An internally controlled virion PCR for the measurement of HIV-1 RNA in plasma

Real-time Fluorescent PCR Techniques to Study Microbial-Host Interactions

This chapter describes how real-time polymerase chain reaction (PCR) performs and how it may be used to detect microbial pathogens and the relationship they form with their host. Research and diagnostic microbiology laboratories contain a mix of traditional and leading-edge, in-house and commercial assays for the detection of microbes and the effects they impart upon target tissues, organs, and systems. The PCR has undergone significant change over the last decade, to the extent that only a small proportion of scientists have been able or willing to keep abreast of the latest offerings. The chapter reviews these changes. It discusses the second-generation of PCR technology-kinetic or real-time PCR, a tool gaining widespread acceptance in many scientific disciplines but especially in the microbiology laboratory.

Liposome encapsulation of the internal control for whole process quality assurance of nucleic acid amplification-based assays

A system intended for whole process quality assurance of nucleic acid amplification assays was developed based on the use of liposomes as cell-mimicking vehicles for the internal control, allowing introduction of the internal control directly into the crude biological specimens. By the proof of principle testing, the Roche Cobas Amplicor CT assay was chosen as model system and the Roche CT/NG Internal Control was thus loaded into the liposomes. The liposome/DNA particles were spiked into a Chlamydia trachomatis-positive urine specimen. A quantitative "in-house" duplex real-time C. trachomatis PCR assay showed that liposomes having Blue Dextran 2000 polysaccharide co-entrapped were the most suited particles as they were efficiently deposited by the centrifugation carried out according to the Roche urine specimen preparation procedure. Furthermore, it was demonstrated that the liposome/DNA particles might be used for whole process quality assurance of Amplicor assay without major modifications of the assay protocol. An additional feature of the use of these liposomes was that the pellet became blue coloured and that might facilitate a thorough removal of the urine supernatant without increasing the risk of disturbance of the pellet. Principally, the liposome/internal control system is versatile and seems to be applicable for whole process quality control of amplification-based assays for detection of various pathogens.

Comparison of competitive and positive control-based PCR quantitative procedures coupled with end point detection

Two PCR methods using internal standards, coupled with our sandwich nonisotopic enzyme-linked oligosorbent assay (ELOSA) in microtiter plate format, were developed for quantitation of human immunodeficiency virus type 1 (HIV-1) provirus. We present an overview of both methodologies focusing on two major features, i.e., the conditions of equivalency of replication efficiency and the definition of criteria of acceptance validating a result. Quantitative competitive PCR (QC-PCR) was based on the coamplification of the HIV-1 nef gene with different amounts of a pNEFmut plasmid that contains the nef gene with different amounts of a pNEFmut plasmid that contains the nef region but with mutations in the capture probe recognition region. The NEF wild-type (NEF) and the NEF mimic (NEFmut) amplification products were differentiated in ELOSA. NEFmut OD to NEF OD ratios were plotted against the number of mimic copies, and the deduced linear curve permitted quantitation of HIV-1 copy number. Internally controlled PCR (IC-PCR) was based on coamplification of the HIV-1 nef gene with an internal endogenous standard, the ras gene, as a positive control of amplification. HIV-1 copy number was determined using external standard of known amounts of HIV-1 DNA. We address the advantages as well as the limitations of individuals protocols and discuss future improvements of quantitative amplification process.

Competitive PCR for quantification of BM5d proviral DNA in mice with AIDS

Murine AIDS in C57BL/6 mice is caused by a unique mixture of murine leukemia viruses. We report the use of a competitive PCR to detect and quantitate BM5d proviral DNA. This assay allowed discrimination among endogenous wild-type murine retroviruses and BM5d sequences. Furthermore, the method was subsequently used to evaluate the amount of BM5d in infected mice and in infected AZT (zidovudine)-treated mice, providing an effective way to quantitatively evaluate drug efficacy in the murine AIDS model.

Microchimerism after liver transplantation: prevalence and methodological aspects of detection

BACKGROUND

Microchimerism after liver transplantation is a readily observed phenomenon. The immunological implications, however, remain unclear. Moreover, methodological approaches and their detection limits in the study of allogeneic microchimerism have not been studied in detail.

