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.     

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.     

Comparison of manual and automated nucleic acid extraction from whole-blood samples

Nucleic acid extraction and purification from whole blood is a routine application in many laboratories. Automation of this procedure promises standardized sample treatment, a low error rate, and avoidance of contamination. The performance of the BioRobot M48 (Qiagen) and the manual QIAmp DNA Blood Mini Kit (Qiagen) was compared for the extraction of DNA from whole blood. The concentration and purity of the extracted DNAs were determined by spectrophotometry. Analytical sensitivity was assessed by common PCR and genotyping techniques. The quantity and quality of the generated DNAs were slightly higher using the manual extraction method. The results of downstream applications were comparable to each other. Amplification of high-molecular-weight PCR fragments, genotyping by restriction digest, and pyrosequencing were successful for all samples. No cross-contamination could be detected. While automated DNA extraction requires significantly less hands-on time, it is slightly more expensive than the manual extraction method.     

实时荧光定量PCR与PCR-ELISA在乙型肝炎病毒DNA定量检测中的应用比较

目的评价应用国产试剂的实时荧光定量聚合酶链反应(PCR)在检测乙型肝炎病毒(HBV)DNA中的临床应用。方法基于TaqMan探针技术的实时荧光定量PCR应用Roche公司LightCycler仪器和国产达安试剂,PCR酶联免疫吸附试验(ELISA)应用Roche公司COBASAmplicor全自动内标法系统,用2种方法检测乙型肝炎患者血清中的HBVDNA,评价其灵敏度、精密度及相关性。结果实时荧光定量PCR方法的灵敏度略低于PCR ELISA全自动内标法,两者变异系数(CV)均较低,用2种方法检测临床标本,相关系数为0.890。结论应用国产试剂配合LightCycler仪器的实时荧光定量PCR具有较高的灵敏度和较好的重复性,并与PCR ELISA全自动内标法有良好的相关性。     

实时荧光定量PCR与PCR-ELISA在乙型肝炎病毒DNA定量检测中的应用比较

目的 评价应用国产试剂的实时荧光定量聚合酶链反应(PCR)在检测乙型肝炎病毒(HBV)DNA中的临床应用。方法 基于TaqMan探针技术的实时荧光定量PCR应用Roche公司Light Cycler仪器和国产达安试剂,PCR-酶联免疫吸附试验(ELISA)应用Roche公司COBAS Amplicor全自动内标法系统,用2种方法检测乙型肝炎患者血清中的HBV DNA,评价其灵敏度、精密度及相关性。结果 实时荧光定量PCR方法的灵敏度略低于PCR-ELISA全自动内标法,两者变异系数(CV)均较低,用2种方法检测临床标本,相关系数为0．890。结论 应用国产试剂配合Light Cycler仪器的实时荧光定量PCR具有较高的灵敏度和较好的重复性,并与PCR-ELISA全自动内标法有良好的相关性。     

Quantification of parvovirus B19 DNA using COBAS AmpliPrep automated sample preparation and LightCycler real-time PCR

The COBAS AmpliPrep instrument (Roche Diagnostics GmbH, D-68305 Mannheim, Germany) automates the entire sample preparation process of nucleic acid isolation from serum or plasma for polymerase chain reaction analysis. We report the analytical performance of the LightCycler Parvovirus B19 Quantification Kit (Roche Diagnostics) using nucleic acids isolated with the COBAS AmpliPrep instrument. Nucleic acids were extracted using the Total Nucleic Acid Isolation Kit (Roche Diagnostics) and amplified with the LightCycler Parvovirus B19 Quantification Kit. The kit combination processes 72 samples per 8-hour shift. The lower detection limit is 234 IU/ml at a 95% hit-rate, linear range approximately 10⁴-10¹⁰ IU/ml, and overall precision 16 to 40%. Relative sensitivity and specificity in routine samples from pregnant women are 100% and 93%, respectively. Identification of a persistent parvovirus B19-infected individual by the polymerase chain reaction among 51 anti-parvovirus B19 IgM-negative samples underlines the importance of additional nucleic acid testing in pregnancy and its superiority to serology in identifying the risk of parvovirus B19 transmission via blood or blood products. Combination of the Total Nucleic Acid Isolation Kit on the COBAS AmpliPrep instrument with the LightCycler Parvovirus B19 Quantification Kit provides a reliable and time-saving tool for sensitive and accurate detection of parvovirus B19 DNA.     

