水痘-带状疱疹病毒RAA检测方法的建立及初步应用

目的建立水痘-带状疱疹病毒(varicella-zoster virus, VZV)的重组酶等温扩增(recombinase-aid amplification, RAA)快速检测方法。方法通过全球共享数据库下载VZV全基因组序列进行比对分析, 针对四个保守基因分别设计特异性引物与探针并筛选出最佳组合, 通过引物与探针浓度梯度筛选出最佳反应体系, 建立荧光型RAA检测方法。用VZV阳性质粒标准品与梯度稀释的临床样本评价方法的灵敏度, 以最低检出极限浓度的阳性质粒标准品进行重复实验评价方法的重复性, 以其他病毒核酸评价方法的特异性, 同时用本方法和荧光定量聚合酶链式反应(quantitative real-time PCR, qPCR)对临床样本进行检测并对检测结果进行比较。结果本方法筛选出针对开放阅读框架(open reading frame, ORF)28基因的引物对F2/R2与探针P2为最佳组合;考虑到成本因素, 最佳引物浓度为500 nmol/L, 最佳探针浓度为280 nmol/L;最低检出极限为101拷贝/μL, 最低可检测到Ct值为36.027的临床阳性样本;重复实验的检测...     

基于RAA-CRISPR/Cas12a的猴痘病毒核酸检测方法的建立

目的建立一种基于RAA-CRISPR/Cas12a的特异性强、灵敏度高的猴痘病毒核酸检测方法。方法根据已知猴痘病毒基因保守区设计合成重组酶介导等温核酸扩增(recombinase-aided amplification, RAA)引物和成簇规律间隔的短回文重复序列RNA(clustered regularly interspaced short palindromic repeats RNA, CRISPR RNA, crRNA), 利用荧光检测技术筛选特异crRNA, 通过荧光计数读取CRISPR/Cas12a检测结果, 同时对所建立方法的灵敏性和特异性进行评价。结果建立了基于RAA-CRISPR/Cas12a的猴痘病毒核酸检测方法, 其灵敏度为2.5拷贝/反应, 且与鼠痘病毒、痘苗病毒无交叉反应, 具有高特异性。结论建立了基于RAA-CRISPR/Cas12a的猴痘病毒核酸检测方法, 为高效、快速、特异性检测猴痘病毒感染提供了有力工具。     

CLIP-PCR直接检测血液中疟原虫雌性配子体特异转录产物s25 mRNA

目的建立一种疟原虫雌性配子体的分子检测法。方法根据疟原虫雌性配子体特异性mRNA靶标(待测靶序列)即动合子表面蛋白(s25)的转录产物,设计特异性的捕获探针和连接探针。血液样品经裂解释放的mRNAs,无需核酸提取,通过"三明治"杂交被捕获到96孔板表面。洗去未结合探针后,将结合在mRNA靶标上的连接探针进行连接,得到两端为特殊设计序列的单链扩增模板。再用通用引物进行染料法qPCR扩增,或在端部设计TaqMan探针序列,用通用引物和通用TaqMan探针进行探针法qPCR扩增。评价这一基于捕获和连接扩增的方法(CLIP-PCR)的灵敏度、特异性和重复性并与普通的RT-qPCR方法进行比较,将其应用于临床样品的检测。结果该CLIP-PCR具有较高的灵敏度和特异性。与普通的RT-qPCR一样,均可检测低至11拷贝数的s25 mRNA靶标;而且该CLIP-PCR操作更简便。该CLIP-PCR可准确检测到疟疾患者血液中的雌性配子体。可将96个样品的检测时间缩短至3 h。结论建立了灵敏高效的染料法和通用TaqMan探针法CLIP-PCR检测疟原虫雌性配子体,为疟疾传播的控制、配子体大规模筛查奠定了基...     

