Development of TaqMan real-time PCR assay for detection and quantitation of reticuloendotheliosis virus

A highly sensitive real-time PCR method was developed in this study for reticuloendotheliosis virus (REV) detection and quantitation. The real-time PCR method, with a minimum detection limit of 10 proviral DNA copies, was 100 times more sensitive than the conventional PCR. It was also shown to be highly specific, as no positive signals were detected for other common avian DNA viruses. The coefficients of variation of intra- and inter-assay reproducibility were both less than 2%. The chicken β-actin gene was co-amplified and used as the internal control to monitor the efficiency of DNA extraction and PCR amplification. Specific pathogen free chickens were infected with REV at different ages and the blood was detected with the real-time PCR method. High levels of proviral DNA were detected in the blood of REV-infected chickens during the experiment and chickens infected early had higher proviral loads from 2 weeks post-infection compared with late infected chickens. This study provides an excellent research and diagnostic tool that can be used for REV detection and quantitation.     

Development of TaqMan real-time RT-PCR for detection of avian reoviruses

Avian reoviruses (ARVs) are an important cause of economic losses in commercial poultry. A TaqMan real-time RT-PCR assay for detecting of ARVs was developed. The primer-probe set was from the conserved region of ARV S4 genome segment. Real-time RT-PCR detected ARV strains including CO8 and ss412 strains, which belonged to different serological subgroups, and the test had no cross-reaction with other avian viruses. The detection limit of this assay was 5 ARV genome copies per 5 μl and was 150 times more sensitive than traditional RT-PCR. Statistical analyses indicated excellent reproducibility. For ARV strain 2408, a titer of 50% embryo infection dose and 50% tissue culture infectious dose equivalent to 3.9 ± 0.8, and 2.9 ± 0.3 ARV genome copies, respectively. This test was rapid, specific, and sensitive for the detection of ARVs and will be useful in veterinary diagnostic laboratories and for the quantitation of vaccine viruses for pharmaceutical companies.     

乙型脑炎病毒TaqMan PCR检测方法的建立及初步应用

目的 利用TaqMan PCR技术，建立乙型脑炎病毒（Japanese encephalitis virus，JEV）实时荧光PCR检测方法，初步应用于蚊虫媒介的JEV监测。方法根据GenBank发表的JEV全基因组序列资料分析结果，在其NS5基因区段设计JEV特异的引物与探针；优化Mg^2＋浓度和引物浓度比例，并利用11株JEV和7株相关病毒株考核检测体系的保守性、特异性、灵敏性和稳定性；利用体外转录的病毒RNA和定量的病毒样品，建立相应的定量分析模型；初步应用于蚊虫媒介的监测与检测分析。结果Mg^2＋优化浓度为5mmol／L，上下游引物浓度比例为4：1，引物探针具有良好的保守性和特异性，灵敏度为10PFU／ml，稳定性分析表明，同一样品Ct值的重复检测5次，变异系数均小于5％；绘制两种标准曲线，构建了JEV基因拷贝数、病毒滴度为分析指标的定量分析模型，检测蚊虫标本结果显示，TaqMan PCR方法较病毒分离法敏感、快捷、简便。结论本研究建立了一种灵敏、特异、简便易行的JEVTaqMan PCR检测方法，为蚊虫媒介检测奠定了基础，为乙型脑炎的预防控制和脑炎相关疾病的诊断与鉴别诊断提供了一种技术手段。     

Molecular beacon real-time PCR detection of swine viruses

Rapid and reliable detection of viral pathogens is critical for the management of the diseases threatening the economic competitiveness of the swine farming industry worldwide. Molecular beacon assays are one type of real-time polymerase chain reaction (PCR) technology capable of fast, specific, sensitive, and reliable viral detection. In this paper, the development of molecular beacon assays as novel tools for the rapid detection of Aujeszky's disease virus, African swine fever virus, porcine circovirus type 2 and porcine parvovirus is described. The assays are capable of rapidly detecting 2 × 10¹ copies of target and are linear between 2 × 10⁹ and 2 × 10² copies. They can detect virus specifically in clinical samples such as whole blood, serum and tissue. In comparison to conventional PCR they are either as sensitive or more sensitive. As such these molecular beacon assays represent a powerful tool for the detection of these viruses in swine.     

