Validation of a quantitative real-time PCR assay for HTLV-1 proviral load in peripheral blood mononuclear cells

The objective of this study was to validate a TaqMan real-time PCR assay for HTLV-1 proviral load detection in peripheral blood mononuclear cells. TARL-2 cells were used to generate a standard curve. Peripheral blood mononuclear cell gDNA from 27 seropositive and 23 seronegative samples was analyzed. The sensitivity, specificity, accuracy, precision, dynamic range of the standard curve and qPCR efficiency were evaluated. All of the positive samples amplified the target gene. All of the negative samples amplified only the control gene (β-actin). The assay presented 100% specificity and sensibility. The intra- and inter-assay variability was 2.4% and 2.2%, respectively. The qPCR efficiency, slope and correlation coefficients (r²) were all acceptable. The limit of detection was 1 copy/rxn. This assay can reliably quantify HTLV-1 proviral load.     

A quantitative PCR method for the assay of HIV-1 provirus load in peripheral blood mononuclear cells

A set of plasmids designed for the construction of recombinant adenoviral vectors is described, which contain two expression cassettes, one in the early region 1 (E1) and the other in the early region 3 (E3). Two cloning steps in E. coli and a transfection of the resulting cosmid into 293 cells are sufficient to recover the recombinant virus. The method has been optimised to facilitate the introduction of the genes of interest in their respective regions and the reconstitution of the entire sequence of the recombinant adenoviral DNA in E. coli. The vectors are easy to handle and generate homogenous virus preparations. To illustrate the efficiency of the method, an adenovirus was constructed expressing the E. coli beta-galactosidase deltaM15 mutant in the E1 region and the complementing lacZ alpha-peptide in the E3 region.     

Development of a real time quantitative PCR assay for detection of porcine endogenous retrovirus

Real time PCR technology was applied to the development of assays for detection and quantitation of porcine endogenous retrovirus (PERV) RNA and DNA sequences in tissues and cells of human or animal origin. A plasmid construct encoding the PERV-pol gene or the in vitro transcribed RNA derived from the plasmid (cRNA) serves as a standard template for amplification of a 178 bp fragment. This study showed that the detection of this target sequence was linear over a range from 20 copies to 2 million copies of the plasmid and from 100 copies to 1 million copies of the cRNA. In addition, amplification of the target sequence was not inhibited by the presence of exogenous genomic DNA. These results demonstrate that a real time (TaqMan-based) PCR or RT-PCR assay can provide a sensitive, reproducible, and robust method for detecting and quantifying PERV DNA or RNA sequences in samples of human or guinea pig origin.     

Analytic validation of a quantitative real-time PCR assay to measure CMV viral load in whole blood.

Cytomegalovirus (CMV) is a significant cause of morbidity and mortality in immunocompromised patients. We compared the CMV pp65 antigenemia test with a less labor intensive quantitative polymerase chain reaction (PCR) assay in 109 whole blood samples predominantly from transplant patients and patients with AIDS. DNA was amplified on an Applied Biosystems 7900 instrument using a TaqMan probe targeting the CMV polymerase gene and the APOB human control gene. The DNA assay was linear over a 6-log range from 8 to 800,000 CMV genomes per reaction; coefficient of variation was 20%. CMV DNA was undetectable in 20 blood samples from healthy donors whereas it was detected in 55 of 109 patient samples. Results were concordant in a nonlinear fashion with those of the antigenemia test in 90/109 (83%). Evaluation of the discrepancies suggested that either PCR or antigenemia assays could be falsely negative when virus levels were quite low. A point mutation interfered with probe binding in 1 sample. A second real-time PCR targeting the immediate early gene was even more likely to be false negative. In summary, CMV viral load measurement targeting the polymerase gene is nearly equivalent to the antigenemia assay for detecting and monitoring active CMV infection in whole blood samples.     

