Development and verification of an automated sample processing protocol for quantitation of human immunodeficiency virus type 1 RNA in plasma

Evaluation of the QIAsymphony™ SP and Artus™ RealTime extraction-quantification systems for measuring HIV-1 virus load

BACKGROUND

Automated HIV-1 RNA extraction and its quantification by real-time PCR assays provide improved sample processing and better analytical performances. The new Artus HIV-1 RealTime assay can be performed after automated extraction with the Qiagen Qiasymphony robot.

OBJECTIVES AND STUDY DESIGN

To evaluate the sensitivity, reproducibility, linearity, ability to detect HIV-1 subtypes of the Qiagen Qiasymphony and RealTime Artus HIV-1 assay system and to compare with the Roche Cobas Ampliprep Cobas TaqMan assay, vs 2.0 (CAP/CTM; Roche Molecular Systems).

RESULTS

The detection limit calculated by probit analysis was 65 c/ml using dilutions of a NIBSC. Assays of serially diluted clinical samples gave very good inter-assay and intra-assay reproducibilities (<10% CV) and linearity (2.2-6.5 log copies/ml). The results Artus™ HIV-1 and CAP/CTM assays provided very similar results: average difference=0.11 log copies/ml. The Artus™ titers for 18 (22%) of the 114 HIV-1 group M samples tested differed by over 0.5 log copies/ml from the CAP/CTM titers. The Artus™ values were lower than the CAP/CTM values in 83% of cases. Discrepant results were not associated with particular subtypes.

CONCLUSION

The Artus™ HIV-1 assay reliably quantified the HIV RNA in clinical specimens. Analytical performances were good and it integrated well with the Qiasymphony automated RNA extraction procedure. It appears to be appropriate for monitoring therapy and the routine management of HIV-1 infections.

Performance evaluation of the automated NucliSens easyMAG nucleic acid extraction platform in comparison with QIAamp Mini kit from clinical specimens

The performance of the NucliSens easyMAG platform for the extraction of nucleic acid from different clinical specimens was compared with a manual procedure. A total of 308 specimens were analyzed: 209 plasma samples collected for virus detection and quantification of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (n = 70), and 29 for HIV genotyping for drug resistance. Linearity of extraction was tested on dilution series of CMV and EBV; the correlation coefficient (R(2)) for standard curves based on repeated extraction runs was 0.99 for CMV and EBV. Inter- and intrarun variability was in accordance with previous studies, and the correlation between automated and manual extraction was very high. The concordant results were 95.7% for CMV and 100% for EBV. The results of sequence analysis for HIV drug resistance showed a concordance in 24 of 29 specimens. The NucliSens easyMAG is extremely easy to perform, is automated, and resulted in a strong reduction of hands-on time compared with manual protocol.

Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens

The objectives of this study were to evaluate the performance of the NucliSens easyMAG platform for nucleic acid extraction from different clinical specimens compared to NucliSens miniMAG platform and manual QIAGEN extraction. The NucliSens easyMAG and the NucliSens miniMAG showed equal performance on 215 throat swabs since real-time nucleic acid sequence-based amplification scored the same samples positive for Mycoplasma pneumoniae (n=9) and Chlamydia pneumoniae (n=5) RNAs, although internal control RNA was slightly better detected with the NucliSens easyMAG (99.3% versus 96.8%). NucliSens easyMAG extracted nucleic acids more efficiently (higher recovery and/or fewer inhibitors) compared to QIAGEN extraction by showing, on average, lower Ct values in real-time LightCycler PCR, although 4 individual specimen out of 45 were found positive only with QIAGEN. For nine M. pneumoniae-positive throat swabs, the mean difference in Ct values between NucliSens easyMAG extraction and QIAGEN extraction was -2.26 (range, -5.77 to +0.60); for the detection of five C. pneumoniae-positive throat swabs, the average difference in Ct values between the two methods was -3.38 (range, -6.62 to -2.02); and for the detection of cytomegalovirus in 24 blood samples, the mean difference in Ct values between the two methods was -0.95 (range, -5.51 to +1.68). The NucliSens easyMAG is considerably easier to perform, efficiently extracts nucleic acids from throat swabs and whole blood, is automated, and has high throughput.

Pathogen Detection in the Genomic Era

In the 21st century, one of the greatest challenges to public health and clinical microbiologists is the rapid detection and identification of emerging and reemerging pathogens. Complex factors such as genetic variation in the host and pathogen, environmental changes, population pressures, and global travel can all influence the emergence of infectious diseases. The SARS epidemic of 2003 highlighted the potential of an emerging pathogen to spread globally in a very short time frame (Peruski and Peruski, 2003). The diagnostics of such infectious diseases has been greatly affected in the past 20 years. No longer is cultivation and microscopy the only means of detecting infectious agents. With the introduction of molecular diagnostics, the ability to detect minute amounts of microbial nucleic acids in clinical specimens has revolutionized clinical microbiology. In particular, the utility of PCR allows the detection and quantitation of specific agents in a matter of hours. PCR sequencing of specific segments of nucleic acid allows for the determination of specific drug resistance that now aids in guiding viral therapies.