肝螺杆菌TaqMan MGB探针实时荧光定量PCR快速检测方法的建立及应用研究

目的 建立特异、敏感、快速检测肝螺杆菌的TaqMan MGB探针实时荧光定量PCR方法.方法 针对肝螺杆菌flaB 基因的保守区设计特异性引物和探针,建立肝螺杆菌TaqMan MGB探针实时荧光定最PCR方检测方法,验证方法的特异性、敏感性和稳定性.对2008-2011年期间采集的1081份临床样本中的肝螺杆菌进行检测,同时进行分离培养和常规PCR检测.结果 建立的TaqMan MGB探针实时荧光定量PCR方法对肝螺杆菌的检测具有高度的特异性,对幽门螺杆菌、空肠弯曲菌、泰泽氏菌、侵肺巴斯德氏菌、大肠埃希菌、铜绿假单胞菌均无交叉反应,检测的灵敏度达8.3拷贝.标准曲线显示各浓度范围内具有良好的线性关系,相关系数为0.999,斜率为-3.227,TaqManMGB探针实时荧光定量PCR效率为100％.对1081份临床样本进行检测,TaqMan MGB探针实时荧光定量PCR和常规PCR均能检出86份肝螺杆菌阳性样本,而细菌分离培养则仅检出4份阳性.结果显示,建立的TaqMan MGB探针实时荧光定量PCR方法比细菌分离培养方法更敏感,能够直接从临床样本中检出肝螺杆菌DNA,检测时间仅为2h.结论 研究建立的TaqMan MGB探针实时荧光定量PCR方法具有可靠、特异、敏感的特点,适用于肝螺杆菌的快速检测.     

SYBR green and TaqMan real-time PCR assays are equivalent for the diagnosis of dengue virus type 3 infections

Dengue is the most important arthropod-borne viral disease in the world. A rapid diagnostic test for dengue is warranted, and real-time polymerase chain reaction may improve diagnosis. TaqMan and Sybr Green systems were evaluated for the diagnosis of dengue virus type 3 (DENV-3) infections. Out of 77 patients with clinical suspicion of dengue infection, specific IgM antibodies were detected in 40 patients. DENV-3 was detected and quantitated in 17 IgM-positive samples by both systems. These assays were shown to be rapid, and specific for detection of DENV-3, and that for diagnostic purposes, there is no difference between these two assays.     

应用定量PCR检测固定矫治器拆除后龈下菌斑中牙龈卟啉单胞菌的动态变化

目的 检测正畸患者在拆除固定矫治器后龈下牙龈卟啉单胞菌(Porphyromonas gingivalis)动态含量和牙周临床指标,研究其动态变化及与临床的关系.方法 选择将要结束正畸治疗的患者20名,在拆除矫治器前即时、之后第1个月、第3个月和第6个月分别检查牙周各项指标:菌斑指数(PLI)、龈沟出血指数(SBI)、探诊深度(PD),同时采集龈下菌斑,采用TaqMan探针荧光实时定量PCR技术对样品进行检测得出每个样品中牙龈卟啉单胞菌和总细菌的数量,牙龈卟啉单胞菌检出率和牙龈卟啉单胞菌占总细菌比例的变化.结果 牙龈卟啉单胞菌检出率在拆后6个月内呈下降趋势,在第6个月差异有统计学意义(P<0.05);牙龈卟啉单胞菌的量在拆后6个月开始呈显著的下降(P<0.05);牙龈卟啉单胞菌的百分含量在拆后6个月开始差异有统计学意义(P<0.05);PLI、SBI、PD都呈显著性下降(P<0.05).结论 拆除固定矫治器后在保持良好口腔卫生保健的情况下,正畸患者在一段时间内牙周组织呈自愈的趋势.牙龈卟啉单胞菌的百分含量的动态变化可以较好地反映牙周组织的健康状况.TaqMan实时荧光定量PCR有较高的特异性和敏感性,且快捷准确,对牙周微生物的检测有一定的应用价值.     

