Effects of Different Temperature and Time Durations of Virus Inactivation on Results of Real-time Fluorescence PCR Testing of COVID-19 Viruses

Summary:The novel coronavirus SARS-CoV-2 caused an outbreak of pneumonia in Wuhan,Hubei province of China in January 2020.This study aims to investigate the effects of different temperature and time durations of virus inactivation on the results of PCR testing for SARS-CoV-2.Twelve patients at the Renmin Hospital of Wuhan University suspected of being infected with SARS-CoV-2 were selected on February 13,2020 and throat swabs were taken.The swabs were stored at room tempcrature(20-25℃),then divided into aliquots and subjected to different temperature for different periods in order to inactivate the viruses(56℃for 30,45,60 min;65,70,80℃for 10,15,20 min).Control aliquots were stored at room temperature for 60 min.Then all aliquots were tested in a real-time fluorescence PCR using primers against SARS-CoV-2.Regardless of inactivation temperature and time,7 of 12 cases(58.3%)tested were positive for SARS-CoV-2 by PCR,and cycle threshold values were similar.These results suggest that virus inactivation parameters exert minimal infuence on PCR test results.Inactivation at 65℃for 10 min may be sufficient to ensure safe,reliable testing.

Detection of Ratoon Stunting Disease in Virus-free Seedcane via Real-time Fluorescence Quantitative PCR

This study was to develop the real-time fluorescence quantitative PCR technique for detecting the ratoon stunting disease （RSD） in virus-free seedcane seedlings. Healthy tissue culture seedlings were obtained from six plants of sugarcane ROC22, which had been confirmed RSD-positive by detecting the sugarcane juice, by employing the sugarcane seedlings production protocol. Real-time fluorescence quantitative PCR was used to detect RSD pathogens in tissue culture sam- pies. The results showed that target fragment of RSD pathogens was not found in all 10 samples in real-time fluorescence quantitative PCR, with the Ct values of 37 - 39. The healthy tissue culture sugarcane seedlings do not carry RSD pathogens, indicating that adopting healthy seedcane seedlings production technique could thoroughly get rid of RSD pathogens.

Development and Preliminary Application of SYBR Green I Real-Time Fluorescence Quantitative PCR Method for Detecting Porcine Parvovirus Virus

According to VP2 gene sequence of the porcine parvovirus virus strain NADL-2 （NC001718） available in GenBank （NC_001718）, a pair of specific primer was designed, and the target fragment of 431 bp was obtained by PCR amplification. The products were ligated with pMD18- T vector and then transformed into bacteria DH5α for recombinant plasmid extraction. After PCR identification and sequencing, recombinant plasmid was used as a standard template to establish the standard curve of SYBR Green I fluorescence quantitative PCR. Sensitivity test, specificity test and repeatability test were also determined. The results indicated that there was a good linear relationship between threshold cycle of the standard curve and template concentration, R2 =0.997 6. Tm ranged from 82.3 to 82.9 ℃, while the sensitivity was 72.1 copies/μl with good specificity and repeatability. The developed SYBR Green I real-time quantitative PCR method to detect PPV VP2 gene laid the basis for further studies on patho- oenesis, early clinical diaonosis of this virus and quantitative analysis of PPV infection.

A Universal Real-Time Fluorescence qPCR Method for Identifying Epidemic Strains of African Swine Fever Virus

Objective Establishing a highly sensitive real-time fluorescence quantitative PCR (qPCR) method for universal testing of epidemic African swine fever virus (ASFV) strains. Methods The ASFV p72 gene was targeted to design primer probes covering 24 p72 genotypes. The optimal amount of dimethylsulphoxide (DMSO) for qPCR amplification was determined, Various sensitivity and limit of detection (LOD) tests were performed, and clinical samples from China and imported goods were tested. Results The optimal primer-probe combination could specifically detect ASFV, 1.5% DMSO was optimal for qPCR, and LOD reached 3.2 copies/μL with good reproducibility (n = 20, p = 0.369). The method was employed to test 142 clinically suspected samples, of which 30 pig blood and 37 pig tissue samples were ASFV-positive. Moreover, the positive testing rate for ASFV was higher than for the standard qPCR method recommended by the Office International Des Epizooties (OIE), and for the commercially available kit. Thus, our method is superior for testing weakly positive samples with low virus titre, and epidemic strains present in imported goods. Conclusion Our method could be employed for universal testing of epidemic ASFV strains worldwide, ensuring wider coverage of hosts and ASFV strains/endemic strains, reducing false negatives, and benefitting early diagnosis.

