一种简易的HIV-1病毒载量定量筛查方法的建立

目的 建立一种基于RT-PCR法的简易的HIV-1感染者或艾滋病患者血浆病毒载量筛查方法.方法 在广西南宁市采集18例HIV-1感染者和18例阴性对照者血液标本,提取RNA,以引物LTR-1/LTR-2对待测样本进行PCR扩增,获得Ct值.同时,应用Nuclisens EasyQ HIV-1 v1.2法作为对照对这些样本进行病毒载量检测.对Ct值与病毒载量之间进行相关性分析,获得相应的回归方程.结果 待测样本中HIV-1感染者Ct值在29.103～31.610个循环之间,阴性对照者未能扩增出产物.RT-PCR法Ct值与Nuclisens EasyQ HIV-1 v1.2法检测出的病毒载量对数值之间具有良好的线性关系（r=-0.51,P=0.03）,回归方程为logY（viral road）=57.55-1.56＆#215;（Ct value）.结论 所建立的HIV-1病毒载量RT-PCR检测方法操作简单,价格便宜,与商业化试剂盒具有较好的一致性,可用于HIV-1感染定量筛查.     

河南某农村艾滋病患者劣势耐药毒株的进化及原发耐药研究

目的 了解河南省部分艾滋病患者抗病毒治疗效果及耐药发生情况,分析劣势耐药毒株在该人群本底存在情况.方法 以河南某农村149名初始接受抗病毒治疗的艾滋病患者为研究埘象,采用自建(In-house)基因型耐药检测方法分析抗病毒治疗失败患者HIV-1耐药发生情况,对抗病毒治疗后产生耐药的病例采用等位基因特异性实时定量PCR(allele-specific real-time PCR,ASPCR)方法检测其抗病毒治疗前样本劣势耐药毒株存在情况.结果 抗病毒治疗后患者的HIV-1病毒载量显著下降(t=275,P＝0.0001),但CD4+T淋巴细胞绝对数无明显变化(t＝1.765 168,P=0.0852).抗病毒治疗失败患者中耐药的发生率为4.88%,ASPCR检测发现,在调查基线时,7例耐药患者伞部存在劣势M184V突变,5例存在劣势K103N突变.结论 河南省部分未治疗的艾滋病患者存在HIV-1原发性耐药毒株,劣势耐药突变可能发展为优势耐药毒株并影响抗病毒治疗的效果.

Abstract：

Objective To evaluate the antiretroviral therapy(ART),analyze the prevalence of resistance in rural areas,Henan,and explore the presence of minor resistant variants in pre-ART.Methods One hundred and forty-nine AIDS patients initiating ART were recruited and investigated at intervals of 6 months. Method of In-house developed by our laboratory for genotypjc resistance test was to analyze the occurrence of resistance among the failure of ART,and the allele-specific real.time PCR(ASPCR)was used to detect the minor resistant variants at the baseline samples once the resistance occurred.Results Vimlload significantly decreased among the patients who received ART(t=275,P=0.0001),but the absolute counts of CD4+T lymphocytes had no significant change(t=1.765 168,P=0.0852).Rate of resistance among the patients of treatment failure was 4.88%.The result of ASPCR in the survey of baseline showed that the minor resistant variants of M184V were detected in 7 patients and mutation K103N presented in 5 patients.Conclusion The primary drug-resistant straias in the untreated patients were found in Henan,and they might develop the dominant resistance strains and bring about the failure of ART.     

体外无药物选择压力条件下HIV-1耐药基因突变的演变

目的 分离培养体外稳定传代的原代HIV-1耐药毒株,观察失去药物压力下,耐药毒株的体外生长以及主要耐药突变的演化趋势.方法 采集15例服用拉米夫定+司他夫定+萘韦拉平(3TC+D4T+NVP)的HIV-1感染者的外周血单个核细胞(PBMC),用体外共培养的方法从中分离原代HIV-1毒株;RT-PCR扩增耐药毒株历代培养上清的HIV-1 pol区基因并测序,在Stanford HIV Drug Resistance Database数据库进行耐药性分析.结果 15例患者中病毒载量>1000拷贝/ml的有8例,均成功分离出稳定传代的原代毒株,其中2株为耐药毒株,所携带的主要耐药突变分别是K103N/K238T和M184V/K103N/Y181C/H221Y,分别对NVP和3TC/NVP高度耐药;无药物压力的体外培养过程中,M184V、K103N、Y181C和H221Y等耐药突变可以稳定传代,但是K238T发生了回复突变.结论 分离出2株稳定传代的HIV-1耐药毒株,无药物压力情况下,携带K103N突变的毒株具有较好的复制适应性,可稳定传代;携带M184V和K103N/Y181C/H221Y的毒株也能够稳定复制;本研究中发现K238T耐药突变在失去药物的条件下稳定性差,提示该位点易发生回复突变.     