A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus

Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0 × 10¹ and 6.0 × 10² copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV.     

Development of duplex real-time PCR for detection of two DNA respiratory viruses

A method was developed for the detection and quantitation of HAdV (human adenovirus) and HBoV (human bocavirus) based on a duplex real-time PCR, the AB PCR, using a Smartcycler instrument. A control real-time PCR was carried out on albumin DNA to standardise the non-homogenous respiratory samples. No cross-reactivity was observed with viruses or bacteria that could be found in the respiratory tract. The diagnosis rate using the AB PCR on clinical samples was 10.7%: 3.4% for HBoV detection, 6.9% for HAdV detection and 0.3% double detection HBoV–HAdV. The clinical and epidemiological characteristics of the HAdV- and HBoV-infected patients were evaluated. In the HAdV-positive group and the HBoV-positive group the samples were classified according to the severity of the disease. The HAdV viral load did not appear to be linked to the severity of the disease. Conversely, the difference between the two HBoV groups, severe and non-severe, was significant statistically when the comparison was based on the viral load (P = 0.006) or after adjustment of the viral load to the number of cells in the samples (P = 0.02).     

Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay

Yellow fever virus quantitation is performed routinely by cultivation of virus containing samples using susceptible cells. Counting of the resulting plaques provides a marker for the number of infectious particles present in the sample. This assay usually takes up to 5 days before results are obtained and must be carried out under L2 or L3 laboratory conditions, depending on the yellow fever virus strain used. For clinical diagnosis of yellow fever virus infections the cell culture-based approach takes too long and is of limited practical relevance. Recently, due to its considerable sensitivity, PCR has become a promising method for virus detection. However, whilst PCR can detect virus-specific nucleic acids, it does not allow conclusions to be drawn regarding the infectious potential of the virus detected. Nonetheless, for diagnostic purposes, a rapid, specific and sensitive virus PCR is preferable. Therefore, two independent yellow fever virus-specific real-time PCR assays were established and compared the viral RNA loads to the results of a traditional plaque assay. The estimated ratio of yellow fever virus genomes to infectious particles was between 1000:1 and 5000:1; both approaches displayed a comparable precision of <45%. A significant correlation between genome number as determined by real-time PCR and the corresponding number of plaques in paired samples was found with a Pearson coefficient of correlation of r=0.88 (P<0.0001).     

H5亚型禽流感灭活疫苗病毒基因的定量检测及其与HI抗体效价之间关系的分析

目的建立H5亚型禽流感病毒灭活疫苗中病毒核酸的特异、敏感、快速的定量检测方法，分析其与HI抗体效价之间的相关性。探索禽流感灭活疫苗效力体外检验的方法。方法选取H5亚型禽流感病毒（avian influenza virus，AIV）血凝素（hemagglutinin，HA）基因保守序列，使用Prinler Express 2．0软件设计了特异性引物和TaqMan MGB（minor groove binder）探针，利用实时荧光PCR技术来定量检测禽流感灭活疫苗，通过体外转录，制备含有选定检测序列的RNA标准品，绘制标准曲线。对50批H5亚型禽流感灭活疫苗进行了荧光定量PCR检测，测定了疫苗的HA基因拷贝数，同时测定了50批疫苗相应的HI抗体效价。进行了疫苗的HA基因拷贝数与HI抗体效价之间相关性的分析。结果该方法的灵敏度为10拷贝，反应，标准曲线的相关系数为0．998003，对H9亚型禽流感灭活疫苗和其他禽病疫苗无交叉反应，特异性好、重复性佳。疫苗的HA基因拷贝数与HI抗体效价不相关。结论荧光定量PCR方法为H5亚型禽流感病毒灭活疫苗检测提供了一种特异、敏感、快速的定量检测方法。     