应用单分子触发式级联指数恒温扩增技术检测长链非编码RNA方法的建立

目的建立一种利用核酸恒温指数扩增技术特异性检测长链RNA的高灵敏度检测方法。方法利用恒温指数扩增(EXPAR)反应对所建立的方法进行反应条件的优化,并对该方法的通用性、特异性和灵敏度进行了系统分析。结果单分子触发反应产物可以作为引物触发指数恒温扩增;柔性引物可以提高检测特异性,柔性臂长7nt;单分子触发式级联指数恒温扩增技术能够有效检测出待检样品浓度在10fmol/L～100pmol/L范围内的靶标RNA,线性响应良好(R 2=0.955)。结论单分子触发级联式恒温指数扩增技术可以快速、准确检测长链RNA。     

应用多聚酶链反应技术检测疟原虫的初步研究

根据编码恶性疟原虫(P．f)红细胞结合抗原(EBA-175)的部分DNA片段和间日疟原虫(P．v．)小亚基核糖体RNA基因序列设计合成恶性疟原虫和间日疟原虫的特异性引物各一对并进行多聚酶链反应(PCR)检测恶性疟和间日疟病人标本。扩增产物经琼脂糖电泳分析，可见在P．f.样本中扩增出特异的492bp大小的DNA片段，P．v．样本中扩增出特异的714bp大小的DNA片段。而在健康人血的白细胞、伯氏疟原虫样本和食触猴疟原虫样本中均不能扩增出以上片段。其结果与镜检符合率分别达95％和93.3％以上，表明该方法是一种特异、敏感的检测方法。     

寨卡病毒可视化RT-LAMP检测方法的建立与应用

本研究建立了一种简单、快速、准确的寨卡病毒可视化逆转录环介导等温扩增(RT-LAMP)检测方法。在线设计3套LAMP引物,利用实时浊度仪筛选最佳引物,加入羟基萘酚蓝,评估可视化RT-LAMP检测方法的灵敏度和特异性。建立的可视化RT-LAMP方法可检测的最低浓度为101copies/μL,高于普通PCR和荧光定量PCR 1~2个数量级;同时,该方法不与其他虫媒病毒产生交叉反应。该方法可为虫媒监测和临床诊断提供实验依据。     

牛瑟氏泰勒虫病PCR诊断方法的建立

为建立一种快速、敏感的牛瑟氏泰勒虫病诊断方法,本实验分离提取牛瑟氏泰勒虫全血基因组DNA,并设计一对编码牛瑟氏泰勒虫32 kDa (P32) 主要表面蛋白基因的引物,进行PCR扩增,预期扩增的片段为875 bp.并对该实验进行特异性、敏感性及临床检测实验.结果成功扩增出了长为875 bp的基因片段,且具有高特异性和很好...     

重组酶聚合酶扩增结合横向流体试纸条快速检测人腺病毒CSCD

目的 建立一种快速、敏感的人腺病毒等温核酸扩增检测方法.方法 针对人腺病毒hexon基因保守区序列设计特异性重组酶聚合酶扩增（RPA）引物及探针、优化反应时间和温度、用横向流体试纸条（LFD）和毛细管电泳检测扩增产物,建立人腺病毒RPA-LFD快速检测方法,评价该方法的敏感度和特异性并与Real-time PCR法比较.结果 RPA-LFD方法检测人腺病毒的最低检出限为2拷贝DNA分子/反应,且与其他呼吸道病原无交叉反应,临床样本检测结果与Real-time PCR法一致性为100％.结论 建立的RPA-LFD方法具有敏感性、特异性高、快速且不需要昂贵的仪器设备等优点,为人腺病毒快速检测提供了新工具.     

基于茎环引物探针法定量检测乙型肝炎病毒miR-3的方法学建立

目的:本研究拟通过广泛筛选特异性引物探针组,建立一套乙型肝炎病毒(HBV)微小RNA-3(miR-3)的绝对定量PCR检测方法。方法:基于茎环引物RT-qPCR方法原理,设计茎环引物进行逆转录,结合SYBR Green法qPCR进行特异性初筛,选择特异性较佳的引物组,再结合TaqMan MBG探针,确定最佳的引物探针组,实现对HBV miR-3的定量检测。结果:共设计和测试了25套茎环引物组,利用基于SYBR Green的RT-qPCR方法,筛选出6套具有良好特异性的引物组,并进一步针对这些引物组设计和测试了相应的探针,获得了可精准定量HBV miR-3的引物探针组。测试结果表明,该引物探针组不但保证了高特异性,而且定量线性范围达到每个反应102～108拷贝,其扩增效率约为88%。结论:本研究确立了一套可用于绝对定量检测HBV miR-3的特异性引物探针组。     

