Quantitation of CMV by real-time PCR in transfusable RBC units

BACKGROUND: CMV is one of the most significant pathogens infecting immunocompromised individuals. CMV is transmissible through transfusion of blood components. The goal of this study was to measure CMV levels in RBC units using a sensitive and quantitative DNA amplification assay. STUDY DESIGN AND METHODS: An assay to measure CMV load was developed by using real-time PCR to target the major immediate early viral gene. A probe (TaqMan, Applied Biosystems) was used to confirm product specificity and to permit quantitation of CMV in blood samples on a sequence detection system (ABI Prism 7700, Applied Biosystems). RESULTS: The assay was shown to be accurate, linear, and sensitive to as few as five copies of CMV DNA per PCR. The assay was applied to aliquots of RBC units from 203 healthy donors, 110 of whom were seropositive for CMV. CMV DNA was not detected in any of the 203 RBC samples. CONCLUSION: The findings statistically imply that at least 98.5 percent of RBC units have a CMV load of less than 250 copies per mL. Future clinical studies on larger numbers of units are required to determine the utility of real-time PCR in evaluating the risk of CMV transmission and in confirming the efficacy of WBC reduction.     

Comparison of 2 highly automated nucleic acid extraction systems for quantitation of human cytomegalovirus in whole blood

The aim of the study was to evaluate analytical performances of the COBAS Ampliprep and to compare extraction from whole blood on the COBAS Ampliprep and on the MagNA Pure instruments (Roche Diagnostics, Mannheim, Germany) for quantifying human cytomegalovirus (HCMV) DNA with real-time polymerase chain reaction (PCR). The limit of detection using the COBAS Ampliprep was 10 copies/run (150 copies/mL, i.e., 2.20 log(10) copies/mL). Quantitation of HCMV-DNA was linear from 3.0 to 6.0 log(10) copies/mL. The intra-assay variations ranged from 11.1 % to 0.4 % and interassay variation was 11.3 %. A total of 107 samples were tested using both extraction systems. Only 3 samples gave discrepant results. Correlation between HCMV virus loads was good (r = 0.73) (P < 0.001). Mean virus load was lower (-0.49 log(10) copies/mL) with COBAS Ampliprep than with MagNA Pure extraction system. Both MagNA Pure and COBAS Ampliprep provide reliable and high-throughput platforms for real-time PCR HCMV quantitation of DNA extracted from whole blood.     

Significance of qualitative polymerase chain reaction combined with quantitation of viral load in the diagnosis and follow-up of cytomegalovirus infection after solid-organ transplantation

Quantitative PCR was evaluated in the monitoring of patients with ongoing posttransplantation cytomegalovirus (CMV) infection and antiviral therapy, compared to leukoDNAemia and serology. From January 1998 until May 1999, 61 patients were followed up weekly during 3 months after transplantation by a qualitative PCR. The quantitative PCR was performed on plasma samples from 21 selected patients, of whom 12 had a primary infection and 9 a reactivation or reinfection. Analysis of the viral load differences showed that the viral loads in patients with a primary infection were significantly higher than viral loads in patients with a reactivation (p < 0.01). Based on the results of our study, we can state that qualitative PCR is a good marker for initiating preemptive therapy. In addition, viral quantitation is clinically useful for accurate diagnosis of established CMV disease, and monitoring of antiviral therapy.     

Prevalence of Cytomegalovirus DNA in Cord Blood and Voided Urine Obtained from Pregnant Women at the End of Pregnancy

Objective

This study was undertaken to determine the prevalence of congenital cytomegalovirus (CMV) infection in pregnant women at the end of pregnancy in Kuwait using cord blood and maternal urine.

Subjects and Methods

Urine samples were collected prior to childbirth, and cord blood was collected immediately after delivery from 983 women. Anti-CMV IgG and IgM antibodies were determined using ELISA; CMV DNA was detected using nested PCR, and viral load was calculated using real-time PCR. CMV concentration in samples was categorized as low when the viral load ≤10³ copies/µl, intermediate when the viral load = 10³−10⁴ copies/µl, and high when the viral load >10⁴ copies/µl. The cord blood serology outcome was compared to cord blood PCR, cord blood viral load, maternal urine PCR and viral load analyses.

