Fully automated quantification of cytomegalovirus (CMV) in whole blood with the new sensitive Abbott RealTime CMV assay in the era of the CMV international standard

Prospective comparison of cytomegalovirus quantification in whole blood and plasma samples among hematopoietic stem cell transplant and kidney transplant recipients

BACKGROUND

Cytomegalovirus (CMV) induces multi-organ pathogenesis in hematopoietic stem cell transplant (HSCT) and kidney transplant (KT) recipients. Effective management involves systematic monitoring for CMV reactivation by quantitative real-time PCR, allowing timely preemptive intervention. However, the optimal blood compartment for CMV surveillance remains undetermined.

OBJECTIVE

The aim of the study was to compare the quantification of CMV DNA in paired plasma and whole blood samples.

STUDY DESIGN

From June and October 2022, we conducted a prospective study with 390 sets of paired plasma and whole blood specimens collected from 60 HSCT and 24 KT recipients. CMV DNA levels were compared between the cobas® CMV assay on the automated cobas® 6800 system for plasma and the reference assay, Abbott RealTime CMV assay on the m2000 RealTime platform for whole blood.

RESULTS

The sensitivity and specificity of CMV quantification in plasma using the cobas® CMV assay were 90.0 % (95 %CI: 81.5 to 95.9) and 94.8 % (95 %CI: 91.8 to 96.8), respectively, compared to whole blood quantification with the Abbott assay. The overall agreement between these two strategies was 0.89 (95 %CI: 0.86-0.91). In samples with quantifiable results, a correlation was observed between the two methods (R2 = 0.62, 95 %CI: 0.65-0.87, p < 0.0001). CMV loads were significantly higher in whole blood, with a mean bias of 0.42 log10 IU/mL (95 %CI: -0.32-1.15).

CONCLUSION

The cobas® CMV assay in plasma showed significant concordance with the Abbott RealTime CMV assay in whole blood, confirming the relevance of plasma samples for CMV monitoring in HSCT and KT recipients.

Performance Evaluation of the Fully Automated NeuMoDx RT-PCR Platform for the Quantification of CMV and EBV DNA in EDTA Plasma: Implications for Clinical Management and Establishment of a Conversion Formula

The NeuMoDx96 platform is a fully automated real-time PCR (RT-PCR) system. To provide continued testing quality with the introduction of new assays, the primary aim of this study was to evaluate the analytical and clinical performance of the NeuMoDx platform for the detection and quantification of CMV and EBV DNA in EDTA plasma. As no conversion from log₁₀ international units per milliliter to copies per milliliter was provided, the secondary aim was to calculate and establish a conversion factor for the output of results in copies per milliliter for CMV and EBV. Archived ETDA plasma samples (cytomegalovirus [CMV], n = 290; Ebstein-Barr virus [EBV], n = 254) were used to evaluate the analytical performance of the NeuMoDx96 platform against the routine real-time quantitative PCR (qPCR) assays. Additionally, the first WHO international standards (WHO-IS) for CMV (n = 70) and EBV (n = 72) were used for the calculation of the intra- and interassay variation. WHO-IS qualitative agreement between the assays was 100%. Intra-assay variability was low for both CMV assays (coefficient of variation [CV], phosphate-buffered saline [PBS], 3 log₁₀ IU/mL NeuMoDx, 3.67%; Abbott RealTime, CMV, 3.35%) and NeuMoDx EBV assay (CV, PBS, 3 log₁₀ IU/mL, 3.05%) but high for the Altona EBV assay (CV, PBS, 3 log₁₀ IU/mL, 26.13%). The overall qualitative concordance in clinical samples was 96.8% (270/279) for CMV and 96.7% (237/245) for EBV. The mean difference between the assays was -0.2 log₁₀ IU/mL (CMV) and -0.18 log₁₀ IU/mL (EBV). High qualitative concordance and a significant correlation of quantitative values for both assays make NeuMoDx CMV and EBV assays suitable for routine diagnostic testing. The new RT-PCR system and conversion formulas to report results in copies per milliliter are now applied in clinical routine testing. IMPORTANCE Clinical management of solid organ transplant (SOT) patients requires the careful monitoring of immunosuppression and viral infection or reactivation. qPCR is the gold standard for the detection and quantification of very small amounts of viral DNA and allows for an early assessment of viral load kinetics. The tested NeuMoDx 96 platform provides faster results than the previously used RT-PCR workflows for CMV (Abbott m2000 and RealTime CMV assay) and EBV (LightCycler 480 II, Roche high pure extraction, and Altona RealStar EBV assay) DNA detection. The implemented conversion formulas allow the continued reporting in clinically established copies per milliliter, important for long-term care of SOT patients.

Impact of CMV reactivation on relapse of acute myeloid leukemia after HCT is dependent on disease stage and ATG

The impact of CMV reactivation on hematologic relapse after HCT is modulated by AML stage (CR1 or advanced) and in vivo T cell depletion.

Following CMV reactivation, NRM was increased in CR1 patients without ATG, but not in patients with ATG or advanced disease stages.