Real-time fluorescent quantitative PCR非特异性扩增的研究进展

Real-time fluorescent quantitative PCR(RT-qPCR)因其高效快速、操作简便、高度敏感等优点获得广泛应用,但因其强大的放大功能而容易出现非特异性扩增的问题,尤其是荧光染料法中更加明显。文章对RT-qPCR的原理、非特异性扩增的发生因素、解决方案及该技术的应用前景进行了综述。

Application of Real-time Fluorescent Quantitative PCR in Plant

Real-time fluorescent quantitative PCR （RQ-PCR） is a detection method by adding fluorescent dye or fluorescent probe into the PCR reaction system, using fluorescent signal accumulation to monitor amplification reactions of PCR reaction process, and finally the unknown template can be quantitatively analyzed through the standard curve. So the detection level of PCR has improved from the qualitative to the quantitative. In order to provide a theoretical reference for further application, the principle, classification, advantages and disadvantages of RQ-PCR were intro- duced, and its application and progress in plants in recent years were reviewed.

Detection of Lactobacillus acidophilus in Fermented Material by Real-time Fluorescent Quantitative PCR

The species distinctive PCR primer of Lactobacillus acidophilus （ L. acidophilus） was designed according to 16S rRNA gene sequences of conunon Lac- tobacillus species in fermented material. Bacterial genome DNA of separated L. acidophilus in fermented sample was taken as template, and L. acidophilus in fer- mented material was conducted the quantitative determination by real-time quantitative PCR （RT-PCR）. Analysis on RT-PCR results shown that contents of L. aci- dophilus in the test sample reached 1.5 billion CFU / g. Test results shown that contents of L. acidophilus in fermented material could be detected accurately by the established RT-PCR method in the test. indicating that the established RT-PCR method could be aookued to the detection of L. acidophilus in fermented material.

Application of Real-time Fluorescent Quantitative PCR in Studies on Plants

Real-Lime fluorescent quantitative PCR is a method for quantitative analysis of gene expression developed in recent years, which has been widely used in various fields such as basic scientific research, clinical diagnosis, disease study, drug research and development since its appearance. It starts relatively late in study on plants, but has already been used for analysis of gene expression in plants and gene identification of exogenous genes. The principles or advantages and dis- advantages of real-time fluorescent quantitative PCR, or its potential problems and condition optimizations in tests were introduced in this study, and then the appli- cation and prospect of real-time fluorescent quantitative PCR in study on plants were also been discussed.

Development of Real-Time Fluorescent PCR for Rapid Detection of Haempohlius parasuis

[ Objective] To develop a real-time fluorescent PCR assay for rapid detection of Haempohlius parasuis （HPS）. [ Method] According to the conservative sequences of 16 S rRNA genes of HPS published in GenBank, a pair of specific primers was designed. The real-time fluorescent PCR was developed by optimizing primer concentration and annealing temperature. And its specificity and reproducibility were evaluated. Ten HPS- suspected samples were detected by the developed method. [ Result] The lowest detection limit of the developed real-time fluorescent PCR was 50 copies/μl. This method had good reproducibility, and its coefficient of variation was lower than 2%. Only HPS rather than Streptococcus suis type 2, Staphylococcus aureus, E. coli DH5 alpha, and swine Salmonella typhi could be detected by the developed real-time fluorescent PCR. The HPS-pesitive samples detected by this method were also positive when they were detected by isolation of bacteria or conventional PCR. [ Conclusion] The developed real-time fluorescent PCR is rapid, sensitive, specific and highly reproducible; thus, it can be used for rapid detection of HPS.