Results

Serology showed that of the 983 cord blood samples, 89 (9%) were positive for anti-CMV IgM antibodies; PCR test showed 44 (4.5%) contained CMV DNA, and there was a high viral load in all. Maternal urine PCR showed that 9 (10.11%) women had CMV DNA, and there was a high viral load in 7 (78%). The kappa test for measures of agreement showed a reasonable agreement (0.45) between cord blood PCR and urine PCR.

Conclusion

This study showed that CMV infection in the cord blood sera of pregnant women is common in Kuwait and highlights the need for more clinically based studies to follow up newborns with congenital CMV infection.Key Words: Active cytomegalovirus infection, Cord blood, Maternal urine, Polymerase chain reaction, Viral load     

Cytomegalovirus gB genotype and clinical features in Chinese infants with congenital infections

OBJECTIVE: To investigate cytomegalovirus (CMV) glycoprotein B (gB) genotypes and clinical features in Chinese infants with congenital infections. METHODS: Urine samples were obtained from 79 infants with human CMV infection confirmed by quantitative fluorescence polymerase chain reaction (PCR). A fragment of the gB gene was amplified by nested PCR. CMV gB genotyping was carried out by restriction fragment length polymorphism, and 24 samples of the amplified DNA fragments were verified by DNA sequencing. RESULTS: The levels of CMV DNA in symptomatic and asymptomatic infants were 2.95 x 10(5) and 4.5 x 10(3) copies/ml, respectively, with a significant difference (p < 0.001). In all these cases, the most prevalent genotype was gB1 (50.63%), followed by gB3 (21.52%), gB2 (17.72%), and coinfection (10.13%); gB4 was not found. Moreover, gB1 was more prevalent in infants with liver damage (22/32) than in other symptomatic infants without liver damage (8/22, p = 0.019) or asymptomatic infants (10/25, p = 0.030). The homology of CMV gB in the 24 strains amplified as compared with the sequences of prototype strains in GenBank ranged from 97.06 to 99.64%. CONCLUSIONS: The restriction fragment length polymorphism analysis of CMV gB genotypes was definite and reliable. The gB1 genotype is the most prevalent in Chinese infants with congenital CMV disease, especially in those with liver damage, followed by genotypes gB3, gB2, and gB4.     

Comparison of QIAsymphony automated and QIAamp manual DNA extraction systems for measuring Epstein-Barr virus DNA load in whole blood using real-time PCR

Automated and manual extraction systems have been used with real-time PCR for quantification of Epstein-Barr virus [human herpesvirus 4 (HHV-4)] DNA in whole blood, but few studies have evaluated relative performances. In the present study, the automated QIAsymphony and manual QIAamp extraction systems (Qiagen, Valencia, CA) were assessed using paired aliquots derived from clinical whole-blood specimens and an in-house, real-time PCR assay. The detection limits using the QIAsymphony and QIAamp systems were similar (270 and 560 copies/mL, respectively). For samples estimated as having ≥10,000 copies/mL, the intrarun and interrun variations were significantly lower using QIAsymphony (10.0% and 6.8%, respectively), compared with QIAamp (18.6% and 15.2%, respectively); for samples having ≤1000 copies/mL, the two variations ranged from 27.9% to 43.9% and were not significantly different between the two systems. Among 68 paired clinical samples, 48 pairs yielded viral loads ≥1000 copies/mL under both extraction systems. Although the logarithmic linear correlation from these positive samples was high (r(2) = 0.957), the values obtained using QIAsymphony were on average 0.2 log copies/mL higher than those obtained using QIAamp. Thus, the QIAsymphony and QIAamp systems provide similar EBV DNA load values in whole blood.     