北京市2006年新确认HIV-1感染者耐药突变的流行性研究

目的 研究北京市2006年新确认HIV-1感染者毒株的耐药突变本底数据.方法 随机选取北京市2006年新确认HIV-1感染者抗凝全血标本50份,提取血浆病毒RNA,用逆转录聚合酶链反应扩增HIV-1 pol区基因片段,并进行序列测定及耐药基因型分析.结果 成功扩增出34份标本的pol区基因;在1例样本的蛋白酶编码区检测出1个主要耐药突变,7例样本检测出7个次要耐药突变,主要耐药突变为M46L,毒株是CRF01_AE亚型,次要耐药突变有4种,出现的频率分别为A71T(2个)、A71V(3个)、Q58E(1个)、V11IV(1个).在14例样本逆转录酶编码区检测出一种或多种核苷类和(或)非核苷类逆转录酶抑制剂耐药突变,9例标本检出核苷类逆转录酶抑制剂耐药突变,出现频率分别为:V118I(42.9%)、M184V(7.1%)、A62V(7.1%)、K70T(7.1%)、K65R(7.1%)、K219N(7.1%)、T69d(7.1%)、V75LV(7.1%)、K219R(7.1%);10例标本检出核苷类逆转录酶抑制剂耐药突变,出现的频率分别为V1061(35.5%)、Y181C(15.4%)、K103KR(7.7%)、K103R(7.7%)、L100LV(7.7%)、V1081(7.7%)、V179D(7.7%)、V179DV(7.7%).结论 北京市2006年新确认HIV-1感染者毒株中已经存在一定比例耐药突变,有必要定期进行耐药性监测研究.     

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.     

甲肝病毒特异性TaqMan荧光定量PCR法检测甲肝病毒核酸的研究

目的 建立甲肝病毒(HAY)特异性TaqMan荧光定量PCR检测方法,并对血清等样品中的HAV进行检测.方法 根据参考文献,选取HAV基因组保守区5'-NCR区引物和探针,建立特异性强、敏感度高、稳定性好的TaqMan HAV Real-time RT-PCR检测体系并应用于甲肝患者血清等病毒核酸的检测.结果 本研究建立的方法能够特异检测出样品中的甲肝病毒,其灵敏度介于每反应0.1CCID50至0.01CCID50之间.同一样本重复检测3次,批内样本Ct值的变异系数最大2.0％,批间样本Ct值的变异系数最大2.6％.急性期甲型肝炎患者血清中甲肝病毒为5.18×102～4.93×107拷贝/ml.结论 本实验建立的HAV Real-time RT-PCR检测方法具有特异、灵敏、快速等优点,可成功应用于临床样本等甲肝病毒的病原学检测.     

人类疱疹病毒6型荧光定量PCR检测方法的建立和应用

目的 建立人类疱疹病毒6型(HHV-6)荧光定量PCR检测方法,并检测临床样本.方法 根据文献合成HHV-6 U65-66基因片段的特异性引物和TaqMan探针,构建质粒制备标准品,评估该方法的特异性、灵敏度和重复性;并用该方法检测93份临床诊断为病毒性脑炎的脑脊液标本.结果 本实验检测HHV-6的灵敏度为3×10(0)拷贝/μl;标准曲线间线性关系(R2)为0.999,扩增效率为97.9％;同一样本重复检测3次,组内Ct值的变异系数最大为0.61％,组间为3.13％;特异性检测中只有HHV-6阳性标本出现扩增曲线.93份临床标本中检出HHV-6阳性2例,检出率为2.15％.结论 本实验所建立的荧光定量PCR检测HHV-6的方法特异强、灵敏高、重复性好,具有应用于临床检测的潜在价值.     

多色荧光PCR法检测HBV耐药位点突变

目的 利用多色荧光PCR技术,建立一套快速检测HBV耐药位点突变的方法 ,并对临床收集的服药患者血清进行耐药位点检测.方法 建立2个反应体系,每个反应体系包含4个耐药位点.对新建的多色荧光PCR法进行灵敏度和特异性分析,并对30例临床收集的服药患者血清进行耐药检测.结果 构建了多色荧光PCR检测HBV耐药位点的体系,其特异性较好,分析灵敏度可达1×103拷贝/ml.30例样本中检测到YVDD 2例（占6.67%）,YIDD 1例（占3.33%）;1896位点变异5例,占总数的16.67%.其他位点未检测到耐药突变.结论 所构建的多色荧光PCR检测体系为临床医院提供快速、简便的HBV耐药位点突变检测手段.HBV基因前C区的1896位点变异率较高.     