Synchronously Detecting Allergenic Ingredients of Peanut and Sesame in Food by Real-time Fluorescent PCR

Peanut,sesame and other raw materials of food are allergens for special populations.In this study,specific primers and TaqMan probes labeled by different fluorescences were designed targeting Ara h 2 gene of peanut and Ses i 1 gene of sesame.After the optimization of reaction conditions,a real-time fluorescent PCR method was established for simultaneous detection of allergenic ingredients of peanut and sesame in food.Genomic DNA samples of peanut,sesame,rice,wheat,barley,soybean,celery,maize,potato,tomato,walnut,groundnut in shell,cashew nut,sunflower seed,almond,apple,pear and strawberry,pork,beef,mutton and fish were used as templates for PCR amplification with deionized water as negative control template.Results indicated that the established real-time fluorescent PCR method could specifically identify allergenic ingredients of peanut and sesame simultaneously.Sensitivity test showed that the minimum detection limit of this method was 0.01%.Therefore,the established real-time fluorescent PCR method is a specific,sensitive and effective assay for simultaneously detecting allergenic ingredients of peanut and sesame in food.

Establishment of a Real-time Fluorescent Quantitative PCR Assay for Detection of Genetically Modified Maize Line MON88017

In order to improve the standardized technical systems of quantitative analyses for genetically modified organisms （GMOs） and products, ensure bio-safety and reduce ecological risk in China, a real-time fluorescent quantitative PCR assay was established for detection of genetically modified maize line MON88017. The established method was evaluated based on the specificity, sensitivity, accuracy and measurement uncertainty. The results showed that the established method had strong specificity in detection of genetically modified maize line MON88017. 1.50% MON88017 sample was detected with 29 replica- tions. The average measured value （ 1. 541% ） was close to the actual value （ 1.50% ） and the relative deviation was 2.70%. The variation coefficient of the measured value was 0.110 g ; the recovery was 100.00% and the measurement uncertainty was 0. 096. The limit of detection for genetically modified maize line MON88017 with the established method was 5 copies at the 97.5% confidence level. Thus, the real-time fluorescent quantitative PCR assay established in this study exhibited high specificity, accuracy and sensitivity, which could provide technical support for the safety supervision of genetically modified organ- isms and products in China.

Real-time TaqMan RT-PCR快速检测犬瘟热病毒方法的研究

按照犬瘟热(CDV)N基因序列,设计合成了特异性引物和探针,经各反应条件的优化,建立了Real-time荧光定量RT-PCR技术,对细胞培养物、肝脏、肺脏、脑、脾脏、淋巴结以及鼻腔拭子等组织病料中的CDV进行了特异性检测和敏感性试验。同时,利用建立的Real-time荧光定量RT-PCR方法与常规RT-PCR以及韩国BIOINDIST生产的BIT RAPID CDV检测试剂盒对57份临床样品进行了检测。结果:用20pmol/mL的引物浓度各1uL和20pmol/mL的探针浓度0．3uL,获得的荧光信号最强,曲线平滑。敏感性高,可检测到1．24×10—3ng/uL的病毒RNA;特异性强,与NDV、AIV、NiPV等RNA病毒不发生交叉反应。试验重复性的变异系数(CV)分别为2．3%、2．5%和4．2%;与常规RT-PCR和BIOINDIST生产的BIT RAPID CDV检测试剂盒相比较,该方法具有快速、特异、敏感、可定量,并可同时检测大量样品等优点。

Comparison of real-time polymerase chain reaction with the COBAS Amplicor test for quantitation of hepatitis B virus DNA in serum samples

AIM:To compare the clinical performance of a real-time PCR assay with the COBAS Amplicor Hepatitis B Virus (HBV) Monitor test for quantitation of HBV DNA in serum samples. METHODS: The reference sera of the Chinese National Institute for the Control of Pharmaceutical and Biological Products and the National Center for Clinical Laboratories of China, and 158 clinical serum samples were used in this study. The linearity, accuracy, reproducibility, assay time, and costs of the real-time PCR were evaluated and compared with those of the Cobas Amplicor test. RESULTS: The intra-assay and inter-assay variations of the real-time PCR ranged from 0.3% to 3.8% and 1.4% to 8.1%, respectively. The HBV DNA levels measured by the real-time PCR correlated very well with those obtained with the COBAS Amplicor test (r = 0.948). The real-time PCR HBV DNA kit was much cheaper and had a wider dynamic range. CONCLUSION: The real-time PCR assay is an excellent tool for monitoring of HBV DNA levels in patients with chronic hepatitis B.