基于ddPCR技术分析EB病毒载量特征及与qPCR技术的比较研究

目的解决临床工作中应用实时荧光定量PCR(qPCR)方法检测EB病毒(EBV)载量与临床诊断不符的问题,探讨微滴式数字PCR(ddPCR)和qPCR方法检测EBV载量的能力并为临床提供可能的解决方案。方法收集510例疑似EBV感染相关疾病患者血浆标本,采用ddPCR和qPCR两种方法测定同一血浆标本的EBV-DNA载量。结果 EBV感染人群中,EBV-DNA载量较其他地区低,载量中位数仅360copies/mL,其中初诊未治鼻咽癌患者中位病毒载量为4 590copies/mL,治疗后鼻咽癌患者中位病毒载量下降为430copies/mL,免疫力低下者中位病毒载量为130copies/mL,而淋巴瘤患者中位病毒载量为840copies/mL;qPCR检测EBV感染以400copies/mL为界值,高于400copies/mL时,ddPCR与qPCR的EBV-DNA测定水平值呈中度相关(r=0.533,P<0.05),低于400copies/mL时,ddPCR与qPCR的EBV-DNA测定水平值呈弱相关(r=0.299 5,P<0.05);以ddPCR为标准,qPCR检测EBV-DNA的灵敏度仅为0.317,以ddPCR检测结果为标准,构建qPCR的受试者工作特征曲线下面积为0.871,此时临界值(qPCR)为10copies/mL,灵敏度为0.824,特异度为0.780。结论采用ddPCR方法或优化qPCR的临界值去检测EBV-DNA载量更能为临床诊断EBV感染提供有利支持。     

Comparison of quantitative competitive polymerase chain reaction-enzyme-linked immunosorbent assay with LightCycler-based polymerase chain reaction for measuring cytomegalovirus DNA in patients after hematopoietic stem cell transplantation

Development of highly sensitive quantitative assays for cytomegalovirus (CMV) DNA detection is crucial for identification of immunodeficient patients at high risk of CMV disease. We designed 2 internally controlled competitive quantitative assays, enzyme-linked immunosorbent assay (ELISA)-based and real-time polymerase chain reaction (PCR) tests, using amplification of the same segment of the CMV genome. The aim of this study was to compare sensitivity, specificity, and laboratory performance characteristics of these assays. In both assays, a 159-bp segment of UL83 gene was amplified. External and internal controls were constructed by cloning the amplification product and heterogenous DNA segment flanked by target sequences for CMV-derived primers into bacterial plasmids, respectively. Real-time PCR was performed on LightCycler (Roche Diagnostics, Mannheim, Germany), and amplicons were detected using fluorescence resonance energy transfer probes. Alternatively, PCR products were labeled by digoxigenin, hybridized to immobilized probes, and detected by ELISA. The assays were tested on genomic DNA isolated from laboratory strains of CMV, QCMD control panel, and CMV DNA-positive peripheral blood DNA samples from hematopoietic stem cell transplant recipients, previously characterized by pp65 antigenemia and qualitative nested PCR. Real-time and ELISA-based PCR assays showed a linear course of 1-10(8) and 10-10(5) copies of CMV DNA per reaction, respectively. When compared with ELISA-based PCR, real-time PCR showed superiority in inter- and intra-assay reproducibility. Both assays were highly specific in detecting CMV DNA. No difference in amplification efficiency of internal or external standards and wild-type CMV DNA was found. The assays exhibited 83% concordance in CMV DNA detection from clinical samples, all discrepant samples having low CMV DNA copy numbers. There was a good correlation between viral DNA loads measured by the 2 assays. Statistically significant correlation was observed between the numbers of CMV DNA copies and pp65-positive leukocytes in the samples tested. Both variants of competitive PCR are adequately sensitive to be used for CMV DNA quantitation in clinical samples. LightCycler PCR, having superior performance characteristics and being less time-consuming, seems to be more suitable for routine diagnosis.     