Cytomegalovirus (CMV) reactivation is a frequent complication after allogeneic hematopoietic cell transplantation (HCT), whose impact on clinical outcome, in particular on leukemic relapse, is controversial. We retrospectively analyzed 687 HCT recipients with acute myeloid leukemia (AML) and ciclosporin-based immunosuppression to better understand the differential impact of CMV on transplant outcomes depending on AML disease stage and in vivo T cell depletion with antithymocyte globulin (ATG). Without ATG, CMV reactivation associated with significantly reduced relapse, yet its effect was more pronounced for advanced disease AML (P = .0002) than for patients in first complete remission (CR1, P = .0169). Depending on the disease stage, ATG exposure abrogated relapse protection following CMV reactivation in advanced stages (P = .796), while it inverted its effect into increased relapse for CR1 patients (P = .0428). CMV reactivation was associated with significantly increased nonrelapse mortality in CR1 patients without ATG (P = .0187) but not in those with advanced disease and ATG. Following CMV reactivation, only patients with advanced disease had significantly higher event-free survival rates as compared with patients without CMV. Overall, our data suggest that both ATG and disease stage modulate the impact of post-HCT CMV reactivation in opposite directions, revealing a level of complexity that warrants future studies regarding the interplay between antivirus and antitumor immunity.

Cytomegalovirus kinetics after hematopoietic cell transplantation reveal peak titers with differential impact on mortality, relapse and immune reconstitution

Even in the era of PCR-based monitoring, prophylaxis, and preemptive therapy, Cytomegalovirus (CMV) viremia remains a relevant cause of non-relapse mortality (NRM) after allogeneic hematopoietic cell transplantation (HCT). However, studies using binary analysis (presence/absence of CMV) reported contradicting data for NRM, overall survival and leukemia relapse. Here, we analyzed CMV replication kinetics in 11 508 whole blood PCR samples of 705 patients with HCT between 2012 and 2017. Using two independent models based on CMV peak titers and on the time point of first CMV reactivation, we stratified patients into risk cohorts. Each cohort had distinct cellular immune reconstitution profiles and differentiated for relevant clinical outcomes. Patients with high CMV peak titers had significantly reduced overall survival (HR 2.13, 95% CI 1.53-2.96; p < .0001), due to high NRM. Early impaired T cell reconstitution was a risk factor for high CMV peak titers, however relevant CMV viremia also related to boosted T cell reconstitution. Importantly, intermediate CMV peak titers associated with a significantly reduced relapse probability (HR 0.53, 95% CI 0.31-0.91; p = .022). In short, CMV kinetics models distinguished relevant clinical outcome cohorts beyond the R+ serostatus with distinct immune reconstitution patterns and resolve in part contradicting results of previous studies exclusively focused on the presence or absence of CMV.

Performance evaluation of the Roche cobas 6800 system for quantifying cytomegalovirus DNA in plasma and urine samples

INTRODUCTION

Cytomegalovirus (CMV) nucleic acid amplification testing is important for CMV infection diagnosis and management. CMV DNA is found in plasma and various other fluids, including urine. If CMV can be reliably detected in urine, it may be considered a non-invasive alternative to blood tests. The cobas 6800 system (Roche Diagnostics, Mannheim, Germany) is a Food and Drug Administration-approved testing platform for measuring CMV DNA in plasma.

OBJECTIVE

To evaluate the analytical performance of the cobas 6800 system and compare the clinical feasibility of CMV detection in plasma and urine samples.

STUDY DESIGN

Imprecision, linearity, limit of quantitation (LOQ), and cross-reactivity of the cobas 6800 system were assessed, and reference interval verification was performed. Plasma CMV DNA quantification was compared to CMV DNA values in urine samples obtained from 129 pediatric patients (<18 years of age) from March 2020 to May 2020 at a tertiary hospital.

RESULTS

The assay precision was within the acceptable range. Linearity was observed within the tested concentration range (2.36-6.33 log IU/mL) with a coefficient of determination of 0.9972. The LOQ was 34.5 IU/mL. The assay did not show cross-reactivity with 15 other viruses. Plasma and urine detection results were stratified into three categories: negative, <LOQ, and positive to analyze the degree of agreement with the results. The quadratic weighted kappa value was 0.623 (P = 0.000), showing substantial concurrence.

CONCLUSION

The cobas 6800 system offers good sensitivity, precision, and linearity and is suitable for monitoring CMV viral loads in the plasma and urine samples.

