香蕉束顶病毒实时荧光PCR检测方法的建立

根据香蕉束顶病毒（Banana bunchy top virus,BBTV）复制酶基因保守序列设计特异性探针及引物,建立了BBTV实时荧光PCR（TaqMan real-time PCR）检测方法。结果显示,所建立的检测方法在检测质粒DNA标准品和发病香蕉植株总DNA时,其灵敏度均比普通PCR高,且与黄瓜花叶病毒（Cucumber mosaic virus,CMV）和香蕉线条病毒（Banana streak virus,BSV）无交叉反应。同浓度样品进行7次重复性试验,各重复扩增结果所得Ct值的变异系数为0.93%,表明建立的荧光定量PCR检测方法重复性好,Ct值保持稳定。利用所建立的方法检测带毒香蕉吸芽繁殖的组培苗中的BBTV,发现BBTV含量随着继代数的增加而增加,并且组培苗顶部叶片中的含量高于其他部位的叶片。     

苹果茎痘病毒TaqMan探针实时荧光定量RT-PCR检测方法的建立

为建立一种检测苹果茎痘病毒（Apple stem pitting virus,ASPV）的TaqMan探针实时荧光定量RT-PCR方法,根据ASPV外壳蛋白基因（coat protein,cp）保守序列设计了特异性引物和TaqMan探针,以体外转录的RNA为标准品构建标准曲线,并对该方法的特异性、灵敏性、重复性进行检验。建立的标准曲线决定系数达0.996,扩增效率为99%;该方法特异性好,与苹果茎沟病毒（ASGV）、苹果褪绿叶斑病毒（ACLSV）、苹果锈果类病毒（ASSVd）均无交叉反应;其最低检测限为1.31 × 102 copies ? μL-1,灵敏度比常规RT-PCR高100倍;批内和批间变异系数均小于1.85%。该方法具有特异性强、灵敏度高、重复性好等优点,适用于田间样品中ASPV的快速定量检测。     

黄瓜绿斑驳花叶病毒核酸试纸条检测技术的建立

以黄瓜绿斑驳花叶病毒(cucumber green mottle mosaic virus,CGMMV)阳性样品为研究对象,根据其外壳蛋白基因设计3条引物和2条探针,探针5′端分别用生物素和荧光进行标记;利用这套引物和探针在59℃进行RT-PCR恒温扩增90min,扩增产物用核酸试纸条进行检测。用其它5种同样侵染葫芦科作物的植物病毒作为对照进行试验,以期确定试纸条检测方法的特异性。将梯度稀释后的总RNA作为模板进行检测,以确定该方法的灵敏度。结果表明:该试验建立的核酸试纸条检测方法对CGMMV具有特异性,能够有效区分CGMMV及同样侵染葫芦科作物的黄瓜花叶病毒(CMV)、辣椒轻斑驳病毒(PMMoV)、烟草花叶病毒(TMV)、番茄花叶病毒(ToMV)和小西葫芦黄花叶病毒(ZYMV);同时该方法也具有较高的灵敏度,可检测低至24.300ng·μL~(-1)的总RNA。因此该试验建立的核酸试纸条法可用于CGMMV的快速检测。     

洋葱黄矮病毒的实时荧光RT-PCR检测方法

洋葱黄矮病毒(Onion yellow dwarf virus,OYDV)是危害葱属植物的主要病毒之一.本试验根据OYDV外壳蛋白(coat protein,CP)基因保守序列设计特异性引物,建立并优化了OYDV实时荧光RT-PCR检测方法,并对其特异性、敏感性和重复性进行了验证.结果显示:标准曲线Ct值与模板拷贝数的...     

番茄黑环病毒液相芯片快速检测方法的建立

为建立番茄黑环病毒(Tomato black ring virus,TBRV)的液相芯片检测技术,对GenBank中的TBRV核苷酸序列进行分析,设计其特异性探针并用生物素标记。探针偶联荧光编码微球后与TBRV的RT-PCR产物进行杂交,用液相芯片检测仪检测荧光信号。结果表明:建立的方法具有良好的特异性,能够有效区分侵染马铃薯的TBRV、马铃薯纺锤块茎类病毒(PSTVd)、马铃薯A病毒(PVA)及番茄斑萎病毒(TSWV);检测灵敏度约为1pg/μL总RNA,与常规RT-PCR灵敏度相当。实际样品检测结果表明该方法可用于TBRV的日常检测。     

柑橘褪绿矮化相关病毒LAMP检测体系的建立

根据GenBank登录的柑橘褪绿矮化相关病毒(Citrus chlorotic dwarf-associated virus,CCDaV)的移动蛋白(MP)基因序列设计了一组特异性引物,经体系优化,建立了CCDaV的环介导等温核酸扩增(LAMP)检测方法。结果显示该方法能特异扩增CCDaV,与其他5种柑橘病原物(柑橘衰退病毒、柑橘碎叶病毒、柑橘裂皮病类病毒、温州蜜柑萎缩病毒和柑橘黄龙病菌)不发生反应;灵敏度为PCR的100倍,与实时荧光PCR的灵敏度相同。用LAMP方法对50个田间样品进行检测,与PCR和实时荧光PCR的检测结果一致,证明该方法可用于田间样品的检测。该LAMP检测方法可特异、灵敏、快速地对CCDaV样品进行检测。     