实时荧光定量PCR监测乙肝抗病毒治疗后部分肝功指标的研究

目的筛选乙肝抗病毒治疗监控新指标,为临床提供更多的信息,满足临床需要。方法对临床确诊的87例慢性乙肝患者使用罗氏Lightcycler实时荧光定量PCR仪检测其血清病毒拷贝数,并以乙肝病毒载量为标准,分为高、中、低组进行研究;用速率法和免疫比浊法借助日立7600型全自动生化分析仪检测患者血清腺苷脱氨酶（adenosinedeaminase,ADA）、前清蛋白（prealbumin,PA）、a—L-岩藻糖苷酶（alpha fucosidase,AFU）、总胆汁酸（total bile acid,TBA）。结果使用实时荧光定量PCR仪检测慢性乙肝患者血清中的病毒拷贝数,据此可将患者血清HBV DNA检测结果分为A、B、C组,A组：10^3～10^4copies／mL;B组：10^5～10^6 eopies／mL;C组：〉10^7copies／mL;分别检测ADA、PA、TBA、AFU指标,结果显示：每组ADA、PA、TBA、AFU指标与健康对照组间比较均有统计学意义（P〈0．01或P〈0．05）,发现B组与A组、C组间比较PA水平显著下降（P〈0．01）,TBA指标显著升高（P〈0．01）,其余组间比较差异无统计学意义（P〉0．05）。结论ADA、PA、TBA、AFU指标检测可作为慢性乙肝患者抗病毒治疗的敏感指标,尤其B组患者通过ADA、PA、TBA、AFU联合检测,将有助于临床诊治。     

Application of real-time PCR for determination of antiviral drug susceptibility of herpes simplex virus

A quantitative real-time PCR (TaqMan) assay was developed for determination of antiviral drug susceptibility of herpes simplex virus (HSV). After short-time culture of the virus, the antiviral drug susceptibility of HSV isolates for acyclovir (ACV) was determined by measuring the reduction of the HSV type 1 (HSV-1) DNA levels in culture supernatants using real-time PCR. The 50% inhibitory concentration was reported as the concentration of antiviral drug that reduced the number of HSV-1 DNA copies by 50%. A total of 15 well-characterized ACV-sensitive or -resistant strains and clinical isolates were used for assay evaluation. The new assay with real-time PCR readout permitted rapid (3 days), objective, and reproducible determination of HSV-1 drug susceptibilities with no need for stringent control of initial multiplicity of infection. Furthermore, the real-time PCR assay results showed good correlation (r = 0.86) with those for the plaque reduction assay. In conclusion, the real-time PCR assay described here is a suitable quantitative method for determination of antiviral susceptibility of HSV-1, amenable for use in the routine diagnostic virology laboratory.     

Early detection of plasma cytomegalovirus DNA by real-time PCR after allogeneic hematopoietic stem cell transplantation

Cytomegalovirus (CMV) infection is an important cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Therefore, preemptive ganciclovir therapy based on early detection of CMV reactivation is widely used to prevent CMV disease. Real-time polymerase chain reaction (PCR) has been widely used for monitoring CMV reactivation as well as the antigenemia assay that detects CMV structural phosphoprotein with a molecular weight of 65,000 (pp65). We developed a real-time PCR assay system for CMV based on a double-stranded DNA-specific dye, SYBR Green I, and quantified DNA, which was extracted automatically from plasma. This real-time PCR assay and the pp65 antigenemia assay were compared in parallel with 357 blood samples obtained from 64 patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT). Real-time PCR assay results correlated with those of the pp65 antigenemia assay (p < 0.0001). It is noteworthy that the detection of CMV DNA by PCR preceded the first positive antigenemia by 14 days. In this study, 10 of 64 patients developed CMV disease. The antigenemia assay detected CMV reactivation earlier than the development of CMV disease only in four of 10 patients. In contrast, our real-time PCR detected CMV-DNA before the development of CMV diseases in eight of 10 patients. The real-time PCR with SYBR Green I as a detection signal is simple and readily performed, and may be a useful system for early detection of CMV reactivation after allo-HSCT.     