Reactivations of Latent Viral Infections Are Associated with an Increased Thr389 p70S6k Phosphorylation in Peripheral Lymphocytes of Renal Transplant Recipients

Reactivations of BK polyoma virus (BKPyV) and human cytomegalovirus (HCMV) frequently cause life- and graft-threatening complications after renal transplantation. Both viruses are dependent on the mTOR pathway for replication. In this study we investigated the association of viral replication with mTOR activity in peripheral lymphocytes of renal transplant recipients. A flow-cytometry based assay for the measurement of Thr389 p70S6k phosphorylation, a surrogate marker of the mTOR pathway was established. Forty-eight adult renal transplant recipients were recruited to measure p70S6k activity in their peripheral blood mononuclear cells. This data set in conjunction with information concerning previous replication of BKPyV and HCMV was examined for correlations. Episodes of BKPyV replication were significantly associated with increased p70S6k phosphorylation in CD4⁺ T lymphocytes (p = 0.0002) and CD19⁺ B lymphocytes (p = 0.0073). HCMV infection of patients with a high-risk HCMV constellation of donor and recipient (D+/R−) was associated with increased p70S6k phosphorylation in CD19⁺ B lymphocytes (p = 0.0325). These associations were found to be independent of the trough levels of the immunosuppressive drugs. Conclusion: P70S6k phosphorylation in peripheral lymphocytes is associated with BKPyV reactivations and to a lesser extent with HCMV infections in renal transplant recipients.

Human Cytomegalovirus-Encoded microRNAs Can Be Found in Saliva Samples from Renal Transplant Recipients

Human cytomegalovirus (HCMV) infections are common following renal transplantation and may have long-lasting effects. HCMV can be measured directly by viral DNA or indirectly via host immune responses. HCMV-encoded microRNA (miRNA) may alter the pathobiology of HCMV infections and contribute to the progression of HCMV disease. HCMV-encoded miRNAs can be detected in blood but have not been sought in saliva. We investigated saliva samples from 32 renal transplant recipients (RTR) and 12 seropositive healthy controls for whom immunological data was available. Five HCMV-encoded miRNAs (miR-UL112-5p, miR-US5-2-3p, miR-UL36, miR-US25-2-3p and miR-UL22A) were sought using primer probe assays. HCMV miRNA species were detected in saliva from 15 RTR and 3 healthy controls, with miR-US5-2-3p most commonly detected. The presence of HCMV miRNAs associated with increased T-cell responses to HCMV IE-1 in RTR, suggesting a link with frequent reactivations of HCMV.

Evaluation of pulmonary complications in patients undergoing allogenic stem cell transplantation

Background

Mature blood cells can be differentiated from hematopoietic stem cells; thus, the latter can play a crucial role in maintaining defense against different microorganisms. Thus, hematopoietic stem cell transplantation is one of the most important lines of immunotherapy. Major systemic complications may occur post transplantation and could be fatal. Pulmonary complications include infectious and non-infectious complications. The aim of this study was to detect the pulmonary complications in allogeneic stem cell transplantation patients.

Results

We studied 20 patients after transplantation of allogeneic stem cells with regular follow-up in outpatient clinic of hematology department of Alexandria Main University Hospital. All the studied patients were subjected to history taking, plain x-ray chest PA view, CT chest, complete blood count, serum creatinine, liver enzymes, and serum cytomegalovirus (CMV) detection by antibodies IgG and IgM. Regarding sputum sampling, 7 patients’ samples (35%) were obtained either spontaneously or by induction via hypertonic saline 3%. One patient (5%) had miniBAL done, while bronchoalveolar lavage using fiber optic bronchoscopy was done for 2 patients (10%). Samples could not be obtained from the remaining patients. Samples were analyzed for culture for bacteria, Pneumocystis jiroveci using immunofluorescence test, CMV PCR, fungal culture, and smear for acid fast bacilli (AFB). Among the examined patients, 2 patients (20%) had pulmonary bacterial infection including streptococcus and multidrug-resistant strain of Klebsiella, 3 patients (30%) had pulmonary candida infection, and one patient (10%) had positive result of pulmonary CMV of low count which was considered insignificant. None of our patients had positive results for pulmonary tuberculosis nor Pneumocystis jiroveci. Six patients (30%) had CMV in serum; 3 patients (15.8%) had manifested CMV reactivation. One patient (5%) of our patients had pulmonary graft versus host disease GVHD. One patient (5%) had died during our study course within 12 days post-transplantation due to ARDS followed by multiple organ failure.

Conclusion

The prevalence of pulmonary infectious complications after allogenic stem cell transplantation was 50% of all studied patients, while 5% of the studied patients presented with non-infectious pulmonary complications.

Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges

Rapid spread of coronavirus disease 2019 (COVID-19) is ravaging the globe. Since its first report in December 2019, COVID-19 cases have exploded to over 14 million as of July 2020, claiming more than 600,000 lives. Implementing fast and widespread diagnostic tests is paramount to contain COVID-19, given the current lack of an effective therapeutic or vaccine. This review focuses on a broad description of currently available diagnostic tests to detect either the virus (SARS-CoV-2) or virus-induced immune responses. We specifically explain the working mechanisms of these tests and compare their analytical performance. These analyses will assist in selecting most effective tests for a given application, for example, epidemiology or global pandemic research, population screening, hospital-based testing, home-based and point-of-care testing, and therapeutic trials. Finally, we lay out the shortcomings of certain tests and future needs.

Advances in Directly Amplifying Nucleic Acids from Complex Samples

Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.

