Linda Cook

Immune surveillance in multiple sclerosis patients treated with natalizumab.

Our objective was to test whether natalizumab, an antibody against very late activating antigen (VLA)‐4, interferes with central nervous system immune surveillance as assessed by leukocyte cell numbers and cellular phenotypes in cerebrospinal fluid (CSF) and peripheral blood.

Marked Variability of BK Virus Load Measurement Using Quantitative Real-Time PCR among Commonly Used Assays

ABSTRACT BK virus (BKV) is the infectious cause of polyomavirus-associated nephropathy. Screening guidelines for renal-transplant recipients define levels of viremia and viruria that are actionable for additional testing or intervention. However, standardized real-time PCR primers, probes, and standards are unavailable, and the extent of agreement among published assays is unknown. We compared seven TaqMan real-time PCR primer/probe sets (three designed at this institution, three described in the literature, and one purchased) in conjunction with two different standards to prospectively measure BKV titers in 251 urine specimens submitted to our clinical laboratory. We observed substantial disagreement among assays attributable both to features of primer and probe design and to choice of reference material. The most significant source of error among individual specimens was primer or probe mismatch due to subtype-associated polymorphisms, primarily among subtype III and IV isolates. In contrast, measurement of the most abundant subtypes (Ia, V, and VI) were typically uniform among all seven assays. Finally, we describe and validate a new clinical assay designed to reliably measure all subtypes encountered in our study population (Ia, Ic, III, IV, and VI). Consideration of available BKV sequence information in conjunction with details of subtype distribution allowed us to develop a redesigned assay with markedly improved performance. These results suggest that both accurate BKV measurement and the uniform application of BKV screening guidelines could be significantly improved by the use of standardized reference materials and PCR primers and probes.

Tolerance of Droplet-Digital PCR vs Real-Time Quantitative PCR to Inhibitory Substances

To the Editor:nnReal-time quantitative PCR (qPCR)1 is a rapid and sensitive method that forms the foundation for many clinical diagnostic tests. Droplet digital PCR (ddPCR) shares these qualities with qPCR, but owing to reaction partitioning, ddPCR is proposed to exhibit increased tolerance to interfering substances, making it an attractive alternative to qPCR for diagnostic applications (1, 2). The data to support this phenomenon and its mechanism, however, are currently lacking in the literature (3).nnHerein, we describe a series of experiments to compare the inhibition tolerance of laboratory-developed CMV qPCR and ddPCR (Bio-Rad Laboratories, QX-100) assays by introducing a panel of clinically relevant inhibitors (SDS, EDTA, and heparin) directly into the PCR reactions (4). Differences in the resulting inhibition curves and the half-maximal inhibitory concentrations (IC50) were then assessed. The laboratory-developed CMV qPCR is a double primer/probe Taqman assay that amplifies and detects the genes UL123 (IE)2 (enhances activation by IE2; interacts with basal transcriptional machinery and cellular transcription factor; disrupts ND10; involved in gene regulation [Human herpesvirus 5]) and UL55 (gB) (type 1 membrane protein; possible membrane fusogen; binds cell surface heparan sulphate; involved in cell entry; involved in cell-to-cell spread [Human herpesvirus 5]) with primers and probes previously described (5). The ddPCR assay uses the same primers and probes, with the dyes HEX replacing 6-FAM on the gB probe and BHQ-1 replacing TAMRA on both probes (Sigma-Aldrich).nnSDS, EDTA, and …