Reduced PCR sensitivity due to impaired DNA recovery with the MagNA Pure LC total nucleic acid isolation kit

The increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. In the present study, we evaluated the performance of the MagNA Pure LC total nucleic acid isolation kit (M extraction) in comparison with the manual method (Si extraction) according to Boom et al. (R. Boom, C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990) for the detection of viral DNA by competitive quantitative PCR. Reconstruction experiments with HindIII-digested phage lambda DNA and HaeIII-digested phiX174 DNA showed that the recovery of DNA from phosphate-buffered saline, cerebrospinal fluid, EDTA-anticoagulated plasma, and EDTA-anticoagulated whole blood by M extraction is, on average, 6.6-fold lower compared to Si extraction. PCR signals of spiked PCR control DNAs for Epstein-Barr virus and varicella-zoster virus were also between 1.9- and 14.2-fold lower after M extraction compared to Si extraction, also suggesting impaired DNA recovery. M extraction of spiked cytomegalovirus strain AD 169 in whole blood showed a 5- to 10-fold reduction in PCR sensitivity compared to Si extraction. This reduction of PCR sensitivity was also observed when clinical whole blood samples were processed by M extraction. Before implementing M extraction, the clinical consequences of the reduced recovery should first be considered, especially when maximal sensitivity is required.

Screening of blood donors for hepatitis C virus RNA with the MagNA Pure-COBAS AmpliScreen method

BACKGROUND

This report describes the validation results and the performance characteristics of a new, semiautomated minipool nucleic acid amplification method for testing of blood products to reduce the transmission of hepatitis C virus (HCV) by transfusions.

STUDY DESIGN AND METHODS

Minipools of 96 donations were prepared with the Tecan Genesis pipettors. Nucleic acids were isolated from plasma samples with the MagNA Pure LC instrument (Roche Diagnostics GmbH) and amplified and detected with the COBAS AmpliScreen second-generation HCV assay (Roche Molecular Systems, Inc.). Sensitivity of the method was determined with the WHO International Standard for HCV RNA (NIBSC 96/790) as a reference. The risk of cross-contamination during the nucleic acid extraction and postelution steps was studied with a highly viremic sample.

RESULTS

Detection limit of the assay (95% hit rate) was calculated to be 11.7 IU per mL. Altogether 2,423 minipools (232,600 donations) were screened with the following performance characteristics: initially false-reactive results (0%), failure of run control detection (0.45%), and failure of internal control detection (0.90%). Two cross-contamination cases caused by a highly viremic sample were found during the validation phase but not in the routine screening period, although nine HCV RNA-positive minipool samples were observed.

CONCLUSION

This combination of HCV RNA screening methods showed the detection limit that is well below the sensitivity requirements of the regulatory bodies. Robustness of the validated HCV RNA screening method has proved to be acceptable for routine screening of blood donors on a large scale.

Comparison of five methods for extraction of Legionella pneumophila from respiratory specimens

The efficiencies of five commercially available nucleic acid extraction methods were evaluated for the recovery of a standardized inoculum of Legionella pneumophila in respiratory specimens (sputum and bronchoalveolar lavage [BAL] specimens). The concentrations of Legionella DNA recovered from sputa with the automated MagNA Pure (526,200 CFU/ml) and NucliSens (171,800 CFU/ml) extractors were greater than those recovered with the manual methods (i.e., Roche High Pure kit [133,900 CFU/ml], QIAamp DNA Mini kit [46,380 CFU/ml], and ViralXpress kit [13,635 CFU/ml]). The rank order was the same for extracts from BAL specimens, except that for this specimen type the QIAamp DNA Mini kit recovered more than the Roche High Pure kit.

Quantitative real-time PCR with automated sample preparation for diagnosis and monitoring of cytomegalovirus infection in bone marrow transplant patients

BACKGROUND

In bone marrow and stem cell transplant patients, the widespread use of preemptive cytomegalovirus (CMV) antiviral therapy necessitates faster, more precise, and more sensitive quantitative laboratory methods for serial viral load monitoring.

METHODS

We developed a novel CMV viral load assay using real-time PCR of plasma DNA prepared by an automated robotic workstation. Fluorescent hybridization probes directed at the glycoprotein B (gB) gene (or EcoRI D region) of CMV were used to detect and quantify PCR products. The beta-globin gene was amplified in parallel to control for the efficiency of the extraction and PCR steps.

RESULTS

The assay was linear (R = 0.999) from a lower detection limit of 125 copies/mL to 5 x 10(9) copies/mL with a PCR efficiency of 1.975 (gB) or 2.02 (EcoRI D). The viral loads determined by PCRs directed at these two different viral targets were no different (n = 53; R = 0.928). The interassay CV was 3.5%, and the intraassay CV was 1-4%. Compared with a commercially available quantitative competitive PCR assay (Roche MONITOR; R = 0.59), the mean CMV viral load by real-time PCR was 3.1 times higher (mean ratio; P = 0.002). The diagnostic sensitivity and specificity of the real-time assay were 96% and 100%, respectively (n = 147), compared with 74% and 98% for a qualitative PCR assay (Roche AMPLICOR). On a subset of samples, the diagnostic sensitivity of viral culture was no greater than 50% (n = 44). Of 1115 clinical referral samples from 252 patients, 10% of the samples and 18% of the patients had low-level CMV viremia (median, 500 copies/mL). In this predominantly (85%) bone marrow transplant testing cohort, serial CMV viral load results were the predominant clinical trigger for the initiation, monitoring, and cessation of preemptive antiviral therapy.

CONCLUSIONS

The combination of automated DNA preparation and semiautomated real-time fluorescent PCR detection allows for a sensitive, precise, and accurate high-throughput assay of CMV viral load that can be used as the laboratory trigger for preemptive antiviral therapy.