Evaluation of the Abbott RealTime quantitative CMV and EBV assays using the maxCycle protocol in a laboratory automation context

Real-time PCR are often used for the diagnosis and monitoring of Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections in susceptible populations. In this context, we evaluated the analytical performances of the Abbott RealTime CMV/EBV maxCycle protocol automated on the m2000 platform (Abbott). It was compared to our routinely-used procedure consisting of a NucleoMag® DNA extraction automated on a STARlet platform followed by manually processed CMV and EBV quantitative real-time PCR (Diagenode). In this study, we showed that both EBV assays exhibited a similar sensitivity but with a better precision for the EBV Abbott RealTime assay. For the CMV performances, the Abbott assay was more sensitive and more precise than our routine method. The use of WHO International Standards also indicated a slight underestimation of the viral loads (-0.25 log₁₀ IU/mL and -0.21 log₁₀ IU/mL for CMV and EBV assays respectively) while these were rather overestimated with the Starlet/Diagenode method (0.48 log₁₀ IU/mL and 0.19 log₁₀ IU/mL for CMV and EBV assays respectively). These trends were confirmed using relevant whole-blood clinical samples and external quality controls. The workflows were also compared and we highlighted a significant technician hands-on time reduction (-63%) using the Abbott CMV/EBV maxCycle automated protocol.

Evaluation of four commercial extraction-quantification systems to monitor EBV or CMV viral load in whole blood

BACKGROUND

Measurement of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) viral loads is commonly used to monitor posttransplant patients. Two new systems (eMAG/eSTREAM and Versant/kPCR) have been recently commercialized.

OBJECTIVES

To evaluate the performance of four systems to quantify CMV and EBV in whole blood.

STUDY DESIGN

Three extraction and real-time PCR amplification systems: m2000SP/RT (M2000), eMAG/eSTREAM (EMAG), and Versant/kPCR (KPCR) were compared with our routine system Qiasymphony/RGQ (QS/RGQ). The 4 systems were tested using 3 dilutions in triplicate according to the WHO international standard (WHO-IS) for intra-assay reproducibility; 56 whole blood samples (24 patients, 4 follow-ups) for CMV and 45 samples (27 patients, 3 follow-ups) for EBV.

RESULTS

For CMV, the mean of the WHO-IS (expected value: 4.7 Log IU/ml) was: QS/RGQ=4.84, M2000=4.61, EMAG=4.33, and KPCR=4.79. One patient (10 samples) presented a major underquantification by QS/RGQ. Of the 46 remaining samples, 41 were quantified with QS/RGQ, 43 with M2000, 33 with EMAG and 24 with KPCR. For EBV, the mean of the WHO-IS was: QS/RGQ=4.70, M2000=4.61, EMAG=4.62, and KPCR=4.57. Among the 45 samples, 43 were quantified with QS/RGQ, 39 with M2000, 40 with EMAG and 32 with KPCR.

CONCLUSION

The results obtained with the WHO-IS were very good. The results of patients' samples were well correlated with the announced sensitivity of each system. The elevated threshold of the KPCR CMV assay may be problematic for the follow-up of highly immunocompromised patients who require early introduction of treatment.

Relationship of Ganciclovir Therapeutic Drug Monitoring with Clinical Efficacy and Patient Safety

The clinical utility of ganciclovir therapeutic drug monitoring (TDM) is unknown. We retrospectively analyzed adult patients treated for cytomegalovirus (CMV) infection with ganciclovir with TDM between 2005 and 2015. The primary outcome was an association between ganciclovir TDM and clinical efficacy endpoints within 30 days, defined by viral load and symptomatology. Secondary outcomes included safety endpoints, evaluated within 7 days of the last administered dose of ganciclovir. Of 175 patients evaluated, 82 patients with CMV infection were included in our analysis with a median (interquartile range) baseline CMV viral load of 5,500 (3,000 to 15,200) copies/ml. The majority achieved undetectable or reduced CMV viral load below the lower limit of quantification (74.4%) with improvement in symptomatology (70.7%) at 30 days. Among patients with detectable CMV viremia at 30 days, the viral load had declined to a median of 1,000 (1,000 to 3,090) copies/ml. We did not observe significant associations between the efficacy outcomes and ganciclovir trough (P = 0.20 and P = 0.20, respectively) or peak concentrations (P = 0.14 and P = 0.14, respectively). Similarly, there was no significant association between ganciclovir trough or peak concentrations and safety endpoints, including leukopenia (P = 0.48 and P = 0.69), neutropenia (P = 0.59 and P = 0.69), thrombocytopenia (P = 0.29 and P = 0.37), anemia (P = 0.51 and P = 0.35), nephrotoxicity (P = 0.41 and P = 0.57), and neurotoxicity (P = 0.22 and P = 0.48). We did not observe any associations between ganciclovir TDM and clinical efficacy or safety endpoints. Routine ganciclovir TDM may be of limited value. Future studies may be warranted to identify specific populations with unpredictable pharmacokinetic and pharmacodynamics profiles in whom ganciclovir TDM may be of benefit.

Prevalence and clinical characteristics of CMV coinfection among HIV infected individuals in Guinea-Bissau: a cross-sectional study

OBJECTIVES

To describe the prevalence of CMV in a cohort of HIV infected individuals in Guinea-Bissau, West Africa and to evaluate differences in patients' clinical characteristics associated with their CMV status.