Clinical Correlates of Herpes Simplex Virus Viremia among Hospitalized Adults

BACKGROUNDnQuantification of herpes simplex virus (HSV) DNA in the peripheral blood is often used to evaluate patients suspected of having disseminated HSV infection. Few studies have examined the clinical correlates of HSV viremia among adults.nnnMETHODSnWe conducted a retrospective analysis of blood samples sent to a molecular virology reference laboratory at a university hospital for quantification of HSV DNA from October 2001 through June 2006. Medical records of patients with detectable HSV DNA were reviewed to abstract relevant clinical characteristics.nnnRESULTSnHSV DNA was detected in 38 (4%) of 951 samples from 29 patients, 19 of whom (66%) were >16 years old. Detailed medical records were available for review from 13 (68%) of 19 adult patients. Of the 10 patients whose HSV infection was typed, 6 (60%) had HSV-2, 3 (30%) had HSV-1, and 1 (10%) had evidence of HSV-1 and HSV-2 coinfection. All patients with viremia were treated with antiviral medications. The most common clinical findings were hepatitis (62%), fever (54%), central nervous system alterations (46%), skin lesions (38%), abdominal pain (31%), and sepsis (31%). Respiratory failure (23%) was uncommon. Patients with HSV viremia were observed to have a high mortality rate (6 of 10 immunocompromised and 1 of 3 immunocompetent individuals).nnnCONCLUSIONSnHSV viremia may be associated with a variety of signs and symptoms of morbidity in immunocompetent and immunocompromised hospitalized adults and is associated with high rates of mortality, although causality can be determined only by additional studies.

Evaluation of Real-Time PCR versus PCR with Liquid-Phase Hybridization for Detection of Enterovirus RNA in Cerebrospinal Fluid

ABSTRACT A LightCycler and two TaqMan real-time PCR assays were evaluated against an older PCR with liquid-phase hybridization method for the detection of enterovirus RNA in 74 patient samples. The two-step LightCycler and the two-step TaqMan formats correlated well with each other (r2 = 0.90) and were equally sensitive compared to the liquid-phase hybridization method, whereas the one-step recombinant Tth DNA polymerase format was rather insensitive, detecting enterovirus RNA in only about one-half of those patient samples previously positive by liquid-phase hybridization. The two-step TaqMan method was optimized utilizing 10 μl of cDNA and demonstrated the highest degree of analytical sensitivity among the methods evaluated in our study, being able to reproducibly quantify down to 510 copies of enteroviral RNA/ml of cerebrospinal fluid. This new assay can be performed in 4 h, is much less labor intensive, and showed less cross-reactivity with rhinovirus than the liquid-phase hybridization assay. Thus, the two-step TaqMan assay should prove useful in the diagnosis of enteroviral meningitis versus bacterial meningitis, thereby resulting in timely and appropriate clinical management that can amount to significant cost savings to the patient and health care system.

Commutability of the First World Health Organization International Standard for Human Cytomegalovirus

ABSTRACT Quantitative detection of cytomegalovirus (CMV) DNA has become a standard part of care for many groups of immunocompromised patients; recent development of the first WHO international standard for human CMV DNA has raised hopes of reducing interlaboratory variability of results. Commutability of reference material has been shown to be necessary if such material is to reduce variability among laboratories. Here we evaluated the commutability of the WHO standard using 10 different real-time quantitative CMV PCR assays run by eight different laboratories. Test panels, including aliquots of 50 patient samples (40 positive samples and 10 negative samples) and lyophilized CMV standard, were run, with each testing center using its own quantitative calibrators, reagents, and nucleic acid extraction methods. Commutability was assessed both on a pairwise basis and over the entire group of assays, using linear regression and correspondence analyses. Commutability of the WHO material differed among the tests that were evaluated, and these differences appeared to vary depending on the method of statistical analysis used and the cohort of assays included in the analysis. Depending on the methodology used, the WHO material showed poor or absent commutability with up to 50% of assays. Determination of commutability may require a multifaceted approach; the lack of commutability seen when using the WHO standard with several of the assays here suggests that further work is needed to bring us toward true consensus.