两种HBV DNA检测试剂的比较

目的 分析两种试剂在HBV DNA定量检测中的相关性,评价其在不同病毒载量时的检测性能.方法 用人AB型血清将WHO第2代HBV DNA国际标准品(编号:97/750)配制成不同浓度的10份样本,10份样本的浓度分别为1×106、5×106、1×105、5×104、1×104、5×103、1×103、5×102、1×102、1×101 kIU/L.采用深圳匹基生物工程股份有限公司生产的HBV DNA荧光定量PCR检测试剂(PG试剂)和美国罗氏公司生产的定量PCR试剂(罗氏试剂)检测78份HBV感染者血清、30份健康献血者血清和10份不同浓度范围的WHO标准品中HBV DNA含量.对两种试剂检测HBV DNA结果相关性进行分析;对试剂在不同病毒载量时的检测性能进行评价;并对漏检情况进行分析.两种试剂每批检测均设有阴性质控、弱阳性质控和强阳性质控.结果 两种试剂对WHO HBV DNA标准物质稀释血清均能正确检出,罗氏试剂能检出最高稀释度样本浓度为2.00(kIU/L,lg),PG试剂能检出最高稀释度样本浓度为3.00(kIU/L,lg);两种试剂检测结果存在线性相关(R2=0.938 7,P<0.01),罗氏试剂检测上限与理论值相符,大于检测上限的标本经稀释重复测定,罗氏试剂检测结果[(8.35±0.20)kIU/L,lg]高于PG试剂检测结果[(7.73±0.42)klU/L,lg],差异有统计学意义(t=3.776,P<0.05).两种试剂检测108份血清标本中HBV DNA含量,罗氏试剂检测值[(5.88±1.64)kIU/L,lg]高于PG试剂检测值[(5.25±1.55)kIU/L,lg],差异有统计学意义(t=12.297,P<0.01);检测高HBV病毒载量[(>5.00～≤7.00)kIU/L,lg和(>7.00～≤9.00)kIU/L,lg]组,两种试剂的相关性较高(R2分别为0.779 7、0.603 7,P均<0.01);对低HBV病毒载量(>3.00～≤5.00 kIU/L,lg)组,两种试剂的相关性较低(R2=0.417 3,P<0.01);病毒载量为>3.00～≤4.00 kIU/L,lg组,PG试剂的漏检率为33.3%(5/15);病毒载量为>1.08～≤3.00 kIU/L,lg组,PG试剂未检出.结论 PG试剂与岁氏试剂检测结果虽存在一定差距,但相关性较好.两种试剂低病毒载量标本的相关性要低于高病毒载量标本,PG试剂检测HBV DNA的线性范围较窄.

Abstract：

Objective To evaluate clinical significance of two real-time fluorescence quantitative PCR kits for quantitative detection of HBV DNA and detection performance at different viral load levels.Methods A series of calibrators with different concentrations(1×106,5×105,1×105,5×104,1×104,5×103,1×103,5×102,1×102,1×101 kIU/L) were prepared with AB-type sera using the second generation WHO international standard (NIBSC code:97/750). HBV viral load in the sera of 78 patients,30 healthy blood donors and 10 calibrators were detected by real-time fluorescence quantitative PCR HBV DNA test kit from PIJI Bio-Technical Development Company Ltd (PG kit) and Cobas AmpliPrep/Cobas TaqMan HBV test kit. The correlation of the two methods was evaluated, and the performance of the two kits different viral load levels was evaluated. The false negative rate was analyzed. Negative control, low positive control and high positive control were included in every batch. Results Both two kits showed the correct results for the 10 specimens from the WHO international standards. The lowest detection limit of HBV DNA for Roche Cobas AmpliPrep/Cobas TaqMan HBV test and PG kit were 2.00 (kIU/L, lg) and 3.00 (kIU/L,lg) ,respectively. There was linear correlation between the results from Roche Cobas AmpliPrep/Cobas TaqMan HBV test and PG kit ( R2=0.938 7, P < 0.01 ), the upper limit of Roche kit had coincided with theoretical value. The samples with HBV DNA level above the upper limit of detection were diluted and retested to obtain the precise result. The result form Roche Cobas AmpliPrep/Cabas TaqMan HBV test [(8.35±0.20) kIU/L, lg] was higher than that from PG kit [(7.73±0.42 ) kIU/L, lg] (t=3. 776, P <0.05) . The detection of 108 serum samples showed that the level of HBV DNA detected by Roche Cobas AmpliPrep/Cobas TaqMan HBV test [(5.88±1.64) kIU/L, lg] was higher than that by PG kit [(5.25±1.55 kIU/L,lg] (t=12. 297 ,P <0.01 ). The correlation coefficients were high in samples with high HBV viral load[HBV DNA(>5.00 and≤7.00) kIU/L,Ig,R2=0. 779 7, P <0.01 ;HBV DNA( >7.00 ands≤9.00) kIU/L,lg,R2=0.603 7, P <0.01]. The correlation coefficient was low in samples with low HBV viral load[HBV DNA ( > 3.00 and≤5.00) kIU/L, lg, R2=0. 417 3, P <0.01 )]. When HBV DNA ( >3.00 and≤4.00) kIU/L,lg,the false negative rate was 33.3% (5/15). When HBV DNA ( > 1.08and≤3.00) kIU/L,lg,none of positive samples was detected with PG kit. Conclusions PG kit is not as good as Cobas AmpliPrep/Cobas TaqMan HBV test . The linear correlation between the results from the two kits is good. The correlation between the results detected with PG kit and Cobas AmpliPrep/Cobas TaqMan HBV test is higher in the high viral load groups than in the low viral load group. It is suggested that PG kit had a narrower linear range.     