基于颜色判定的逆转录环介导恒温扩增技术检测HIV-1病毒

目的 建立一种基于颜色判定的用于人类免疫缺陷病毒Ⅰ型(HIV-1)检测的逆转录环介导恒温扩增(RT-LAMP)技术.方法 根据HIV-1 gag基因保守区的序列设计RT-LAMP引物,利用 已建立好的基于羟基萘酚蓝(HNB)颜色判定的RT-LAMP体系验证其灵敏度与特异性,并对实时荧光逆转录PCR(qRT-PCR)确认的临床样本进行一致性对比.结果 RT-LAMP引物特异性高,检出限为1000个拷贝RNA,对43份临床样本检测的灵敏度和特异性分别为94.6％ ～ 100％.结论 基于颜色判定的环介导恒温扩增方法摆脱了对昂贵仪器的依赖,有望应用于HIV-1感染的现场筛选,为快速检测HIV-1病毒提供了新方法和新思路.     

Development of a PCR assay followed by nonradioactive hybridization using oligonucleotides covalently bound to CovaLink NH microwells for detection of four Plasmodium species in blood samples from humans

We developed and evaluated a PCR-based assay to detect four Plasmodium species in 79 blood samples from 56 travelers returning from areas where malaria is endemic. DNA amplification targeting a small region of the 18S rRNA gene was performed with Plasmodium genus-specific primers. The biotinylated PCR products were then identified by PCR-colorimetric Covalink NH microwell plate hybridization (CMPH) using species-specific phosphorylated probes covalently bound to a pretreated polystyrene surface. The results from PCR-CMPH showed high specificity, and for 47 of the 56 patients (84%), microscopy and PCR-CMPH results were in agreement. Discordant results were reevaluated with microscopy examination, other molecular methods, and DNA sequencing. Except for one patient, discrepancies were resolved in favor of PCR-CMPH: three mixed infections were detected, four species identification errors were corrected, and two negative results were shown to be positive. Our results indicate that PCR-CMPH is a simple, rapid, and specific method for malaria diagnosis. It employs stable reagents and inexpensive equipment, making it suitable for routine epidemiological use.     

PCR assay for species-specific identification of Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is the second most frequently encountered species of the anaerobes isolated from clinical specimens. We developed a PCR-based assay for the rapid identification of B. thetaiotaomicron. Specific primers were based on shared amplicons of about 1.2 kb generated from B. thetaiotaomicron by randomly amplified polymorphic DNA. This 1.2-kb fragment was sequenced and then used to design a set of PCR amplification primers. This PCR generated an amplification product of 721 bp, which was unique to all 65 isolates of B. thetaiotaomicron tested. There was no amplification with isolates of other bacterial species. Restriction enzyme digestion of the amplification product and dot blot hybridization further verified the specificity of the assay. These results suggest that this PCR assay targets a nucleotide sequence that is strongly conserved in B. thetaiotaomicron. This simple and rapid PCR assay provides a rapid and accurate method for identification of B. thetaiotaomicron and shows promise for the detection of B. thetaiotaomicron in clinical samples.     

Sensitive and rapid detection of the new Delhi metallo-beta-lactamase gene by loop-mediated isothermal amplification

New Delhi metallo-β-lactamase 1 (NDM-1), which is associated with resistance to carbapenem, was first reported in 2008. A sensitive and rapid molecular assay to detect the plasmid bla(NDM-1) in clinical isolates is needed to control its spread. We describe a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of bla(NDM-1) from pure culture and sputum, urine, and fecal samples. Eight sets of primers were designed to recognize six or eight distinct sequences on target bla(NDM-1), and one set was selected as the most appropriate set of primers for its rapid detection. The specificity and sensitivity of the primers in the LAMP reactions for bla(NDM-1) detection were determined. The sensitivity of the LAMP assay for bla(NDM-1) detection in sputum, urine, and fecal samples was also tested. Two methods, namely, monitoring of turbidity and addition of calcein to the reaction tube, were used to determine negative and positive results. The results showed that target DNA was amplified and visualized by the two detection methods within 70 min at an isothermal temperature of 65°C. The sensitivity of LAMP, with a detection limit of 10.70 pg/μl DNA, was 100-fold greater than that of PCR. Thirteen infection bacterial strains without bla(NDM-1) were selected for testing of specificity, and the results of the amplification were negative, which showed that the primers had good levels of specificity. The LAMP method reported here is demonstrated to be a potentially valuable means for the detection of bla(NDM-1) and rapid clinical diagnosis, being fast, simple, and low in cost.     