METHODS

Newly diagnosed HIV infected adults were invited to participate in this cross-sectional study, from May until December 2015. Enrolled patients were interviewed and underwent a full physical examination focusing on CMV disease manifestations. Blood samples were analysed for CMV serology, QuantiFERON-CMV response and CMV DNA. Mortality follow-up were registered for one year after inclusion.

RESULTS

In total, 180 patients were enrolled. Anti-CMV IgG positivity was found in 100% (138/138) and 2.8% (4/138) were anti-CMV IgM positive. A positive QuantiFERON-CMV response was found in 85.7% (60/70) of the patients and 60.6% (83/137) had CMV viraemia. QuantiFERON-CMV response and detectable CMV DNA were associated with lower CD4 cell count, older age and upper gastrointestinal complaints. During one year of follow-up, the IRR for death among CMV DNA positive patients was 1.5 (P = 0.5).

CONCLUSIONS

CMV coinfection was detected among all enrolled patients and CMV viraemia was highly prevalent. Only age and upper gastrointestinal complaints were associated with the patients' CMV status.

Assessing the risk of CMV reactivation and reconstitution of antiviral immune response post bone marrow transplantation by the QuantiFERON-CMV-assay and real time PCR

BACKGROUND

CMV reactivation is a major cause of severe complications in allogeneic hematopoietic stem cell transplant (HSCT) recipients. The risk of CMV reactivation depends on the serostatus (+/-) of the donor (D) and recipient (R). The reconstitution of CMV-specific T-cell responses after transplantation is crucial for the control of CMV reactivation.

OBJECTIVES

The study aimed to determine the cellular immune status correlating with protection from high-level CMV viremia (>5000 copies/ml) and disease.

STUDY DESIGN

We monitored CMV-specific cellular immune responses in 9 high-risk (D-/R+), 14 intermediate risk (D+/R+) and 3 low risk individuals (D+/R-), and 8 CMV negative controls (D-/R-). Interferon- γ (IFN-γ) levels as a marker for the CD8+ T-cell response were determined by the QuantiFERON-CMV-assay and compared to viral loads determined by PCR.

RESULTS

Early CMV reactivation was detected in all high-risk and 13/14 intermediate risk individuals. High-level viremia was detected in 5/7 high and 7/14 intermediate risk patients. Reconstitution of the CMV-specific cellular immune response started from 3 months after transplantation and resulted in protection against CMV reactivation. Re-establishing of CMV-specific T-cell immune responses with IFN- γ levels >8.9 IU/ml is crucial for protection from high-level CMV viremia.

CONCLUSIONS

Monitoring of HSCT-recipients with the QuantiFERON-CMV-assay might be of great benefit to optimize antiviral treatment.

Comparison of two commercial quantitative PCR assays and correlation with the first WHO International Standard for human CMV

Comparability between CMV assays could be facilitated by the first WHO International Standard for human CMV (standard). Standard dilutions were submitted to nucleic acid extraction with Versant kPCR Molecular systems SP or MagNA Pure LC System followed by the kPCR PLX™ CMV DNA (kPCR) or the CMV R-gene™ assay (R-gene), respectively; 139 clinical specimens were tested. Both assays correlated well with the standard (R² > 0.96) and a matrix effect was observed. Quantitative results correlated reasonably between both assays for whole blood (R² = 0.79) and well for other specimen types (R² = 0.93). Quantification differences were within one log₁₀ of the averaged log₁₀ results for 25/27 blood specimens and for 32/33 other specimens. Calibration to the standard did not increase this percentage. In conclusion, results of both assays showed reasonable correlation with each other and good correlation with the standard. Calibration to the standard did not improve comparability of quantitative results.

HIV patients, healthy aging and transplant recipients can reveal the hidden footprints of CMV

Cytomegalovirus (CMV) is a β-herpesvirus. Latent infections are common in all populations. However age-associated increases in levels of CMV-reactive antibody are testament to repeated reactivations and periods of viral replication. CMV has been associated with several diseases of aging, including vasculopathy and neurocognitive impairment. These conditions occur at a younger age in persons with particularly high burdens of CMV - transplant recipients and people living with HIV. Here we define the "clinical footprints" as immunopathologies triggered by CMV that develop over many years. A high burden of CMV also drives accumulation of multifunctional terminally-differentiated αβ T-cells, a novel population of Vδ2^- γδ T-cells, and a population of CD56^lo NK cells lacking a key regulatory molecule. An understanding of these "immunological footprints" of CMV may reveal how they collectively promote the "clinical footprints" of the virus. This is explored here in transplant recipients, HIV patients and healthy aging.

Analytical and Clinical Validation of Six Commercial Middle East Respiratory Syndrome Coronavirus RNA Detection Kits Based on Real-Time Reverse-Transcription PCR

Background

During the 2015 outbreak of Middle East Respiratory Syndrome coronavirus (MERS-CoV), six different commercial MERS-CoV RNA detection kits based on real-time reverse-transcription polymerase chain reaction (rRT-PCR) were available in Korea. We performed analytical and clinical validations of these kits.