建立一种PCR产物直接测序检测HBVYMDD突变的方法

目的 建立检测HBV YMDD变异的PCR产物直接测序法,并与传统实时荧光PCR检测YMDD突变的结果进行比较分析.方法 选取103份慢性乙型肝炎患者血清标本,提取血清HBVDNA.用实时荧光PCR检测YMDD突变;用巢式pcR扩增HBV逆转录酶基因,对PCR产物进行DNA双向测序,NTI软件比对结果.采用Kappa一致性检验对DNA测序法检测的rt204位点突变与实时荧光PCR检测的YMDD突变结果进行比较.结果 PCR产物直接测序法可有效检测低病毒载量标本(500拷贝/ml)和高病毒载量(1010拷贝/ml)标本,同时可以避免高病毒载量标本的抑制效应.与实时荧光PCR相比较,YIDD突变检测符合率为100%,YVDD突变检测符合率97.1%,YIDD与YVDD共生突变符合率76.2%(Kappa=0.853,P<0.01).结论 本研究建立的PCR产物直接测序法检测HBV耐药相关基因突变,灵敏度高,检测范围宽,与实时荧光PCR检测结果有较高的符合率,并可同时检出YMDD、YIDD和YVDD.     

Evaluation of COBAS AmpliPrep/COBAS TaqMan CMV Test for use in hematopoietic stem cell transplant recipients

Introduction: Cytomegalovirus (CMV) is a common opportunistic infection that contributes to poor outcomes in hematopoietic stem cell transplant (HSCT) recipients. Prevention of CMV end-organ disease in allogeneic HSCT recipients is commonly achieved by preemptive antiviral therapy of asymptomatic CMV reactivation that is detected by serial nucleic acid testing (NAT). However, there was no standardized CMV NAT until the development of the World Health Organization (WHO) International Standard.

Areas covered: This article provides a comprehensive review on COBAS AmpliPrep/TaqMan (CAP/CTM) CMV assay (Roche) and emphasizes the limitations in the clinical use of CMV NAT in HSCT recipients.

Expert commentary: The CAP/CTM CMV Test is the first US FDA approved commercial quantitative NAT for CMV viral load monitoring of plasma samples in solid organ transplant and HSCT recipients. The CAP/CTM assay has wide linear range of DNA quantification and demonstrates colinearity to the WHO International Standard. Studies of CAP/CTM CMV assay in HSCT recipients are still limited, but are now being reported to define viral thresholds for diagnosis, surveillance and monitoring. Results from these early studies in HSCT recipients suggest that, while the WHO IS has improved the inter-laboratory result variances, there are still important factors that continue to contribute to assay variability. This lack of harmony among NAT highlights the need for further standardization.     