实时荧光PCR快速检测嗜肺军团菌的研究

目的 建立TaqMan-MGB探针实时荧光PCR快速检测嗜肺军团菌技术,为临床和环境样品检测嗜肺军团菌提供可实用工具.方法 在对嗜肺军团菌mip序列进行分析、比较基础上,设计一对特异性引物和TaqMan-MGB探针,通过实时荧光PCR反应条件和反应体系的优化,实现对嗜肺军团菌的快速检测;用克隆到pMD-19T载体上的嗜肺军团菌mip基因阳参片段和不同菌株验证方法的敏感性和特异性.结果 当用热裂解法提取DNA,25μl的反应体系中包括上、下游引物(20μmol/L)各0.6μl,探针(20μmol/L)0.4μl,模板DNA 6.0μl,反应条件为预变95℃20 S,变性95℃10 s,退火50℃ 40 s,40个循环时,TaqMan-MGB探针实时荧光PCR技术对嗜肺军团菌mip基因阳参片段最低检测浓度为0.71拷贝/μl,其循环阈值(Ct值)与模板浓度具有极好的对应关系(r=0.999);1株嗜肺军团菌标准株、12株嗜肺军团菌分离株的Ct值在13.23～16.04之间,而包括金黄葡萄球菌、鼠伤寒沙门菌、副溶血性弧菌、大肠埃希菌、铜绿假单胞菌、痢疾志贺菌共计76株其他菌PCR Ct值均大于30;整个检测过程仅需1.5 h.结论 TaqMan-MGB探针的嗜肺军团菌实时荧光PCR检测方法具有特异性和敏感性、易操作、结果准确可靠等优点,可用于嗜肺军团菌检测.     

New design and optimization of an in-house quantitative TaqMan Real-Time PCR-based assay for the detection and monitoring of occult hepatitis B virus (genotype A-J) infection

PurposeHBV DNA quantification is used for individuals with uninterpretable serological tests, occult HBV infections, decreasing the window period of the disease, and treatment follow-up. Although there are commercial qPCR assays, they are expensive. In this study, we developed a highly sensitive quantitative TaqMan Real-Time PCR with an exogenous internal control to quantify HBV DNA in serum/plasma.MethodsA specific primer/probe set was designed for the S conserved region of various HBV genotypes. The primer/probe set was evaluated experimentally and in-silico. An exogenous internal control was included to monitor the effects of inhibitors. The standard plasmid was titrated using three different methods to prepare the seven standards for the assay. The functional characteristics of the in-house assay were evaluated using the standards. Two hundred clinical specimens were also tested.ResultsThe LOD of the in-house assay was 40 IU/mL, and the assay was linear from 3.26Log10 to 9.26Log10 IU/mL. The analytical and clinical sensitivity of the assay was 100% and 92.15%, respectively. The analytical and clinical specificity of the assay was 100% and 98.97%, respectively. The positive and negative predictive values of the assay were determined to be 98.94% and 92.38%, respectively. The highest coefficient of variation of the inter/intra-assay was 5.1%. The accuracy was close to 100% for all standards, and the correlation between the in-house assay and commercial kit AltoStar® PCR Kits 1.5 was remarkable. The results of the clinical samples using the standards titrated using AcroMetrix? HBV Panel, Artus® HBV RG PCR Kit, and AltoStar® PCR Kits 1.5 were comparable (r ?= ?0.942, 0.951, 0.951).ConclusionsThe results indicate that the in-house assay is highly sensitive and specific, reproducible, and cost-benefit. Thus, it can be used to detect and quantify HBV DNA in research and clinical settings.     