A real time PCR assay for the detection and quantification of orf virus

A real time quantitative PCR assay based on TaqMan technology was developed for orf virus (ORFV) DNA quantification in clinical samples, infected cells and organotypic cultures. This method was based on the amplification of a 70 bp fragment from the ORFV B2L gene (orthologue of the Vaccinia virus Copenhagen F13L gene) that encodes the major envelope protein. Both intra- and inter-assay variability were well within +/-0.25 log(10) S.D. showing the high efficiency and reproducibility of the assay. The TaqMan PCR was subsequently used to determine the titre of several batches of the ORFV strain NZ-2, with it being possible to quantify virus solutions in the range of 1 x 10(1) to 1 x 10(6) TCID(50)/ml. A good correlation between the titre determined by the TaqMan PCR and by conventional endpoint dilution was found. The PCR assay is reproducible and can be used for a rapid quantification of ORFV in vitro and ex vivo, being readily achievable within 1h.     

Design and performance testing of quantitative real time PCR assays for influenza A and B viral load measurement.

BACKGROUND: The antiviral effect of anti-influenza drugs such as zanamivir may be demonstrated in patients as an increased rate of decline in viral load over a time course of treatment as compared with placebo. Historically this was measured using plaque assays, or Culture Enhanced Enzyme Linked Immunosorbent Assay (CE-ELISA). OBJECTIVES: to develop and characterise real time quantitative PCR (qPCR) assays to measure influenza A and B viral load in clinical samples, that offer improvements over existing methods, in particular virus infectivity assays. STUDY DESIGN: The dynamic range and robustness were established for the real time qPCR assays along with stability of the assay components. Cross validation of the real time PCR assays with CE-ELISA was performed by parallel testing of both serial dilutions of three different subtypes of cultured virus and a panel of influenza positive throat swab specimens. RESULTS: the assays were specific for influenza A and B and the dynamic ranges were at least seven logs. The assay variability was within acceptable limits but increased towards the lower limit of quantification, which was 3.33 log(10) viral cDNA copies/ml of virus transport medium (ten viral RNA copies/PCR). The components of the assay were robust enough to withstand extended storage and several freeze-thaw cycles. For the real time PCR assays the limit of quantification was equivalent to the virus infectivity cut off, which equates to a 93-fold increase in sensitivity. CONCLUSION: Well characterised real time PCR assays offer significant improvements over the existing methods for measuring the viral load of strains of influenza A and B in clinical specimens.     

化学发光法和实时荧光定量PCR法检验EB病毒的临床效果对比

目的 分析化学发光法和实时荧光定量PCR法检测肝癌患者血清中的EB病毒载量,探讨EB病毒在肝癌检测中的意义.方法 以化学发光法和实时荧光定量PCR对正常对照组、乙肝组、丙肝组及肝癌组患者血清中的EB病毒载量进行检测,并将两种检测结果进行对比分析.结果 化学发光检测肝癌组患者EB表达水平为1.99,均显著高于乙肝(1.25,u=5.129,P＜0.05)、丙肝(1.31,u =4.497,P＜0.05)、正常组(0.03,u=10.927,P＜0.05).实时荧光定量PCR方法检测肝癌组患者的EB表达水平为1.89,高于乙肝(1.26,u=5.295,P＜0.05)、丙肝(1.32,u=4.983,P＜0.05)及正常组(0.04,u=11.394,P＜0.05),差异具有统计学意义;肝癌患者术前EB表达水平(化学发光:1.87;实时荧光定量PCR:1.85)明显高于术后(化学发光:0.03,u=12.873,P＜0.05);实时荧光定量PCR:0.04,u =11.936,P＜0.05),差异具有统计学意义.两种检测方法结果无统计学差异(P＞0.05).结论 化学发光法和荧光定量PCR具有特异性强、灵敏度高等优点,可以用于检测肝癌的早期诊断和分期.     

