Polymerase chain reaction kinetics when using a positive internal control target to quantitatively detect cytomegalovirus target sequences

A highly sensitive assay for detection and quantitation of human cytomegalovirus DNA in serum and plasma by PCR and electrochemiluminescence

We describe a diagnostic PCR assay (D-PCR) and a quantitative PCR assay (Q-PCR) for the detection of human cytomegalovirus (CMV) in plasma and serum. In the D-PCR, DNA was purified from plasma or serum together with internal control (IC) DNA, which monitored both DNA extraction efficiency and PCR efficiency. DNA was subjected to PCR with a single primer pair, and the amount of PCR products was determined by electrochemiluminescence (ECL) in the QPCR System 5000 (Perkin-Elmer) after hybridization with Tris (2,2'-bipyridine) ruthenium (II) chelate-labeled probes. The lower limit of sensitivity of the D-PCR was reached at about 25 CMV particles/ml. Even with extremely low DNA inputs (four molecules of IC DNA/200 microl of plasma), very high yields (near 100%) were reached. DNA extracted from specimens that were CMV positive by the D-PCR was subsequently used in the Q-PCR, which was similar to the D-PCR. The viral load was calculated directly from the ratio of CMV and IC signals obtained by ECL. The Q-PCR assay is quantitative in the range of 100 to 150,000 copies of CMV/ml, independent of the anticoagulant. Interassay variation, intra-assay variation, and interspecimen variation were about 25%, suggesting that the Q-PCR will reliably detect fourfold differences in viral load. Comparison of paired serum and plasma specimens from CMV-infected individuals showed that serum CMV loads were frequently more than 10-fold lower than plasma CMV loads.

Polymerase chain reaction based assessment of leukoreduction efficacy using a cytomegalovirus DNA transfected human T-cell line

BACKGROUND AND OBJECTIVES

Detection of CMV DNA by PCR in seropositive blood donors is affected by nucleic acid extraction, amplification conditions and PCR product detection sensitivity. Clinical studies have shown that leukoreduced blood products are as effective as CMV-seronegative blood products in minimizing transfusion-associated CMV infection. We developed a PCR-based test model to assess the efficacy of leukoreduction on the removal of CMV DNA from blood donations.

MATERIALS AND METHODS

Whole blood units were spiked with a human Jurkat T-lymphocyte cell line which had been stably transfected with a CMV DNA immediate early sequence. All blood units were either CMV seronegative or shown to be CMV PCR negative. The amount of CMV DNA by PCR before, during and after filtration of blood units with third-generation leukocyte reduction filters were determined using a semi-quantitative adaptation of the Digene SHARP Signal System Assay (DSSSA).

RESULTS

Whole blood units spiked with 1-2 x 10(6) CMV transfected Jurkat cells contained no detectable CMV DNA after leukoreduction. With a higher inoculum of 2.9 x 10(8) transfected Jurkat cells per unit, CMV DNA was detected after leukoreduction; however, there was an approximate 3 log decrease in the amount of CMV DNA detected.

CONCLUSION

This CMV DNA transfected human Jurkat cell line in conjunction with semi-quantitative CMV PCR may be used to model leukoreduction efficacy and provides evidence that leukoreduction of blood products can decrease the amount of cellular CMV DNA by approximately 3 logs.

Analysis of cAMP RI alpha mRNA expression in breast cancer: evaluation of quantitative polymerase chain reaction for routine use

A quantitative polymerase chain reaction (PCR) method for determining concentrations of mRNA for the cyclic AMP (cAMP)-binding protein RI alpha, a regulatory subunit of cAMP-dependent protein kinase, was developed using site-directed mutagenic primers and mix-melt PCR. The PCR product for RI alpha mRNA was modified to include an EcoRV restriction site for use as an internal standard. This mutant utilised the same primers as the target mRNA and differed in sequence by only four bases. As only one of these base changes results in a purine/pyrimidine switch the effective change in labelling with [32P]dCTP was less than 0.5%. Reverse transcription of mRNA was performed and quantitative PCR was carried out using fixed levels of mutant RI alpha vs varying amounts of both normal RI alpha sequence of known concentration and unknown samples. Validation of the technique using rigourous quality control established that reverse transcription, determined by incorporation of labelled nucleotides, gave intra- and interassay variations of 16.2 and 9.3% respectively. Using crossover evaluation of cDNA concentrations with cloned RI alpha sequences as controls intra- and interassay variations of 14.3% and 4-8% respectively were obtained. Using compounded errors, the limits of precision for this technique demonstrate that values that are altered by 50% or more represent a true alteration in mRNA levels between samples tested. This value compares favourably to similar values for radioimmunoassays of between 10% and 30% precision. Analysis of a series of patient samples during routine follow-up of treatment demonstrated clear changes in mRNA levels. Using site-directed mutagenesis to establish a quantitative PCR-based assay for expression of mRNA this study demonstrates the potential usefulness and some limitations of quantitative PCR for applications within a clinical biochemistry laboratory. However, based on compounded error, values that vary by less than 50% within assays, and by less than 70% in separate assays could not be clearly separated. Assessment of paired patient samples has demonstrated clear changes in mRNA for the target protein RI alpha. With the use of normal quality control procedures this study has established that the degree of reproducibility of this quantitative PCR technique would allow assessment of mRNA levels for markers of interest in clinical samples in a routine laboratory context.