Methods

PowerChek (Kogene Biotech, Korea), DiaPlexQ (SolGent, Korea), Anyplex (Seegene, Korea), AccuPower (Bioneer, Korea), LightMix (Roche Molecular Diagnostics, Switzerland), and UltraFast kits (Nanobiosys, Korea) were evaluated. Limits of detection (LOD) with 95% probability values were estimated by testing 16 replicates of upstream of the envelope gene (upE) and open reading frame 1a (ORF1a) RNA transcripts. Specificity was estimated by using 28 nasopharyngeal swabs that were positive for other respiratory viruses. Clinical sensitivity was evaluated by using 18 lower respiratory specimens. The sensitivity test panel and the high inhibition panel were composed of nine specimens each, including eight and six specimens that were positive for MERS-CoV, respectively.

Results

The LODs for upE ranged from 21.88 to 263.03 copies/reaction, and those for ORF1a ranged from 6.92 to 128.82 copies/reaction. No cross-reactivity with other respiratory viruses was found. All six kits correctly identified 8 of 8 (100%) positive clinical specimens. Based on results from the high inhibition panel, PowerChek and AccuPower were the least sensitive to the presence of PCR inhibition.

Conclusions

The overall sensitivity and specificity of all six assay systems were sufficient for diagnosing MERS-CoV infection. However, the analytical sensitivity and detection ability in specimens with PCR inhibition could be improved with the use of appropriate internal controls.

Performance Evaluation of the Real-Q Cytomegalovirus (CMV) Quantification Kit Using Two Real-Time PCR Systems for Quantifying CMV DNA in Whole Blood

Standardized cytomegalovirus (CMV) DNA quantification is important for managing CMV disease. We evaluated the performance of the Real-Q CMV Quantification Kit (Real-Q assay; BioSewoom, Korea) using whole blood (WB), with nucleic acid extraction using MagNA Pure 96 (Roche Diagnostics, Germany). Real-time PCR was performed on two platforms: the 7500 Fast real-time PCR (7500 Fast; Applied Biosystems, USA) and CFX96 real-time PCR detection (CFX96; Bio-Rad, USA) systems. The WHO international standard, diluted with CMV-negative WB, was used to validate the analytical performance. We used 90 WB clinical samples for comparison with the artus CMV RG PCR kit (artus assay; Qiagen, Germany). Limits of detections (LODs) in 7500 Fast and CFX96 were 367 and 479 IU/mL, respectively. The assay was linear from the LOD to 10⁶ IU/mL (R² ≥0.9886). The conversion factors from copies to IU in 7500 Fast and CFX96 were 0.95 and 1.06, respectively. Compared with the artus assay, for values <1,000 copies/mL, 100% of the samples had a variation <0.7 log₁₀ copies/mL; >1,000 copies/mL, 73.3% and 80.6% of samples in 7500 Fast and CFX96, respectively, had <0.5 log₁₀ copies/mL. The Real-Q assay is useful for quantifying CMV in WB with the two real-time PCR platforms.

Automated quantification of Epstein-Barr Virus in whole blood of hematopoietic stem cell transplant patients using the Abbott m2000 system

BACKGROUND

Accurate quantification of Epstein-Barr virus (EBV) load in blood is essential for the management of post-transplant lymphoproliferative disorders. The automation of DNA extraction and amplification may improve accuracy and reproducibility. We evaluated the EBV PCR Kit V1 with fully automated DNA extraction and amplification on the m2000 system (Abbott assay).

METHODOLOGY

Conversion factor between copies and international units (IU), lower limit of quantification, imprecision and linearity were determined in a whole blood (WB) matrix. Results from 339 clinical WB specimens were compared with a home-brew real-time PCR assay used in our laboratory (in-house assay).

RESULTS

The conversion factor between copies and IU was 3.22 copies/IU. The lower limit of quantification (LLQ) was 1000 copies/mL. Intra- and inter-assay coefficients of variation were 3.1% and 7.9% respectively for samples with EBV load higher than the LLQ. The comparison between Abbott assay and in-house assay showed a good concordance (kappa = 0.77). Loads were higher with the Abbott assay (mean difference = 0.62 log10 copies/mL).

SIGNIFICANCE

The EBV PCR Kit V1 assay on the m2000 system provides a reliable and easy-to-use method for quantification of EBV DNA in WB.

Performance of a completely automated system for monitoring CMV DNA in plasma

BACKGROUND

Completely automated systems for monitoring CMV-DNA in plasma samples are now available.

OBJECTIVES

Evaluate analytical and clinical performances of the VERIS™/MDx System CMV Assay(®).

STUDY DESIGN

Analytical performance was assessed using quantified quality controls. Clinical performance was assessed by comparison with the COBAS(®) Ampliprep™/COBAS(®) Taqman CMV test using 169 plasma samples that had tested positive with the in-house technique in whole blood.