A case of refractory cytomegalovirus-related thrombocytopenia that achieved complete remission without antiviral therapy

Cytomegalovirus (CMV) is one of the major infectious etiologies that induce thrombocytopenia. Although immune thrombocytopenic purpura (ITP) in children is often preceded by viral infections, thrombocytopenia associated with active CMV infection is considered CMV-related thrombocytopenia (CMV-thrombocytopenia), which can be distinguished from ITP. CMV-thrombocytopenia is reported to be less responsive to standard therapies for ITP and may require antiviral therapies. We herein report a case of refractory CMV-thrombocytopenia that achieved complete remission without antiviral therapy.A 20-month-old boy presented with a 2-day history of fever and systemic petechiae. There were no abnormal findings except for an extremely low platelet count (8000/μl) on blood examinations. He was clinically diagnosed with ITP, and intravenous immunoglobulin was administered twice, but his platelet count did not increase. CMV infection was suspected serologically, and a high CMV DNA load was detected in serum by real-time quantitative polymerase chain reaction (PCR). Without antiviral treatment, the CMV DNA load decreased below the detection limit on the 11th day of admission, followed by complete remission of the thrombocytopenia. The present case suggests that spontaneous recovery of thrombocytopenia can be expected in immunocompetent patients with CMV-thrombocytopenia in whom decreased CMV DNA load is observed.     

Evaluation of the Epstein-Barr virus R-gene quantification kit in whole blood with different extraction methods and PCR platforms

Reliable real-time quantitative PCR assays to measure Epstein-Barr virus (EBV) DNA load (EBV) are useful for monitoring EBV-associated diseases. We evaluated a new commercial kit, EBV R-gene Quantification kit (Argene, Varilhes, France) to quantify EBV DNA load in whole blood. Assay performance was assessed with two PCR platforms (LightCycler 2.0 and SmartCycler 2.0) and three commercial DNA extraction methods. The assay was compared with our in-house real-time EBV PCR using samples from the Quality Control for Molecular Diagnostics 2006 EBV proficiency program and using 167 whole-blood specimens from individuals with infectious mononucleosis, from transplanted or HIV-infected patients, and from EBV-seropositive healthy carriers. The EBV R-gene assay was sensitive to 500 copies of EBV DNA per milliliter of whole blood with the two PCR platforms and the three extraction methods and was linear across 4 orders of magnitude. Intra- and interassay coefficients of variations were less than 20%. Nine of 10 samples tested with the EBV R-gene were in agreement with the expected qualitative results of the Quality Control for Molecular Diagnostics 2006 EBV proficiency program, and 7 of 10 samples were within +/-0.5 log units of the expected quantitative values, with discrepant results mostly observed for low viral load (ie, <1000 copies/ml). In the clinical specimens, the correlation between the R-gene assay and the in-house PCR was high (r=0.92). In conclusion, the EBV R-gene assay accurately assesses the EBV DNA load in whole blood of patients with various forms of EBV infections.     

Single tube multiplex real-time PCR for the rapid detection of herpesvirus infections of the central nervous system

Human herpesvirus infection of immunocompromised hosts may lead to central nervous system (CNS) infection and diseases. In this study, a single tube multiplex real-time PCR was developed for the detection of five herpesviruses (HSV-1, HSV-2, VZV, EBV and CMV) in clinical cerebrospinal fluid (CSF) specimens. Two primer pairs specific for the herpesvirus polymerase gene and five hybridization probe pairs for the specific identification of the herpesvirus types were used in a LightCycler multiplex real-time PCR. A singleplex real-time PCR was first optimized and then applied to the multiplex real-time PCR. The singleplex and multiplex real-time PCRs showed no cross-reactivity. The sensitivity of the singleplex real-time PCR was 1 copy per reaction for each herpesvirus, while that of the multiplex real-time PCR was 1 copy per reaction for HSV-1 and VZV and 10 copies per reaction for HSV-2, EBV and CMV. Intra and inter-assay variations of the single tube multiplex assay were in the range of 0.02%–3.67% and 0.79%–4.35%, respectively. The assay was evaluated by testing 62 clinical CSF samples and was found to have equivalent sensitivity, specificity and agreement as the routine real-time PCR, but reducing time, cost and amount of used sample.     

Effects of storage and viral load on hepatitis C viral genotyping.