荧光定量PCR检测查菲埃立克体

依据查菲埃立克体16SrRNA基因序列设计特异性引物和TaqMan-MGB探针,以克隆的查菲埃立克体16SrRNA基因片段作DNA模板,建立实时荧光定量PCR检测方法。与套式PCR相比较,荧光定量PCR检测的灵敏度是其30倍;用荧光定量PCR检测其他相关立克次体和细菌DNA样本,检出结果为0;对荧光定量PCR检测重复性进行分析,变异系数(CV)批内和批间误差在0·2%~2·0%之间。结果证明本研究建立的荧光定量PCR方法具有种特异性和良好的重复性,可用于检测感染样本中的微量查菲埃立克体DNA。     

聚合酶链反应诱导丙型肝炎病毒(HCV)蛋白酶活性位点的突变及突变HCVNS3/4a蛋白的表达

目的 以聚合酶链反应（PCR）突变方法诱导丙型肝炎病毒（HCV）蛋白酶活性位点ser1165的突变，获得全长非结构基因3（NS3）／4a的表达与纯化。方法 分别以NS3 N端正向引物与诱变反向引物，诱变正向引物与NS4a C端反向引物获得2个PCR产物，产物纯化后在新的PCR反应体系中加入以上2个PCR产物与NS3 N端正向引物、NS4a C端反向引物。再次PCR扩增突变模板，分别与野生型模板重组入表达载体pET26-Ub，转化大肠杆菌BL21（DE3）pCG1，诱导表达后经菌体裂解、纯清化、硫酸铵沉淀、DEAE－Sepharose、NTA纯化，Western blot分析表达蛋白的特异性及PCR诱导突变使HCV蛋白酶活性位点失活的作用。结果 获得诱导突变的模板，Western blot证实该突变可完全阻断对NS3丝氨酸蛋白酶与NS3螺旋酶间的切割，部分阻断了螺旋酶与NS4a间的切割，纯化后的HCV NS3／4a蛋白在SDS－PAGE胶上显示为双带。结论 PCR突变方法简便、有效，获得丝氨酸蛋白酶失活的NS3蛋白表达，NS3蛋白与NS4a蛋白以复合物形式存在。     

Real-time PCR detection of multiple lamivudine-resistant mutations with displacing probes in a single tube.

BACKGROUND: Detection of lamivudine-resistant hepatitis B virus (HBV) is essential to clinical diagnosis and treatment. OBJECTIVES: To establish a single tube, real-time PCR assay for simultaneous detection of multiple lamivudine-resistant mutations in serum samples. STUDY DESIGN: By using four sequence-specific displacing probes labeled with different fluorophores, a single real-time PCR reaction can tell whether a sample contains any of the following HBV variants: wild-type, rtM204 mutant; mixtures of wild-type and rtM204 mutant; mixtures of rtM204 and rtL180 mutant; mixtures of wild-type, rtM204 mutant and rtL180 mutant. The assay was evaluated with 50 HBV mutation(s)-containing samples and 36 HBeAg-positive samples. RESULTS: The results of the real-time PCR assay were consistent with the DNA sequencing, but with much higher sensitivity for detecting a mixture of quasispecies. As few as 10(2)-10(3)copies/ml HBV of all four sequences in pure population and as little as 5% mutant DNA in the presence of wild-type DNA can be detected. CONCLUSIONS: Application of this high throughput assay into clinical use should enable earlier diagnosis and better treatment of lamivudine-resistant HBV.     

锁核酸结合分子信标技术检测乙型肝炎病毒DNA G1896A点突变研究

目的研究和评估乙型肝炎病毒（HBV）DNA G1896A点突变的实时荧光PCR检测方法。方法收集经测序验证HBV DNA G1896A未突变的野生型样本150例和已发生突变的突变型样本58例,在突变区域设计分子信标探针,点突变处进行锁核酸处理,利用荧光PCR方法检测HBV前C区G1896A点突变;再从临床标本中随机抽取18例、8例和19例荧光PCR结果分别显示为G1896A突变的标本、杂合的标本以及野生型的标本的PCR产物进行序列测定。结果突变型质粒和野生型质粒的检测灵敏度均可以达到100copies/ml;突变型探针检测高浓度的野生型质粒时无检测信号,野生型探针检测高浓度突变型质粒时无检测信号;突变型模板在总杂合模板中的比例达到5%时则都可以将突变型检测出来;序列测定的8例G1896A突变标本、6例杂合标本和19例野生型标本的PCR产物结果和荧光PCR检测结果完全吻合。结论实时荧光PCR检测方法可以快速、简便、准确地检测HBVDNAG1896A点突变,是检测点突变的重要方法,具有重要的临床应用价值。     