Clinical Utility of Droplet Digital PCR for Human Cytomegalovirus

ABSTRACT Human cytomegalovirus (CMV) has historically been the major infectious cause of morbidity and mortality among patients receiving hematopoietic cell or organ transplant. Standard care in a transplant setting involves frequent monitoring of CMV viral load over weeks to months to determine when antiviral treatment may be required. Quantitative PCR (qPCR) is the standard molecular diagnostic method for monitoring. Recently, digital PCR (dPCR) has shown promise in viral diagnostics, although current dPCR systems have lower throughput than qPCR systems. Here, we compare qPCR and droplet digital PCR (ddPCR) for CMV detection in patient plasma samples. Droplet digital PCR exhibits increased precision over qPCR at viral loads of ≥4 log10 with equivalent sensitivity. However, retrospective analysis of longitudinal samples from transplant patients with CMV viral loads near therapeutic thresholds did not provide evidence that the improved precision of ddPCR would be of clinical benefit. Given the throughput advantages of current qPCR systems, a widespread switch to dPCR for CMV monitoring would appear premature.

Rapid Detection Directly from Patient Serum Samples of Human Cytomegalovirus UL97 Mutations Conferring Ganciclovir Resistance

ABSTRACT Ganciclovir-resistant cytomegalovirus can cause disease and death in transplant recipients. We describe here a rapid PCR- and sequencing-based assay for ganciclovir resistance that can be performed in 1 to 2 working days directly from patient specimens, without the need for amplification of the virus by cell culture. An evaluation of 120 sequential samples submitted for clinical testing revealed a variety of silent and amino acid mutations.

The incidence of hepatocellular carcinoma in US white women with breast cancer after the introduction of tamoxifen in 1977

SummaryIt has been hypothesized that hepatocellular carcinoma might be a long-term adverse effect of tamoxifen therapy. Data from nine population-based cancer registries in the United States were used to investigate time trends in the incidence of hepatocellular carcinoma in white women previously diagnosed with invasive breast cancer during 1974–1987 and followed until 1989. Of particular interest were the rates after 1977, the year tamoxifen was licensed by the FDA. Compared to rates in all white women, no increased risk of hepatocellular carcinoma was found in women most likely to have received tamoxifen - those 50 years of age or more at diagnosis of breast cancer and diagnosed after 1977. These results suggest that tamoxifen does not cause a large increase in the incidence of hepatocellular carcinoma within the first decade after use. However, smaller and/or later increases in the risk for hepatocellular carcinoma are possible and warrant continued monitoring of women treated with tamoxifen.

Multiplex Real-Time Reverse Transcription-PCR Assay for Determination of Hepatitis C Virus Genotypes

ABSTRACT A variety of methods have been used to determine hepatitis C virus (HCV) genotypes. Because therapeutic decisions for chronic HCV-related hepatitis are made on the basis of genotype, it is important that genotype be accurately determined by clinical laboratories. Existing methods are often subjective, inaccurate, manual, time-consuming, and contamination prone. We therefore evaluated real-time reverse transcription-PCR (RT-PCR) reagents that have recently become commercially available (Abbott HCV Genotype ASR). The assay developed by our laboratory starts with purified RNA and can be performed in 4 to 5 h. An initial evaluation of 479 samples was done with a restriction fragment length polymorphism (RFLP) method and the RT-PCR assay, and discrepant samples were sequenced. An additional 1,200 samples were then tested, and data from all assays were used to evaluate the efficiency and specificity of each genotype-specific reaction. Good correlation between results by the two methods was seen. Discrepant samples included those indeterminate by the RT-PCR assay (n = 110) and a subset that were incorrectly called 2a by the RFLP method (n = 75). The real-time RT-PCR assay performed well with genotype 1, 2, and 3 samples. Inadequate numbers of samples were available to evaluate fully genotypes 4, 5, and 6. Analysis of each primer-probe set demonstrated that weak cross-reactive amplifications were common but usually did not interfere with the genotype determination. However, in about 1% of samples, two or more genotypes amplified at roughly equivalent amounts. Further studies are necessary to determine whether these mixed-genotype samples are true mixtures or a reflection of occasional cross-reactive amplifications.