Complete nucleotide sequence and genomic organization of hepatopancreatic parvovirus (HPV) of Penaeus monodon

We have determined the genome of hepatopancreatic parvovirus (HPV), a minus, single-stranded DNA virus isolated from infected Penaeus monodon in Thailand. Its genome consisted of 6321 nucleotides, representing three large open reading frames (ORFs) and two non-coding termini. The left (ORF1), mid (ORF2), and right (ORF3) ORFs on the complementary (plus) strand may code for 428, 579, and 818 amino acids, equivalent to 50, 68, and 92 kDa, respectively. The 5' and 3' ends of viral genome contained hairpin-like structure length of approximately 222 and 215 bp, respectively. No inverted terminal repeat (ITR) was detected. The ORF2 contained conserved replication initiator motif, NTP-binding and helicase domain similar to NS-1 of other parvoviruses. Therefore, it most likely encoded the major nonstructural protein (NS-1). The ORF1 encoded putative nonstructural protein-2 (NS-2) with unknown function. The ORF3 of the HPV genome encoded a capsid protein (VP) of approximately 92 kDa. This may be later cleaved after arginine residue to produce a 57-kDa structural protein. A phylogenetic tree based on conserved amino acid sequences (119 aa) revealed that it is closely related to Brevidensoviruses, which are shrimp parvovirus (IHHNV) and mosquito densoviruses (AaeDNV and AalDNV). However, the overall genomic organization and genome size of HPV were different from these parvoviruses, for instance, the non-overlapping of NS1 and NS2, the larger VP gene, and the bigger genome size. This suggested that this HPV virus is a new type in Parvoviridae family. We therefore propose to rename this virus P. monodon densovirus (PmDNV).     

Development of a primer-probe energy transfer real-time PCR assay for improved detection of classical swine fever virus

Classical swine fever (CSF) is a contagious and devastating disease, causing serious losses in the pig industry worldwide. Vaccination of pigs with the conventional C-strain vaccine has been practised in different regions of the world in order to prevent the disease. In the control programmes of CSF, rapid detection and identification of the causing agent, classical swine fever virus (CSFV) is a crucial step. This study describes a novel real-time PCR assay based on primer-probe energy transfer (PriProET) technology for improved detection of CSFV. The assay is able to detect 20 copies of viral cDNA per reaction, showing a high sensitivity. The specificity has been evaluated by testing 57 pestiviruses, representing all species and unclassified pestiviruses. The assay has been found to be highly reproducible. Following PCR amplification, melting curve analysis allows confirmation of specific amplicons, and differentiation between wild-type CSFV and certain C-strain vaccines. This study provides a new tool for the diagnosis of CSF.     

实时PCR检测HSV-2的方法学建立

目的建立一种快速、特异、准确定量的单纯疱疹病毒2型(HSV-2)检测方法。方法构建重组质粒pMD18-T-gG作为标准品。以HSV-2的gG基因区为靶基因区,设计合成引物和探针,采用TaqMan MGB技术对HSV-2进行实时定量PCR检测,优化反应体系,并进行方法学评价。结果成功构建重组质粒pMD18-T-gG。建立利用TaqMan MGB技术的,real-time PCR方法,其重复性较好[批内 CV(变异系数)值为2．29％,批间CV值为4．76％]、特异性较好(对HSV-1、Vero细胞、巨细胞病毒、弓形虫等无特异性扩增)、线性范围好(4．75×10~1-4．75×10~6 copies／μ1,r=0．998),灵敏度达到47．5 cop- ies／μl;与ELISA法进行比较,认为前者的灵敏度更高、检测时间更短。结论建立的TaqMan MGB PCR 方法能够快速准确、特异、灵敏地对HSV-2进行定量分析,可为临床诊断提供帮助。     

Recurrent high level parvovirus B19/genotype 2 viremia in a renal transplant recipient analyzed by real-time PCR for simultaneous detection of genotypes 1 to 3

