The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.

/pdf/real-time-pcr-in-virology-cln3j5i0kf.pdf

Real-time PCR in virology

https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)63100-1/pdf

Real‐time PCR in the microbiology laboratory

Quantitation of viral load using real-time amplification techniques.

High incidence of human herpesvirus 6 infection with a high viral load in cord blood stem cell transplant recipients

A real-time quantitative PCR assay has been developed to measure human herpesvirus 6 (HHV-6) DNA in biological specimens. The assay sensitivity was 10 copies of DNA per well, with a linear dynamic range of 10 to 10(7) copies of HHV-6 DNA. Intra- and interassay variations were, respectively, 0.88 and 0.8% for samples containing 10(2) DNA copies, 0.99 and 0.96% for samples containing 10(4) copies, and 0.76 and 0.9% for samples containing 10(6) copies. Among 34 saliva samples from healthy subjects, 26 were found to contain HHV-6 DNA (76.5%; median, 23,870 copies/ml), and following a single freeze-thaw cycle, 25 of the same samples were found to be positive for HHV-6 DNA, although at a statistically significantly lower concentration (median, 3,497 copies/ml). The assay enabled detection of HHV-6 DNA in lymph node biopsies from patients with Hodgkin's disease (HD) (13 of 37 patients [35.1%]), B-cell neoplasms (8 of 36 patients [22.2%]), and T- or NK-cell neoplasms (3 of 13 patients [23.1%]), with concentrations ranging from 100 to 864,640 HHV-6 copies per microg of DNA (HHV-6B being found in every case except two). All HD patients infected with HHV-6 presented clinically with the nodular sclerosis subtype of HD. The real-time quantitative PCR assay developed here was simple to perform and was sensitive over a wide range of HHV-6 concentrations. It therefore appears to be of potential value in clinical investigation or diagnosis of HHV-6 infection.

Real-Time PCR for Quantification of Human Herpesvirus 6 DNA from Lymph Nodes and Saliva

Reactivation of human herpesvirus 6 (HHV-6) is common following allogeneic marrow transplantation, however, little is known about the immune control and pathogenic potential of HHV-6 infection after transplantation. In order to determine whether reactivation of HHV-6 plays an important role in the development of complications in patients undergoing allogeneic bone marrow transplantation or not, we developed a very rapid quantification of viral DNA using a LightCycler. The amount of viral DNA was determined using a supernatant of a chronically infected cell line [TaY(OK)] which contains a known amount of viral DNA. Peripheral blood cells were collected from 5 patients undergoing allogeneic bone marrow transplantation once before transplant and once per week after transplant for 8-24 weeks. The real-time PCR system revealed that there was a linear correlation in the range of 101 to 105 molecules of reference. Using this system, we have found the presence of non-diagnosed HHV-6 reactivation as well as symptomatic infection, indicating the potential for routine implementation of this technology for laboratory diagnosis of HHV-6 infection. Our study shows that this method of rapid quantification of HHV-6 genomes by the real-time PCR using a LightCycler may be useful not only to understand the reconstitution of the immune system following marrow transplantation but also to manage the care of patients.

Use of real-time PCR to monitor human herpesvirus 6 reactivation after allogeneic bone marrow transplantation.

Summary: To establish a practical monitoring system of human herpesviruses reactivation in patients undergoing stem cell transplantation, we developed a new, very rapid, highly sensitive, and quantitative PCR assay for accurate measurement of human cytomegalovirus (CMV), human herpesvirus 6 (HHV-6) and Epstein–Barr virus (EBV) DNA using LightCycler. The LightCycler system revealed that there was a linear correlation in the wide range of viral template DNA at the indicated number of PCR cycles. Peripheral blood cells were collected from 16 patients undergoing stem cell transplantation. The cut-off level of CMV and HHV-6 was assessed as 10 2 copies/g and that of EBV as 10 3 . High numbers of CMV genomes were detected in 3/13 patients after transplant, and reactivation of HHV-6 was frequently seen, whereas none of the patient showed an elevation of EBV genome copies until the end of the observation period. In the present study, the reactivation of herpesviruses is associated with the occurrence of thrombotic microangiopathy (TMA) in two patients undergoing allogeneic BMT. Therefore, it may contribute in clarifying the pathological potential of human herpesviruses using a large number of clinical samples. Our results suggest that this system may be useful for monitoring viral reactivation. Bone Marrow Transplan

Technical report A rapid monitoring system of human herpesviruses reactivation by LightCycler in stem cell transplantation

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Use of real-time PCR to monitor human herpesvirus 6 reactivation after allogeneic bone marrow transplantation.

Technical report A rapid monitoring system of human herpesviruses reactivation by LightCycler in stem cell transplantation