilla
New England Research Institutes, Inc., Watertown, Massachusetts 02472,1 and
Suzanne Granger
New England Research Institutes, Inc., Watertown, Massachusetts 02472,1 and
Cheryl Jennings
Rush Medical College, Chicago, Illinois 606122
James W. Bremer
Rush Medical College, Chicago, Illinois 606122

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