Comparative evaluation of automated and manual commercial DNA extraction methods for detection of Francisella tularensis DNA from suspensions and spiked swabs by real-time polymerase chain reaction

This study evaluated commercial automated and manual DNA extraction methods for the isolation of Francisella tularensis DNA suitable for real-time polymerase chain reaction (PCR) analysis from cell suspensions and spiked cotton, foam, and polyester swabs. Two automated methods, the MagNA Pure Compact and the QIAcube, were compared to 4 manual methods, the IT 1-2-3 DNA sample purification kit, the MasterPure Complete DNA and RNA purification kit, the QIAamp DNA blood mini kit, and the UltraClean Microbial DNA isolation kit. The methods were compared using 6 F. tularensis strains representing the 2 subspecies which cause the majority of reported cases of tularemia in humans. Cell viability testing of the DNA extracts showed that all 6 extraction methods efficiently inactivated F. tularensis at concentrations of ≤10⁶ CFU/mL. Real-time PCR analysis using a multitarget 5′ nuclease assay for F. tularensis revealed that the PCR sensitivity was equivalent using DNA extracted by the 2 automated methods and the manual MasterPure and QIAamp methods. These 4 methods resulted in significantly better levels of detection from bacterial suspensions and performed equivalently for spiked swab samples than the remaining 2. This study identifies optimal DNA extraction methods for processing swab specimens for the subsequent detection of F. tularensis DNA using real-time PCR assays. Furthermore, the results provide diagnostic laboratories with the option to select from 2 automated DNA extraction methods as suitable alternatives to manual methods for the isolation of DNA from F. tularensis.     

EB病毒VCA-IgA抗体及病毒DNA载量在系统性红斑狼疮患者中的表达

目的 检测EB病毒VCA-IgA抗体及病毒DNA载量在系统性红斑狼疮（SLE）患者外周血中的表达，探讨EB病毒与SLE的相关性。方法 分别采用酶联免疫吸附试验（ELISA）法和实时定量PCR方法检测EB病毒VCA-IgA抗体和EB病毒DNA载量。同时分析EB病毒VCA-IgA抗体与SLE患者的实验室指标抗Sm抗体、抗dsDNA抗体、补体C3和C4的相关性。结果 248例SLE患者中，49例为EBV-VCA-IgA抗体阳性，167例健康对照者中12例阳性，SLE患者阳性率明显高于对照组(19.8% vs 7.2%; P < 0.001)；SLE患者EB病毒载量也明显高于对照组。EB病毒VCA-IgA抗体阳性与抗Sm抗体、抗dsDNA抗体、补体C3和C4不相关。结论EB病毒感染与SLE相关，EB病毒VCA-IgA抗体阳性者有较高的DNA载量，SLE的发病危险性亦高，EB病毒重新活化与SLE活动有关。     

Successful use of saliva without DNA extraction for detection of macrolide-resistant Mycoplasma pneumoniae DNA in children using LNA probe-based real-time PCR

It is not known that saliva is useful to diagnose Mycoplasma pneumoniae (M. pneumoniae) infection by PCR. We evaluated prospectively whether crude saliva samples without the DNA extraction process were useful for the detection of M. pneumoniae DNA in a locked nucleic acid (LNA) probe-based real-time PCR assay. Fifty-one clinical specimens (29 sputum, 22 saliva) that were positive by conventional M. pneumoniae-specific PCR were evaluated in this study. We designed an LNA probe-based real-time PCR that could discriminate the mutant strain (A2063G mutation) from the wild-type strain. All the 51 samples treated with DNA extraction were positive using the LNA probe-based real-time PCR. The results of the real-time PCR with DNA extraction were consistent with the sequence analysis. Of the 51 samples without DNA extraction, on the other hand, 41 (80.4 %) were positive by real-time PCR. Of 29 sputum samples without DNA extraction, 23 (79.3 %) were positive by real-time PCR; of the 22 saliva samples without DNA extraction, 18 (81.8 %) were positive by real-time PCR. There was a statistically significant difference in the amplified DNA levels with extraction between the direct real-time PCR-positive samples (mean ± SD, 7.5 ± 1.6 log copies/ml) and PCR-negative samples (4.2 ± 0.8 log copies/ml) (P < 0.001). Saliva was useful for a template for PCR as well as sputum. In addition, crude samples were useful for real-time PCR when the samples had medium or high DNA levels. However, samples with low DNA levels sometimes showed false-negative results in direct real-time PCR.     