RESULTS

The specificity of the VERIS™/MDx System CMV Assay(®) was 99% [CI 95%: 97.7-100]. Intra-assay reproducibilities were 0.03, 0.04, 0.05 and 0.04 log10IU/ml (means 2.78, 3.70, 4.64 and 5.60 log10IU/ml) for expected values of 2.70, 3.70, 4.70 and 5.70 log10IU/ml. The inter-assay reproducibilities were 0.12 and 0.08 (means 6.30 and 2.85 log10IU/ml) for expected values of 6.28 and 2.80 log10IU/ml. The lower limit of detection was 14.6IU/ml, and the assay was linear from 2.34 to 5.58 log10IU/ml. The results for the positive samples were concordant (r=0.71, p<0.0001; slope of Deming regression 0.79 [CI 95%: 0.56-1.57] and y-intercept 0.79 [CI 95%: 0.63-0.95]). The VERIS™/MDx System CMV Assay(®) detected 18 more positive samples than did the COBAS(®) Ampliprep™/COBAS(®) Taqman CMV test and the mean virus load were higher (0.41 log10IU/ml). Patient monitoring on 68 samples collected from 17 immunosuppressed patients showed similar trends between the two assays. As secondary question, virus loads detected by the VERIS™/MDx System CMV Assay(®) were compared to those of the in-house procedure on whole blood. The results were similar between the two assays (-0.09 log10IU/ml) as were the patient monitoring trends.

CONCLUSION

The performances of the VERIS™/MDx System CMV Assay(®) facilitated its routine use in monitoring CMV-DNA loads in plasma samples.

New strategies against drug resistance to herpes simplex virus

Herpes simplex virus (HSV), a member of the Herpesviridae family, is a significant human pathogen that results in mucocutaneous lesions in the oral cavity or genital infections. Acyclovir (ACV) and related nucleoside analogues can successfully treat HSV infections, but the emergence of drug resistance to ACV has created a barrier for the treatment of HSV infections, especially in immunocompromised patients. There is an urgent need to explore new and effective tactics to circumvent drug resistance to HSV. This review summarises the current strategies in the development of new targets (the DNA helicase/primase (H/P) complex), new types of molecules (nature products) and new antiviral mechanisms (lethal mutagenesis of Janus-type nucleosides) to fight the drug resistance of HSV.

Commutability of Cytomegalovirus WHO International Standard in Different Matrices

Commutability of quantitative standards allows patient results to be compared across molecular diagnostic methods and laboratories. This is critical to establishing quantitative thresholds for use in clinical decision-making. A matrix effect associated with the 1st cytomegalovirus (CMV) WHO international standard (IS) was identified using the Abbott RealTime CMV assay. A commutability study was performed to compare the CMV WHO IS and patient specimens diluted in plasma and whole blood. Patient specimens showed similar CMV DNA quantitation values regardless of the diluent or extraction procedure used. The CMV WHO IS, on the other hand, exhibited a matrix effect. The CMV concentration reported for the WHO IS diluted in plasma was within the 95% prediction interval established with patient samples. In contrast, the reported DNA concentration of the CMV WHO IS diluted in whole blood was reduced approximately 0.4 log copies/ml, and values fell outside the 95% prediction interval. Calibrating the assay by using the CMV WHO IS diluted in whole blood would introduce a bias for CMV whole-blood quantitation; samples would be reported as having higher measured concentrations, by approximately 0.4 log IU/ml. Based on the commutability study with patient samples, the RealTime CMV assay was standardized based on the CMV WHO IS diluted in plasma. A revision of the instructions for use of the CMV WHO IS should be considered to alert users of the potential impact from the diluent matrix. The identification of a matrix effect with the CMV WHO IS underscores the importance of assessing commutability of the IS in order to achieve consistent results across methods.

Response to antiviral therapy in haematopoietic stem cell transplant recipients with cytomegalovirus (CMV) reactivation according to the donor CMV serological status

Pre-emptive antiviral treatment efficiently prevents occurrence of cytomegalovirus (CMV) disease in allogeneic stem cell transplant recipients. However, successive treatment courses can be necessary. The current study was aimed at determining factors that could influence the response to antiviral treatment, in particular the donor CMV serostatus. A total of 147 consecutive CMV-seropositive recipients (R+) were included and prospectively monitored for 6 months after transplantation. Reactivation of CMV occurred in 111 patients, 61 of 78 with a CMV-positive donor (D+) and in 50 of 69 with a CMV-negative donor (D-) (p 0.45). Baseline viral loads and initial viral doubling times did not differ between D+/R+ and D-/R+. Fifteen D+/R+ and four D-/R+ had self-resolving CMV infections. A total of 92 patients received antiviral treatment and 81 (88%) had a significant decrease in CMV load under therapy. Repeated CMV episodes were observed in 67% of those and were significantly more frequent in D-/R+ than in D+/R+ (p <0001). Half-life of CMV under treatment was significantly longer in D-/R+ than in D+/R+. Treatment failure observed in eight recipients was associated with low leucocyte count at reactivation onset, and was significantly more frequent in D-/R+ (six patients) than in D+/R+ (two patients) (p <0.0001). CMV strains resistant to antivirals were found in two D-/R+. Donor CMV serostatus influenced neither CMV reactivation occurrence nor the kinetics of CMV DNA load in the early phase of CMV replication but had a significant impact on response to antiviral therapy. Virological drug-resistance remained rare.