Development of real-time PCR method for rapid detection and quantification of Heterosigma akashiwo

To rapidly detect the harmful algae H.akashiwo qualitatively and quantitatively, sequences of the 18S rDNA deduced from H.akashiwo were used for designing species-specific primers, and a RFQ-PCR (Real-time Fluorescent Quantitative Polymerase Chain Reaction) method was developed for quantitative detection of H.akashiwo. Primer H.akashiwo and TaqMan probe were designed, and the specificity of primer was checked with PCR. A calibration curve was constructed with cycle threshold value against visual counted cell number. And the value of the curve was tested with other H.akashiwo samples, which were assayed with both the RFQ-PCR method and visual count under microscope.

诺如病毒TaqMan荧光定量PCR检测方法的设计与优化

为设计一种快速、高灵敏度检测诺如病毒(Norovirus,NV)的方法.本文通过检索参考NCBI数据库中收录的国内典型流行的NV毒株BJSMQ的基因序列NC_039476.1,合成了NV的标准重组质粒,根据NV的ORF1基因保守序列设计一组特异性引物和荧光探针;通过正交试验进行程序及试剂反应体系的优化,设计TaqMan荧光定量PCR检测方法.结果表明该检测方法具有高灵敏度,最低检测限可达1.2 copies/μL,且在标准重组质粒浓度1.2×10^(5)~1.2×10^(0) copies/μL范围内具有较好的线性关系,其R^(2)=0.9907;该方法特异性强,在病毒的混合重组质粒样液中仅与NV病毒反应;组内和组间的重复性良好,变异系数(CV)值均小于2%;在数字PCR试验中进一步验证了该方法的可行性.本文设计的TaqMan荧光定量PCR检测方法可用于NV毒株的快速准确检测,有望成为NV诊断的有效工具.

奶牛乳房炎病原微生物20联核酸检测试剂盒(PCR-荧光探针法)的临床应用评估

为了评估商品化的奶牛乳房炎病原微生物20联核酸检测试剂盒(PCR-荧光探针法)(后文简称为“检测试剂盒”)在临床应用中的适用性,本试验采用传统细菌分离培养、检测试剂盒、16S rRNA基因扩增子测序和药物敏感性试验对宁夏回族自治区9个牧场155份奶牛乳房炎奶样分别进行菌株鉴定和耐药性检测,并将检测试剂盒与其他3种检测结果进行比较和分析。结果显示,检测试剂盒与传统细菌分离培养在病原菌检出情况上基本保持一致,均主要检出了大肠杆菌、芽孢杆菌属和凝固酶阴性葡萄球菌(CNS)等;检测试剂盒与16S rRNA基因扩增子测序结果在菌属组成上一致性较高,均主要检出了假单胞菌属、链球菌属和葡萄球菌属等;药物敏感性试验结果显示,检出率较高的66株病原菌分离株对β-内酰胺类抗菌药物的耐药率普遍偏高;奶样中β-内酰胺酶耐药基因blaZ的检测试剂盒检出结果与同一奶样中分离菌株的药物敏感性试验结果一致率达58%(7/12)。综上所述,该检测试剂盒具有较高的准确度和病原覆盖率,可为牧场奶牛乳房炎主要病原的快速诊断和耐药基因(blaZ)监测提供有效的技术支持,从而降低抗菌药物的使用量,以减少牧场经济损失。

TaqMan实时荧光PCR快速检测与鉴定单核细胞增生李斯特氏菌能力验证样品

利用TaqMan实时荧光PCR技术对单核细胞增生李斯特氏菌能力验证样品进行快速鉴定和验证。依据GB 4789系列标准的第一法对ACAS-PT526能力验证中的样品D15和样品D16进行检测,通过增菌、分离、初筛和鉴定等传统培养法检测。鉴定过程中还使用了鉴定试剂条API Listeria和全自动微生物鉴定系统。同时采用TaqMan实时荧光PCR技术对经过增菌的样品D15与样品D16的培养物和单核细胞增生李斯特氏菌标准菌株的培养物进行快速鉴定。结果表明,经API Listeria试剂条鉴定,样品D15为单核细胞增生李斯特氏菌,鉴定百分率为98.6%,T值为1;经全自动微生物鉴定系统检测,样品D15为单核细胞增生李斯特氏菌,99%可能性;样品D16为金黄色葡萄球菌,99%可能性;经实时荧光PCR鉴定,样品D15 LB1增菌液培养物及李斯特显色培养基平板上的单菌落都具有显著的S型扩增曲线。综上得出,实时荧光PCR与GB 4789.30—2016的第一法试验结果一致,样品D15为单核细胞增生李斯特氏菌检出,样品D16为单核细胞增生李斯特氏菌未检出,TaqMan实时荧光PCR方法可用于微生物的快速检验,尤其是对盲样检测的辅助验证。