Hepatitis C virus (HCV) genotyping is important for determining the treatment protocol for hepatitis C patients. Since amplified material from the Roche HCV Monitor kit is compatible with the Innogenetics INNO-LiPA HCV II kit (line probe assay), amplicons from the Monitor assay can be used to identify the HCV genotype. The Monitor package insert recommends using amplicons within a 7-day period (at 4 degrees C) following amplification. It was hypothesized that storage of amplicons for 4 weeks and longer (at -20 degrees C) would not affect the sensitivity of the genotyping assay. After denaturation, amplicons from two genotypes were stored for 7-386 days prior to performing the genotyping assay. Storage of amplicons did not hamper the ability to identify the genotype. Additionally, the sensitivity of the assay was evaluated by analyzing five genotypes with low viral loads. HCV genotypes were detected most consistently at viral levels of 10,000 copies/mL. In conclusion, the Innogenetics genotyping assay can use stored amplicons, thus reducing the cost of the assay by avoiding additional PCR reactions. Determining the sensitivity of this assay facilitates the efficient use of this test by incorporating a sensitivity cutoff of >or=10,000 copies/mL.     

Sensitivity of multiplex real-time PCR reactions,using the LightCycler and the ABI PRISM 7700 Sequence Detection System,is dependent on the concentration of the DNA polymerase

The introduction of multiplex PCR techniques to clinical laboratories has provided a means to streamline assays and to produce multiple results with minimal effort. While this methodology is very beneficial, care must be taken to ensure that reactions are properly optimized to allow for maximum sensitivity. This study was conducted to determine whether the sensitivity of multiplex-real-time PCR assays could be improved by increasing the concentration of DNA polymerase within a reaction. Multiplex reactions were designed to simultaneously detect the human HLA-DQ gene and a sequence from the UL83 region of the CMV genome. Two real-time PCR systems, one utilizing AmpliTaq Gold DNA polymerase and the ABI 7700 Sequence Detection System, and one utilizing FastStart Taq DNA polymerase and the Roche LightCycler were tested. The results indicated that increasing the AmpliTaq Gold concentration from 0.050 to 0.10 U/microl and the FastStart Taq concentration from 0.1875 to 0.375 U/microl increased detection sensitivity from 5,000 to 50 CMV copies per PCR reaction. In separate experiments, commercially prepared mastermixes were utilized for both real-time PCR platforms as per the manufacturer's suggestions or with the addition of supplemental DNA polymerase. In assays designed to detect 4 CMV genome copies per reaction, the addition of 2.5 U of AmpliTaq Gold to TaqMan Universal Mastermix increased the detection rate from 21 to 67%, and the addition of 5 U of FastStart Taq to FastStart DNA Master Hybridization Probes mastermix increased the detection rate from 17 to 56%. These results indicate that increasing the DNA polymerase concentration in multiplex real-time PCR reactions may be a simple way to optimize assay sensitivity.     

Rapid detection and differentiation of human pathogenic orthopox viruses by a fluorescence resonance energy transfer real-time PCR assay

BACKGROUND: The orthopox viruses that are pathogenic for humans include variola major virus (VAR), monkeypox virus (MPV), cowpox virus (CPV), and to a lesser extent, camelpox virus (CML) and vaccinia virus (VAC). PCR is a powerful tool to detect and differentiate orthopox viruses, and real-time PCR has the further advantages of rapid turnaround time, low risk of contamination, capability of strain differentiation, and use of multiplexed probes. METHODS: We used real-time PCR with fluorescence resonance energy transfer technology to simultaneously detect and differentiate VAR, MPV, CPV/VAC, and CML. An internal control generated by cloning and mutating the PCR target gene facilitated monitoring of PCR inhibition in each individual test reaction. RESULTS: Strain differentiation results showed little interassay variability (CV, 0.4-0.6%), and the test was 100-fold more sensitive than virus culture on Vero cells. Low copy numbers of DNA could be detected with > or =95% probability (235-849 genome copies/mL of plasma). CONCLUSIONS: The real-time PCR assay can detect and differentiate human pathogenic orthopox viruses. The use of an internal control qualifies the assay for high sample throughput, as is likely to be needed in situations of suspected acts of biological terrorism, e.g., use of VAR.