α变形菌纲磁螺菌属TaqMan探针实时荧光定量PCR快速检测方法的建立

目的建立一种快速有效检测环境中q变形菌纲磁螺菌属细菌的方法。方法本研究以α变形菌纲磁螺菌属保守且特异的16SrRNA片段为靶序列,化学合成基因序列,制备重组质粒作为磁螺菌属检测的标准品;用实时荧光定量聚合酶链反应（FQ—PCR）技术,针对目的片段基因设计特异性引物和TaqMan荧光探针,进行实时荧光定量PCR检测,运用统计学方法评价该方法的特异性、敏感性及重复性。结果本实验成功构建了质粒PUC19-QC,引物、探针特异性良好,标准曲线在5．10×10^1～5．10×10^7拷贝数之间具有较好的线性关系,相关系数R2=0．999。该法最低可检测到5．10x10个DNA拷贝数,灵敏度明显高于普通PCR;重复性试验表明．荧光定量PCR检测结果Ct值波动范围较小,α值的标准差均小于0．23,表明该法重复性好,可靠性高。析因方差分析表明不同稀释度之间的ct值差异有统计学意义（F=3125．305,P〈0．001）,三个批次的再现性良好,差异无统计学意义（F=0．057,P=0．945）,而浓度分组与时间之间也无交叉效应（F=0．533,P=0．873）。结论本实验所建立的TaqMan探针实时荧光定量PCR检测技术,能够快速有效地检测仅变形菌纲磁螺菌属细菌,且检测结果稳定,受外界条件如时间、气温等影响小。     

A quantification of human cells using an ERV-3 real time PCR assay

A novel approach to quantifying human cells using a real time PCR assay was developed. The target sequence used in the assay is a 135 bp segment within the unique 1.7 kb Hind III / Pst I fragment of the ERV-3 envelope gene. ERV-3 is a full-length human endogenous retrovirus present in known copy number in all human cells. The detection range of ERV-3 by real time PCR is from 10(6) to 10(1). The precision described, sensitivity and specificity of the assay indicate that the ERV-3 sequence is an accurate cell quantitation marker. The quantitative ERV-3 assay enables simple, fast, and reproducible detection and quantitation of the cell number. The assay can be used to determine the sample DNA conditions and also it can be used to adjust the quantitative DNA measurements of other target gene assays relative to the number of cell equivalents.     

Development and validation of a quantitative PCR assay for diagnosis of scedosporiosis

Scedosporium apiospermum and Scedosporium prolificans are fungal pathogens that can cause severe human infections, including disseminated mycosis in immunocompromised patients. Two real-time PCR (RT-PCR) assays for the diagnosis of these species were developed and validated for the classification of clinical strains and for the detection of DNA in clinical samples by use of a murine model of invasive infection. A total of 14 clinical strains and 141 samples, including blood, serum, and lung samples from infected CD1 mice, were analyzed. Each RT-PCR methodology used a species-specific molecular beacon probe targeting a highly conserved region of the fungal ribosomal DNA gene. Results showed 100% specificity and a detection limit of 10 fg of DNA for both assays. The sensitivities for the S. prolificans-specific PCR assay were 100% for cultured clinical strains, 95.5% for lung tissues, 85% for serum, and 83.3% for blood. For S. apiospermum, the sensitivities were 100% for clinical strains and 97.2%, 81.8%, and 54.5% for lung tissues, serum, and blood, respectively. Both techniques can be useful for clinical diagnosis, and further studies are warranted.     

Detection of equine herpesvirus type 1 by real time PCR

A real-time PCR assay was developed for detection and quantitation of equid herpesvirus type 1 (EHV-1). The sensitivity of the assay was compared with an established nested-PCR (n-PCR). The real-time PCR detected 1 copy of target DNA, with a sensitivity 1 log higher than gel-based n-PCR. The assay was able to detect specifically EHV-1 DNA in equine tissue samples and there was no cross-amplification of other horse herpesviruses. Real-time PCR was applied to determine EHV-1 load in tissue samples from equine aborted fetuses. The high sensitivity and reproducibility of the EHV-1-specific fluorogenic PCR assay, combined with the wide dynamic range and the high throughput, make this method suitable for diagnostic and research applications.     