Organ transplant recipients infected with parvovirus B19 frequently develop persistent viremia associated with chronic anemia and pure red cell aplasia. In this study, a male renal transplant recipient who had been infected with parvovirus B19/genotype 2 after renal transplantation at the age of 34 years is described. The patient was repeatedly treated with high dose intravenous immunoglobulin (IVIG) that resulted in the resolvement of symptoms but not in virus eradication. During an observation period of 33 months after transplantation three phases associated with high parvovirus B19 viremia were observed. Both the first and the second viremic phases were combined with severe anemia. Parvovirus B19 specific IgM-antibodies were initially detected at the beginning of the second phase in continually rising concentrations. Initially eradication of the virus by immunoglobulin therapy was reported after the first viremic phase [Liefeldt et al. (2002): Nephrol Dial Transplant 17:1840-1842]. Retrospectively this statement has to be corrected. It was based on the use of a qualitative PCR assay specific for parvovirus B19 genotype 1 associated with reduced sensitivity for detection of genotype 2. After sequence analysis of the viral DNA and adjustment of a real-time PCR assay (TaqMan) for quantitative detection of all three B19 virus genotypes analysis of consecutive serum samples allowed the demonstration of long lasting phases with reduced viral loads following IVIG-treatment. These results demonstrate that IVIG treatment of parvovirus B19-triggered anemia in transplant recipients offers an opportunity to resolve symptoms, but does not guarantee eradication of the virus. Since reactivation of parvovirus B19 infection can result in high virus load associated with the recurrence of symptoms repeated screening for viral DNA is recommended using the TaqMan system established for quantitative detection of all three genotypes of parvovirus B19.     

Development of a Plexor real-time PCR assay for the detection of porcine circovirus type 2

A novel, real-time PCR system for the detection of porcine circovirus type 2 (PCV2) was developed. The system employed Plexor technology and detected 10⁸-10¹ copies per reaction of PCV2 DNA within a recombinant plasmid. The examination of clinical material showed consistent diagnostic sensitivity when samples contained more than 10³ viral copies per reaction. Specificity of Plexor real-time PCR was confirmed using the porcine viruses PCV1, PRRSV, CSFV, TTSuV1 and TTSuV2 employing the melting curve analysis of PCR products. The low values of coefficient of variation in the intra- (1.74%) and inter-assay (2.41%) analysis suggested that the assay was a highly reproducible. The Plexor real-time PCR was compared with three other real-time PCR systems (SYBR Green, TaqMan, LUX) with conclusion that it can be used as a method of choice for the detection and quantitation of PCV2.     

实时荧光RT-PCR检测活性单核细胞增生李斯特菌方法的建立

目的 采用逆转录结合实时荧光定量PCR技术,建立一种快速、准确、特异甄别单核细胞增生李斯特菌(Listeria monocytogenes,简称单增李氏菌)死活状态的定量方法.方法 根据单增李氏菌hlyA基因序列设计引物和探针;对实时荧光PCR反应体系进行优化后,提取菌体mRNA,通过随机引物进行逆转录反应;产生的cDNA通过实时荧光定量PCR进行鉴定.进一步评价逆转录结合实时荧光定量PCR方法的特异性、灵敏度、重复性后,对20份模拟双盲样本进行检测.结果 本实验所建立的逆转录结合实时荧光定量PCR方法可准确、特异地检测单增李氏菌,其他菌株和失活的单增李氏菌均无阳性结果出现;该方法检测纯菌和模拟样本的灵敏度分别可达到10 CFU/ml和1000CFU/ml;定量检测的批间和批内的变异系数均小于5%;对20份模拟样本进行检测,其中10份含有活性单增李氏菌样本的检测结果均为阳性,其他含有失活单增李氏菌的5份样本和其他致病菌的5份样本检测结果为阴性.结论 本文建立的检测活性单增李氏菌实时荧光定量PCR方法快速、准确,结果可靠,实用性强,可进行定量分析,为食品安全监测和现场流行病学调查提供较好的分析手段和完整的数据.