Detection of cytomegalovirus in blood donors by PCR using the digene SHARP signal system assay: effects of sample preparation and detection methodology

Cytomegalovirus (CMV) is an important cause of transfusion-associated morbidity and mortality; however, only 0.4 to 12% of the blood products obtained from seropositive blood donors transmit infection. The effects of three commercially available whole-blood sample preparation kits on the detection of CMV PCR products by a semiquantitative adaptation of the Digene SHARP Signal System Assay (DSSSA) in samples from volunteer blood donors was assessed. Of 101 samples from seropositive blood donors, CMV was detected in 0 (0%) of the samples extracted with a QIAamp blood kit (QIAGEN), 1 (1%) of the samples extracted with an Amplicor whole-blood specimen preparation kit (Roche), and 8 (8%) of the samples extracted with an Isoquick nucleic acid extraction kit (modified by the addition of carrier tRNA) (Microprobe). CMV DNA was not detected in samples from seronegative blood donors (n = 13). Nested PCR of selected samples confirmed the detection of CMV in the sane eight samples extracted with the modified Isoquick nucleic acid extraction kit and detected an additional nine CMV-positive samples (n = 50). Samples from volunteer blood donors contain low copy numbers of CMV DNA. PCR amplification of such specimens can result in analytical sampling errors, giving results similar to the variations in titers recognized during determinations of the 50% tissue culture infective dose. The detection of CMV in blood samples from volunteer blood donors by PCR is a function of sample preparation, amplification conditions, and detection methodology. Accurate assessments of the clinical utility of CMV DNA detection by nucleic acid amplification for blood product screening and patients will require highly standardized and quantitative methodology.

Viral serology and detection

Viral detection is an important part of clinical hepatology. For many years practical clinical tests have been serological but recently newer molecular techniques have become available for virus detection, although these have yet to become routine and some, such as PCR of viral nucleic acid in blood or tissue are not yet consistently reliable. Serology remains the mainstay at present for routine diagnosis. Hepatitis A testing in clinical practice is entirely serological, the IgM response representing acute infection and the IgG response immunity, although more sophisticated molecular techniques have been applied experimentally. A second agent of epidemic enteral hepatitis, the hepatitis E virus, has recently been cloned and sequenced and serological tests for this virus are available, although experience in their use is necessarily limited and a commercial IgM assay has yet to be produced. Serological tests for the hepatitis B virus are well developed. The IgM anticore response differentiates acute infection from chronic, the latter being characterized by the persistence of hepatitis B surface antigen for over six months. Chronic carriers are at risk of liver damage and this risk is best assessed by the amount of viral DNA circulating, which can be determined using a hybridization assay. More sensitive techniques such as the branched chain DNA assay or PCR can detect lower levels of viral DNA but their clinical relevance remains to be established. The hepatitis D virus is defective and relies on hepatitis B to replicate. Serology for antibody and antigen is well established although PCR for circulating viral genome may come to supplant hepatic viral antigen as a test for hepatitis D replication. For hepatitis C serology is feasible only for antibodies, not antigens; although early tests were prone both to false positives and false negatives, current versions are more reliable. PCR has been much used for detection of hepatitis C RNA in blood and tissues and a bDNA assay is now commercially available. Cytomegalovirus detection is confounded by the problem of distinguishing asymptomatic viral replication from disease. Serology is helpful, especially in primary infections, but viral culture is a widely used method. PCR (especially quantitative modifications) or the pp65 antigenaemia assay are experimental approaches which may prove specific enough for general use.

Molecular detection of hepatitis C virus: impact of detection methodology on clinical and laboratory correlations

The clinical manifestations of hepatitis C virus (HCV) infection are generally indistinguishable from other causes of viral hepatitis. HCV infections are usually anicteric, asymptomatic, and rarely cause acute fulminant liver failure. Serological testing for HCV in conjunction with epidemiological studies have verified that HCV was the major cause of parenterally transmitted non-A, non-B hepatitis (NANBH). With the widespread introduction of serological screening of blood products for HCV antibody, the risk of transfusion-associated HCV infection has been dramatically reduced (to < 3 cases per 10,000 units transfused). Despite the virtual elimination of transfusion-associated infections, the diagnosis of HCV remains important because > 50% of infections are sporadic in origin, 50 to 70% of infected individuals develop chronic hepatitis, and these individuals are at risk of developing cirrhosis (> 20%) as well as hepatocellular carcinoma. Although currently available anti-HCV immunoassays function well as blood-donor screening assays, they are poor at detecting acute infection because of the prolonged lag time between infection and detection of seroconversion (approximately 10 to 26 weeks for second-generation immunoassays). In contrast, polymerase chain reaction (PCR)-based detection of HCV RNA in serum can detect infection in as little as 1 to 2 weeks after exposure. This review focuses on the impact of modern serologic and nucleic acid-based HCV detection methodology on the clinical understanding of HCV infection, its associated illnesses, and its transmissability. Quantitative and reproducible nucleic acid-based detection assays will be required to provide additional insights into the clinical spectrum of HCV infections as well as to assess the efficacy of antiviral agents.