Automated extraction and quantification of human cytomegalovirus DNA in whole blood by real-time PCR assay

The measurement of human cytomegalovirus (HCMV) DNA in blood is becoming the standard method for monitoring HCMV infection in immune-suppressed and unsuppressed patients. As various blood compartments can be used, we have compared the HCMV DNA measured in whole blood (WB), peripheral blood leukocytes (PBL), and plasma by real-time PCR. We tested 286 samples: HCMV DNA was extracted automatically from WB and PBL with the MagNA Pure instrument (Roche Molecular Biochemicals) and manually from plasma samples. The HCMV DNA from WB, PBL, and plasma was measured by real-time Light Cycler PCR. Primers and probe were located in the UL 83 region. HCMV DNA was detected more frequently in WB (88.5%) than in the PBL (65.7%) (P < 0.0001) or the plasma (55.2%) (P < 0.0001). There was a good correlation between the positive results in WB and in PBL (r = 0.68; P < 0.0001), and 3.15 log(10) genome copies in 200000 PBL, equivalent to the threshold value of 50 pp65-positive polymorphonuclear cells per 200000 leukocytes, was equivalent to 3.4 log(10) genome copies in 200 microl of WB. WB was shown to be suitable for automated extraction and the quantitation of HCMV DNA by real-time Light Cycler PCR by analysis of serial samples from representative patients of various populations. This system may be very useful for monitoring of immune-suppressed and unsuppressed patients.     

Prevalence of human T-cell lymphotropic virus type 1 (HTLV-1) and HTLV-2 infection among Spanish drug users measured by HTLV-1 assay and HTLV-1 and -2 assay. HTLV-1 and HTLV-2 Spanish Study Group.

The prevalence of human T-cell lymphotropic virus type 1 (HTLV-1) and HTLV-2 infection in 1992 and 1993 was determined by testing 2,152 specimens from injection drug users living in 11 geographic areas in Spain. Results obtained by an authentic HTLV-1 and -2 test were compared with those obtained by an HTLV-1 assay. HTLV infection was identified in 7 of 11 regions, with an overall prevalence of 2.5% (range, 0.4 to 11.5%). Fourty-four (81%) of 54 subjects were infected with HTLV-2; the viral strains in the remaining 10 subjects could not be serologically typed. Underestimation of HTLV infection because of the low sensitivities of HTLV-1 enzyme immunoassays for HTLV-2 antibody was relatively low (< 20%). Therefore, previous epidemiologic findings generated with HTLV-1 enzyme immunoassays appear to be reasonably accurate. Our results suggest that the rate of HTLV infection may have been increasing recently among Spanish drug users.     

Development of a real-time PCR assay using SYBR Green I for provirus load quantification in a murine model of AIDS

A real-time PCR assay using SYBR Green I for quantification of provirus load in a murine model of AIDS (i.e., LP-BM5 infection) was developed and validated. In this method, data are normalized against the 18S rRNA gene. The method has a dynamic range of 8 logs and a sensitivity of one copy.     

辛德毕斯病毒荧光PCR检测方法的建立

目的建立辛德毕斯病毒核酸的SYBRGREENΙ荧光PCR检测方法。方法根据辛德毕斯病毒基因组核苷酸序列特性设计引物。病毒在BHK21细胞上繁殖扩增后提取RNA和逆转录。以病毒cDNA为模板分别进行SYBRGREENΙ荧光PCR和常规RTPCR扩增,并对SYBRGREENΙPCR法的灵敏性、特异性、重复性等进行分析。结果最适退火温度为55℃,最适引物浓度为0.5μmol/L。用该方法检测2株SIN病毒株YN87448和XJ160结果均为阳性,而对其他虫媒病毒如甲病毒属Geta病毒、乙脑病毒、Batai病毒、Banna病毒、环状病毒及西方马脑炎病毒合成模板检测时结果均为阴性。根据病毒空斑形成实验结果,将YN87448病毒悬液进行连续10倍稀释后分别用常规PCR和SYBRGREENΙ荧光PCR方法进行检测。结果SYBRGREENΙ荧光PCR检测敏感性比常规PCR方法要高近100倍,检出下限可达0.1PFU/ml。对模拟感染的人血清标本检测结果表明人血清中成分对检测体系无明显影响。对151份不明原因发热和病毒性脑炎患者的血清或脑脊液标本进行检测,结果检测到6份标本阳性。结论本实验建立了辛德毕斯病毒特异性核酸的SYBRGREENΙ荧光PCR检测方法,实验结果显示了较好的特异性、广谱性,初步证实可应用于临床标本的检测,为将来用于临床和调查辛德毕斯病毒在我国的流行情况提供了新的技术手段。