实时荧光定量PCR检查在献血者乙型肝炎病毒核酸检测中的应用

目的探究献血者乙型肝炎病毒(HBV)核酸检测中,实时荧光定量PCR检查的应用价值。方法选取2022年10月至2023年9月宁德市中心血站10403份献血者标本,对其进行乙型肝炎病毒检测。ELISA检测用A、B两种不同试剂进行初检、复检,对检测阴性的血液标本进一步行核酸检测。结果经ELISA检测,A试剂初检乙型肝炎病毒表面抗原(HBsAg)阳性率为0.57%(59/10403);B试剂复检HBsAg阳性率为0.65%(68/10403)。对阴性血液标本进一步核酸检测,A试剂初检HBsAg阴性标本的阳性率为0.261%(27/10344);B试剂复检HBsAg阴性标本的阳性率为0.174%(18/10335)。结论献血者HBV检测使用核酸检测有助于提高血液筛查的准确性,保障用血安全。

SAT-TB联合FQ-PCR检测在痰涂片阴性肺结核诊断中的效能

目的:分析RNA恒温扩增实时检测技术(SAT-TB)联合荧光定量聚合酶链反应(FQ-PCR)检测在痰涂片阴性肺结核患者诊断中的效能。方法:选取2020年7月至2022年7月该院收治的75例疑似痰涂片阴性肺结核患者进行前瞻性研究。采集所有患者肺泡灌洗液标本,采用SAT-TB、FQ-PCR法进行检测,以结核分枝杆菌痰培养结果为“金标准”,比较SAT-TB、FQ-PCR单项及联合检测在痰涂片阴性肺结核诊断中的效能。结果:金标准结果显示,75例疑似痰涂片阴性肺结核患者中,阳性48例,阴性27例;SAT-TB检测结果显示,阳性36例,阴性39例;FQ-PCR检测结果显示,阳性37例,阴性38例;SAT-TB联合FQ-PCR检测结果显示,阳性47例,阴性28例;SAT-TB联合FQ-PCR检测诊断痰涂片阴性肺结核的灵敏度、准确度均高于SAT-TB、FQ-PCR单项检测诊断,漏诊率低于SAT-TB、FQ-PCR单项检测诊断,差异有统计学意义(P<0.05)。结论:SAT-TB联合FQ-PCR检测诊断痰涂片阴性肺结核的效能高于二者单项检测诊断效能。

实时荧光定量RT-PCR在麻疹和风疹病毒检测中的应用

目的探讨实时荧光定量RT-PCR在麻疹和风疹病毒检测中的应用效果。方法选取2021年12月—2022年12月盘锦市疾病预防控制中心接收的麻疹与风疹患者76例为研究对象,入院后所有研究对象均接受酶联免疫吸附试验法和实时荧光定量RT-PCR法检测,以检测患者恢复期血免疫球蛋白G(IgG)抗体水平(相对急性期是否4倍升高)为麻疹诊断金标准,对比两种检测方法的检测准确率、不同检测时间的阳性检出率。结果实时荧光定量RT-PCR法总诊断准确率为97.37%;酶联免疫吸附试验法中总诊断准确率为88.16%,比较两种方法的诊断准确率差异有统计学意义(P<0.05)。第1d,实时荧光定量RT-PCR法阳性检出率高于酶联免疫吸附试验法,差异有统计学意义(P<0.05)。第5d,实时荧光定量RT-PCR法阳性检出率低于酶联免疫吸附试验法,差异有统计学意义(P<0.05)。第2d、第3d、第4d实时荧光定量RT-PCR法和酶联免疫吸附试验法阳性检出率对比差异无统计学意义(P>0.05)。结论实时荧光定量RT-PCR对麻疹、风疹检测有一定诊断作用,可以有效提高检测准确率,同时操作简单,灵敏性较高,值得在麻疹与风疹病毒检测中推广。