Fast and sensitive quantitative detection of HIV DNA in whole blood leucocytes by SYBR green I real-time PCR assay

The aim of this study was the development of a real-time PCR for HIV DNA quantification in whole blood leucocytes providing an alternative assay to those already described, almost based on the gag gene detection. The technique (pbs-rtPCR assay) is more rapid (the whole assay required less than 5h), easy to perform, omitting both PBMC purification step and data normalization to a housekeeping gene, when compared to previously published assays. Our method is able to detect all group M HIV-1 subtypes in the highly conserved primer-binding site (PBS) region and to avoid the interference by retroviral endogenous sequences in HIV DNA quantification. The sensitivity was 100% for 2 copies even in the presence of high amounts of genomic DNA (1 microg). To monitor the HIV DNA level in all possible clinical conditions, the assay has been validated and compared with a previously developed gag-PCR assay on 73 HIV-1 HAART-treated patients with a plasma HIV-1 RNA range from <50 to >500,000 copies/ml. The 50% of the samples with a viremia below the limit of detection (50 copies/ml) was found to contain HIV DNA between 2 and 10 copies/microg DNA. The pbs-rtPCR offers a significant improvement in the percentage of quantitatively detectable sample (99%) compared with the gag-PCR (42%) suggesting caution in the choice of HIV DNA assay.     

手工与全自动核酸提取仪提取石蜡包埋组织DNA的比较

目的：比较手工与全自动核酸提取仪提取石蜡包埋组织DNA的浓度和纯度之间的差异,探讨不同提取方法、不同消化方式对DNA提取的影响。方法：选取27例中性福尔马林固定石蜡包埋组织标本,同一技师分别用手工提取与全自动核酸提取仪提取DNA的方法以及分别置于金属浴和恒温箱中消化,进行DNA提取。结果：使用金属浴对组织进行消化,手工提取DNA的浓度为107.1±30.1 ng/μL,全自动核酸提取仪提取DNA的浓度为39.1±16.5 ng/μL；使用恒温箱对组织进行消化,手工提取DNA的浓度为75.5±28.2 ng/μL,全自动核酸提取仪提取DNA的浓度为29.6±17.1 ng/μL,手工提取DNA的浓度均较高,差异有统计学意义(两者均为P<0.01)。手工提取和全自动DNA提取中,使用金属浴消化提取的DNA浓度均比使用恒温箱消化的高(107.1±30.1 VS 75.5±28.2,39.1±16.5 VS 29.6±17.1),差异有统计学意义(两者均为P<0.05)。不同提取方法及消化方式提取DNA的纯度无显著性差异。 结论：手工提取石蜡包埋组织DNA的浓度较高,使用金属浴消化组织提取DNA较恒温箱消化好,不同方式提取的DNA质量均满足分子病理检测需求。     

Long-term stability of human immunodeficiency virus viral load and infectivity in whole blood

BACKGROUND: We intended to evaluate the stability of human immunodeficiency virus (HIV) type 1 virions in whole blood and in culture medium. MATERIALS AND METHOD: EDTA whole-blood samples taken from 12 patients were left at room temperature for up to 7 days, and aliquots of a laboratory virus stock spiked in EDTA, in heparinized or in citrated whole blood, with or without the addition of Triton X-100, or spiked in culture medium were left at room temperature for up to 120 days before plasma was separated and frozen at -80 degrees C. Viral load was measured for all frozen plasma samples using different viral load assays. p24 antigen and infectivity were also measured in the spiked samples. RESULTS: The patient whole-blood samples did not show any decrease in viral load during this 7-day period. The spiked samples decayed by not more than 1 log after 120 days (about 4 months), with the fastest decay in medium. Virus infectivity decayed very slowly from 20,000 units mL-1 to undetectable amounts after 56 days. CONCLUSIONS: These results indicate that HIV-1 virions in whole blood possess a long-term stability in terms of viral load, p24 antigen level and infectivity, which is not sufficiently recognized by laboratory and health care workers.     