Therapeutic strategies for cytomegalovirus in allogeneic hematopoietic cell transplantation

Cytomegalovirus (CMV) remains a major cause of morbidity and mortality in allogeneic hematopoietic cell transplantation. Advances in surveillance of cytomegalovirus reactivation using sensitive techniques and a preemptive strategy to treat virus reactivation has reduced incidence of cytomegalovirus end organ disease. However, severe immunosuppression associated with extensive T-cell depletion resulting from graft-versus-host disease prevention for cases of mismatched or others such as haploidentical allogeneic hematopoietic cell transplantation (allo-HCT) and graft-versus-host disease therapy itself create clinical challenges in managing cytomegalovirus infection. Novel anticytomegalovirus therapies including newer pharmacologic interventions, vaccines, and adoptive cellular therapies to restore anticytomegalovirus immunity appear promising and are expected to continue to shape our treatment armamentarium. Eradication of CMV disease altogether, rather than simply suppressing viremia, should be the ultimate desirable goal.

Assessing assay agreement estimation for multiple left-censored data: a multiple imputation approach

Agreement between two assays is usually based on the concordance correlation coefficient (CCC), estimated from the means, standard deviations, and correlation coefficient of these assays. However, such data will often suffer from left-censoring because of lower limits of detection of these assays. To handle such data, we propose to extend a multiple imputation approach by chained equations (MICE) developed in a close setting of one left-censored assay. The performance of this two-step approach is compared with that of a previously published maximum likelihood estimation through a simulation study. Results show close estimates of the CCC by both methods, although the coverage is improved by our MICE proposal. An application to cytomegalovirus quantification data is provided.

Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses

Nucleic acid-based tests for infectious diseases currently used in the clinical laboratory and in point-of-care devices are diverse. Measurement challenges associated with standardization of quantitative viral load testing are discussed in relation to human cytomegalovirus, BK virus, and Epstein-Barr virus, while the importance of defining the performance of qualitative methods is illustrated with Mycobacterium tuberculosis and influenza virus. The development of certified reference materials whose values are traceable to higher-order standards and reference measurement procedures, using, for instance, digital PCR, will further contribute to the understanding of analytical performance characteristics and promote clinical data comparability.

Favorable impact of natural killer cell reconstitution on chronic graft-versus-host disease and cytomegalovirus reactivation after allogeneic hematopoietic stem cell transplantation

Natural killer cells are the first lymphocyte subset to reconstitute, and play a major role in early immunity after allogeneic hematopoietic stem cell transplantation. Cells expressing the activating receptor NKG2C seem crucial in the resolution of cytomegalovirus episodes, even in the absence of T cells. We prospectively investigated natural killer-cell reconstitution in a cohort of 439 adult recipients who underwent non-T-cell-depleted allogeneic hematopoietic stem cell transplantation between 2005 and 2012. Freshly collected blood samples were analyzed 3, 6, 12 and 24 months after transplantation. Data were studied with respect to conditioning regimen, source of stem cells, underlying disease, occurrence of graft-versus-host disease, and profiles of cytomegalovirus reactivation. In multivariate analysis we found that the absolute numbers of CD56(bright) natural killer cells at month 3 were significantly higher after myeloablative conditioning than after reduced intensity conditioning. Acute graft-versus-host disease impaired reconstitution of total and CD56(dim) natural killer cells at month 3. In contrast, high natural killer cell count at month 3 was associated with a lower incidence of chronic graft-versus-host disease, independently of a previous episode of acute graft-versus-host disease and stem cell source. NKG2C(+)CD56(dim) and total natural killer cell counts at month 3 were lower in patients with reactivation of cytomegalovirus between month 0 and month 3, but expanded greatly afterwards. These cells were also less numerous in patients who experienced later cytomegalovirus reactivation between month 3 and month 6. Our results advocate a direct role of NKG2C-expressing natural killer cells in the early control of cytomegalovirus reactivation after allogeneic hematopoietic stem cell transplantation.

Quantification of cytomegalovirus viral load

Cytomegalovirus (CMV), a member of the Herpesviridae family, is worldwide distributed. After the primary infection, CMV induces a latent infection with possible reactivation(s). It is responsible for severe to life-threatening diseases in immunocompromised patients and in foetuses and newborns of infected mothers. For monitoring CMV load, classical techniques based on rapid culture or pp65 antigenemia are progressively replaced by quantitative nuclear acid tests (QNAT), easier to implement and standardize. A large variety of QNAT are available from laboratory-developed assays to fully-automated commercial tests. The indications of CMV quantification include CMV infection during pregnancy and in newborns, and viral surveillance of grafted and non-grafted immunocompromised patients, patients with bowel inflammatory diseases and those hospitalised in intensive care unit. A close cooperation between virologists and clinicians is essential for optimizing the benefit of CMV DNA monitoring.