Direct detection of Mycobacterium tuberculosis in respiratory specimens in a clinical laboratory by polymerase chain reaction.

The emergence of epidemic multiple-drug-resistant (MDR) strains of Mycobacterium tuberculosis in conjunction with an increase in the number of reported cases of tuberculosis (TB) represents a major public health problem. In light of a recent outbreak of MDR M. tuberculosis at our center, we began the development of a polymerase chain reaction (PCR) assay for the rapid diagnosis of pulmonary TB using two sets of primers, one based on the IS6110 repeated sequence of M. tuberculosis and the other based on the protein antigen b (PAB). Reaction conditions were first optimized as to the appropriate extraction protocol and the concentrations of primer pairs, nucleotides, and MgCl2. Following a preliminary evaluation of the assay with clinical specimens, extraction and amplification procedures were further modified. PAB and IS6110 primers detected between 2 and 23 and 0.023 and 0.23 CFU of M. tuberculosis, respectively, in pooled, M. tuberculosis-negative sputa by our optimized PCR assay. After routine processing for mycobacteria, 734 specimens were subsequently amplified. DNA for amplification was obtained by boiling and beating the sediments with Tween 20. For each reaction, DNA (10 microliters) was added to an amplification mixture containing 12 pmol of IS6110 primers, 20 pmol of PAB primers, 2 mM MgCl2, 200 microM nucleotides, and 2.5 U of Taq polymerase and the mixture was then amplified for 40 cycles. The sensitivity and specificity of our PCR assay were 87.2 and 97.7%, respectively. We were unable to interpret the results for seven specimens (1%). In our experience, PCR proved to be a useful rapid diagnostic test for TB in a clinical setting and a valuable epidemiological tool for determining exposure groups in the hospital setting. Our findings also underscore the need for the systematic optimization of PCR assay conditions.     

Detection of porcine parvovirus by loop-mediated isothermal amplification

Loop-mediated isothermal amplification is a novel method for rapid amplification of DNA. It has been adopted widely for the detection of virus because of its simplicity, rapidity, and specificity. A loop-mediated isothermal amplification assay was developed for the detection of porcine parvovirus. Four primers specific for six regions of PPV non-structural protein 1 gene were designed with an online software. After amplifying at a constant temperature of 59-65 degrees C by Bst enzyme, a clear result was visible after 2.5% agarose gel electrophoresis. The sensitivity and specificity of this assay were evaluated by comparison with the polymerase chain reaction. The detection limit of the assay was shown to be equivalent to 5 PPV copies/reaction. Due to its specificity and simplicity, the assay should be a useful diagnostic tool for epidemiologic studies of PPV.     

猴空泡病毒40核酸序列检测法的优化研究

目的 对通常使用的猴空泡病毒40(Simian vacuolating virus 40,SV40)核酸序列检测法进行优化,寻找敏感性高、特异性强、适用面广的SV40核酸序列检测引物.方法 以21个SV40毒株完全基因组为基础数据,用Primer Premier 5.00软件重新设计两对SV40 DNA检测引物,用Oligo 6.71软件和DNAMAN 6.0.40软件对引物参数进行分析,将分析结果与通常使用的检测引物进行比较.用不同稀释度SV40核酸序列作模板,比较4对引物检测的敏感性.分别用无菌水、Vero细胞DNA、SV40 DNA作模板检测4对引物的特异性.结果 对于21个SV40病毒株,优化引物对VP1和T的序列是保守的;对于接受号为J02400、NC_001669、AF316139和AF316141的4个病毒株,通常使用的引物对GCVP1和GCT的序列是保守的;用同一稀释度的SV40 DNA作模板,引物对VP1和T的扩增效率明显高于引物对GCVP1和GCT;在特异性检测比较中,引物对VP1和T没有出现非特异性扩增条带,引物对GCVP1和GCT在100 bp处出现非特异性扩增条带.结论 优化的SV40核酸序列检测法具有敏感性高、特异性强、检测面广、引物及其PCR产物序列保守等特点.