Ultrasensitive Amplification Refractory Mutation System Real-Time PCR (ARMS RT-PCR) Assay for Detection of Minority Hepatitis B Virus-Resistant Strains in the Era of Personalized Medicine

Resistance to antiviral treatment for chronic hepatitis B virus (HBV) has been associated with mutations in the HBV polymerase region. This study aimed at developing an ultrasensitive method for quantifying viral populations with all major HBV resistance-associated mutations, combining the amplification refractory mutation system real-time PCR (ARMS RT-PCR) with a molecular beacon using a LightCycler. The discriminatory ability of this method, the ARMS RT-PCR with molecular beacon assay, was 0.01 to 0.25% for the different HBV resistance-associated mutations, as determined by laboratory-synthesized wild-type (WT) and mutant (Mut) target sequences. The assay showed 100% sensitivity for the detection of mutant variants A181V, T184A, and N236T in samples from 41 chronically HBV-infected patients under antiviral therapy who had developed resistance-associated mutations detected by direct PCR Sanger sequencing. The ratio of mutant to wild-type viral populations (the Mut/WT ratio) was >1% in 38 (63.3%) of 60 samples from chronically HBV-infected nucleos(t)ide analogue-naive patients; combinations of mutations were also detected in half of these samples. The ARMS RT-PCR with molecular beacon assay achieved high sensitivity and discriminatory ability compared to the gold standard of direct PCR Sanger sequencing in identifying resistant viral populations in chronically HBV-infected patients receiving antiviral therapy. Apart from the dominant clones, other quasispecies were also quantified. In samples from chronically HBV-infected nucleos(t)ide analogue-naive patients, the assay proved to be a useful tool in detecting minor variant populations before the initiation of the treatment. These observations need further evaluation with prospective studies before they can be implemented in daily practice.     

Analysis of HCV resistance mutations during combination therapy with protease inhibitor boceprevir and PEG-IFN alpha-2b using TaqMan mismatch amplification mutation assay

TaqMan Mismatch Amplification Mutation Assay (TaqMAMA) is a highly sensitive allelic discrimination method. The mismatch amplification mutation assay (MAMA) is based on preferential amplification of mutant allele by the 'MAMA' primer, which is designed to have two mismatches with the wild-type allele and only one mismatch with the mutant allele. In this report, the TaqMAMA method was adapted for the detection and quantitation of minor HCV variants resistant to the protease inhibitor boceprevir (SCH 503034) from clinical samples. A good correlation of mutant frequency was observed between TaqMAMA and the results of clonal sequencing. TaqMAMA detected consistently minor variants at a level as low as 0.1%. Using TaqMAMA, it was demonstrated that resistant variants existed in the viral population before boceprevir treatment. The frequency of two resistant mutants (T54A and V170A) increased significantly during treatment with boceprevir, but was suppressed by combination treatment of PEG-IFN alpha-2b and boceprevir. The prevalence of both mutants decreased at the end of the two-week follow-up period. These results show that TaqMAMA can be used to detect minor resistant variants in pretreatment samples and to study in detail the evolution of mutant viruses during targeted antiviral therapy.     

Quantitative real-time PCR for detection of monkey B virus (Cercopithecine herpesvirus 1) in clinical samples

A TaqMan based real-time PCR assay was developed for rapid detection and quantitation of herpes B virus (Cercopithecine herpesvirus 1) in clinical samples. The assay utilizes B virus-specific primers and a probe to the non-conserved region of the gG gene to discriminate B virus from closely related alphaherpesviruses. Fifty copies of B virus DNA could be detected with 100% sensitivity with a wide range of quantitation spanning 6 logs. The assay was highly reproducible with intra- and inter-assay coefficients of variation of 0.6 and 2.4%, respectively. Clinical utility of the developed real-time PCR was evaluated by testing genomic DNA prepared from B virus clinical isolates (n=23) and human and monkey clinical specimens (n=62). This novel method was also compared with conventional cell culture with respect to sensitivity and specificity. TaqMan PCR assay was shown to be equally specific and more sensitive than culture method (culture vs. PCR sensitivity 50%) and was able to identify all B virus clinical isolates tested. Fast, reliable assessment of B virus DNA in infected cells and tissues makes real-time PCR assay a valuable tool for diagnosis and management of B virus infections.