METHODS

Therefore, the aim of this study was to evaluate the single-step and nested formats of the polymerase chain reaction/sequence-specific priming (PCR-SSP) approach under standardized conditions. For that purpose, a panel of recombinant plasmid clones was generated by PCR cloning. The panel contained the allelic sequences of the second exon of DRB1 covering all DR specificities on a low-resolution level. Using this panel, limiting dilution assays for various DR sequences in the presence and absence of competitor DNA were carried out to determine the minimal number of copies required for detection by single-step and nested PCR-SSP. Subsequently, 22 liver transplant recipients were analyzed in a retrospective study for the presence of allogeneic microchimerism by nested PCR-SSP.

RESULTS

Although at least 10 copies of template DNA could be detected by nested PCR-SSP overall, single-step PCR-SSP was on average 10(2) to 10(3) times less sensitive. Upon the addition of human competitor DNA, the detection limits decreased on average by a factor of 10. In addition, sequence-specific differences in amplification efficiency could be appreciated. Using nested PCR-SSP, peripheral blood allogeneic microchimerism could be observed in 17 of 22 HLA-DR-mismatched liver recipients. Recombinants representing recipient DRB1 specificities were used to exclude false-positive results by lack of cross-reactivities of the donor-specific primers and to evaluate negative results due to sample-related reduced amplification efficiencies in microchimerism-negative recipients. In donor/recipient combinations that differed by at least one DR specificity, allogeneic microchimerism was seen in 87.5% of the cases. In five chimerism-negative cases, sample-related problems were detected in two cases.

CONCLUSION

The optimization and standardization of the detection of genomic HLA sequences at low copy number may be greatly facilitated using a clonal reference system. Furthermore, a clonal reference system may be used to conduct cross-priming experiments to exclude false-positive results and may allow the determination of sample-specific detection limits for donor-derived HLA-DR specificities in chimerism-negative patients. Our evaluation of the PCR-SSP approach for the study of allogeneic microchimerism indicated that nested PCR-SSP provides the most sensitive format when HLA sequences are targeted. Yet, the detection sensitivity may vary between individual alleles and specificities. Allogeneic microchimerism in liver recipients can be observed in the majority of patients. However, the detection may be subject to the degree of mismatching, the HLA-DR alleles involved, and sample-related impaired PCR amplification efficiency.

Developments in quantitative PCR

In recent years the growing interest in quantitative applications of the polymerase chain reaction (PCR) has favoured the development of a large number of assay procedures suitable for this purpose. In this paper we review some basic principles of quantitative PCR and in particular the role of reference materials and calibrators and the different strategies adopted for nucleic acid quantification. We focus on two methodological approaches for quantitative PCR in this review: competitive PCR and real-time quantitative PCR based on the use of fluorogenic probes. The first is one of the most common methods of quantitative PCR and we discuss the structure of the competitors and the various assay procedures. The second section is dedicated to a recent promising technology for quantitative PCR in which the use of fluorogenic probes and dedicated instrumentation allows the development of homogeneous methods. Assay performance of these methods in terms of practicability and reliability indicates that these kinds of technologies will have a widespread use in the clinical laboratory in the near future.

Quantitative molecular methods in virology

During the past few years, significant technical effort was made to develop molecular methods for the absolute quantitation of nucleic acids in biological samples. In virology, semi-quantitative and quantitative techniques of different principle, complexity, and reliability were designed, optimized, and applied in basic and clinical researches. The principal data obtained in successful pilot applications in vivo are reported in this paper and show the real usefulness of these methods to understand more details of the natural history of viral diseases and to monitor specific anti-viral treatments in real time. Theoretical considerations and practical applications indicate that the competitive polymerase chain reaction (cPCR) and competitive reverse-transcription PCR (cRT-PCR) assay systems share several advantages over other quantitative molecular methodologies, thus suggesting that these techniques are the methods of choice for the absolute quantitation of viral nucleic acids present in low amounts in biological samples. Although minor obstacles to a wide use of these quantitative methods in clinical virology still remain, further technical evolution is possible, thus making the quantitative procedures easier and apt to routine applications.