Comparison of two automated nucleic acid testing systems for simultaneous detection of human immunodeficiency virus and hepatitis C virus RNA and hepatitis B virus DNA

BACKGROUND: Recently developed nucleic acid testing (NAT) assays incorporating simultaneous detection of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV) have made HBV NAT screening more feasible for blood services. This study compared the performance of two "multiplex" NAT assays and their automated testing platforms. STUDY DESIGN AND METHODS: The HBV NAT yield rate was estimated by testing 10,397 Hong Kong (HK) donor samples concurrently on the PROCLEIX ULTRIO (Ultrio) assay as individual donor samples with the TIGRIS and on the cobas TaqScreen multiplex (cobas MPX) test in pools of 6 with the cobas s 201. Analytical sensitivity was assessed by probit analysis of diluted international standards and operational performance was compared. RESULTS: Each system detected two different HBV NAT yield samples for a combined rate of 0.04 percent. One additional sample was reactive on the cobas MPX test but remained unresolved. The 95 percent detection limits for HIV-1, HBV, and HCV were 42.2, 12.2, and 2.0 IU per mL, respectively, for Ultrio and 50.5, 8.4, and 6.0 IU per mL for the cobas MPX. The invalid test and failed run rates were 0.05 and 2.92 percent, respectively, for the TIGRIS and 2.39 and 5.53 percent for the cobas s 201. CONCLUSION: Clinical sensitivity for HBV in HK blood donors was equivalent, as was the analytical sensitivity for HIV-1 and HBV; however, the Ultrio assay had a higher analytical sensitivity for HCV. Despite a shorter downtime and mean time of repair for the cobas s 201, the TIGRIS demonstrated better overall operational performance.     

Real-time automated polymerase chain reaction (PCR) to detect Candida albicans and Aspergillus fumigatus DNA in whole blood from high-risk patients

We report the development and evaluation of a real-time PCR assay using the LightCycler instrument for the detection of C. albicans and A. fumigatus DNA in whole blood. Recently published consensus criteria for the diagnosis of invasive fungal infection (IFI) were used for all patient samples. Unique and published primer pairs were developed and assessed for sensitivity, specificity, and reproducibility to detect C. albicans and A. fumigatus DNA in samples spiked with purified DNA, and whole blood samples from 8 high-risk patients and 45 negative controls. The real-time assay demonstrated an analytical sensitivity of 10 fg of purified C. albicans and A. fumigatus DNA and was found to be specific for each species. The standardized approach was highly reproducible and detected C. albicans and A. fumigatus DNA in two patients with proven IFI and in one patient with a possible IFI. In addition, we report for the first time the use of recently published international consensus criteria for the diagnosis of IFI in the evaluation of a mildly invasive fungal diagnostic assay. Standardized clinical criteria and a more standardized approach to detect fungal DNA in less invasive patient samples, may permit a more reliable comparison of future studies. A rapid real-time detection of fungal DNA in whole blood, combined with standard clinical markers of response, may be more useful for monitoring patients at risk of developing IFI than other diagnostic methods currently available.     

Comparison of manual and automated ELISA methods for serum ferritin analysis

Serum ferritin concentration is a sensitive measure of body iron stores. The aim of this study was to compare the performance of two commercially available enzyme-linked immunoassays (ELISAs) for serum ferritin: a widely used manual assay kit (Spectro Ferritin MT), and a new fully automated assay (Immulite). We analyzed serum samples from Moroccan school-aged children (n=51) from a rural area with a high prevalence of iron deficiency anemia (IDA). Four replicates of each sample were analyzed using both assays. For the manual method, the interassay repeatability was 24%, 22%, and 11%, and intraassay precision was 18.3%, 9.2%, and 9.1% at increasing serum ferritin concentrations. Using the automated assay, the interassay repeatability was 7%, 6%, and 6%, and intraassay precision was 1.5%, 5.4%, and 5.5% at increasing serum ferritin concentrations. The two assays were well correlated (y=1.16x+1.83; r=0.98). However, the limits of agreement (LOAs) were wide, particularly at low concentrations. A comparison of the assay results with recommended cutoffs for serum ferritin generated sharply different estimates of the prevalence of iron deficiency (ID) in the sample. We conclude that the automated assay has several potential advantages compared to the manual method, including better precision, less operator dependence, and faster sample through-put.     

实时定量逆转录PCR测定EB病毒DNA负荷的临床应用

EB病毒(EBV)是1964年由Epstein和Barr在对非洲Burkitt淋巴瘤来源的瘤细胞进行体外培养时发现的。全球估计EBV成人感染率高达90％以上。已有的证据证明EBV感染可引起传染性单核细胞增多症和器官移植及艾滋病感染等免疫功能降低后的淋巴增生性疾病(lymphoproliferative disease，LPD)。此外，还发现EBV与一些疾病，如淋巴瘤、鼻