应用实时荧光RT-PCR检测柑橘黄化脉明病毒

为更快速准确检测柑橘黄化脉明病毒（Citrus yellow vein clearing virus,CYVCV）,根据病毒外壳蛋白基因的保守序列设计特异性引物,通过体系优化得到最佳反应条件,建立基于SYBR GreenⅠ的CYVCV实时荧光RT-PCR检测方法。该方法可特异性检测CYVCV,而测试的柑橘衰退病毒、碎叶病毒等5种柑橘病毒均不能检测出。灵敏度较普通RT-PCR提高了100倍,标准曲线循环阈值与模板浓度呈良好的线性关系,扩增效率和相关性系数分别为102%和0.999。对田间样品的检测结果表明,建立的实时荧光RT-PCR适用于检测不同柑橘品种中CYVCV的含量。     

柑橘脉突病毒实时荧光定量RT-PCR检测体系的建立与应用

为了快速、灵敏地检测柑橘脉突病毒(Citrus vein enation virus,CVEV),通过设计特异性引物(EVq F4/EVq R4),优化反应条件,建立了CVEV的实时荧光定量RT-PCR检测体系。该方法特异性良好;检测灵敏度比常规RT-PCR高100倍;标准曲线循环阈值与模板浓度呈良好的线性关系,相关系数为0.992,扩增效率101.8%;检测组内和组间变异系数均小于2.85%,重复性较好。利用所建立的实时荧光定量方法对柑橘植株进行检测发现,‘代代酸橙’和‘象山红’植株中CVEV分布不均匀,其中根部病毒滴度最高,分别为162.52和45.32拷贝·ng~(-1) RNA,皮及叶部病毒滴度相对较低。     

葡萄A病毒的IC-RT-PCR检测研究

葡萄A病毒是葡萄皱木综合证的病原之一,通常与其它病毒混合发生,造成葡萄产量的损失。为有效检测葡萄A病毒,该研究建立了免疫捕获-反转录-聚合酶链式反应检测方法(IC-RT-PCR),将免疫学和核酸扩增技术结合起来使用。结果表明:IC-RT-PCR方法检测的特异性较强,检测葡萄A病毒2个株系的结果为阳性,检测葡萄扇叶病毒、南芥菜花叶病毒、烟草环斑病毒结果为阴性。该方法检测提纯葡萄A病毒的灵敏度为10ng/mL,检测葡萄A病毒感染的Nicotiana benthamiana叶片可稀释到10-6。     

应用Real Time PCR法进行mRNA表达量相对定量分析方法的探讨

为了便于对所检测样本进行比较,在real-time Q-PCR反应的指数期,首先需设定一定荧光信号的域值,以PCR反应的前15个循环的荧光信号作为荧光本底信号(baseline),荧光域值的默认设置是3~15个循环的荧光信号的标准偏差的10倍。如果检测到荧光信号超过域值被认为是真正的信号,它可用于定义样本的临界循环数(Ct)即每个反应管内的荧光信号达到设定的域值时所经历的循环数。本研究表明每个模板的Ct值与该模板的起始拷贝数的对数存在线性关系,即起始拷贝数越多,Ct值越小。利用已知起始拷贝数的标准品可作出标准曲线,因此只要获得未知样品的Ct值,即可从标准曲线上计算出该样品的起始拷贝数,可以对科研和生产起到一定的参考价值。     

Study of long-distance movement of Plum pox virus (Sharka) as an alternative resistance-evaluation method in Prunus

During the breeding programs for Plum pox virus (PPV, Sharka) resistance in Prunus, the evaluation of the new releases through symptoms observation on leaves has been contradictory and represents one of the main handicaps in these programs. In order to increase the accuracy of this traditional evaluation method, we here analyze an alternative method based on the study of the ability of a genotype to allow the long-distance movement of the virus through its vascular vessels. Two different plant models have been assayed: (a) in Model I, the inoculation was performed in the ‘GF305’ rootstock with a later grafting of the genotype under evaluation and a scion of healthy control ‘GF305’, to evaluate the long-distance movement through the studied genotype from the rootstock to the scion (xylem transport), and (b) in Model II, the inoculation with ‘GF305’ diseased scions was performed by grafting these diseased scions onto the studied genotypes, which were grafted onto healthy ‘GF305’ peach seedlings, to evaluate the long-distance movement through the studied genotype from the scion to the rootstock (phloem transport). The results show that, regardless of the presence of symptoms, susceptible genotypes allowed the movement of the virus through their vascular vessels in both directions studied. However, the resistant apricot ‘Stark Early Orange’ did not allow this movement. We propose the study of the ability of a genotype to allow the long-distance movement of the virus as an alternative and more accurate method for the evaluation of PPV resistance. However, this protocol is much more tedious than the traditional one and could be used mainly in the evaluation of a reduced number of more interesting genotypes.     

Simultaneous detection of stone fruit tree viruses by one-step multiplex RT-PCR

A protocol of multiplex RT-PCR in a one-tube system for the detection of the most common stone fruit trees viruses [e.g., plum pox virus (PPV), prune dwarf virus (PDV), and Prunus necrotic ringspot virus (PNRSV)], including the internal control of NADH dehydrogenase subunit 5 (nad5) gene are described here. The method specificity was tested on more than 80 different samples with various isolates and strains of the viruses. It showed that the targeted viruses produced the expected amplicons, whereas all other related viruses produced only the nad5 internal control amplicon. The method sensitivity was evaluated by comparing it with Simplex RT-PCR with the same primers; no significant differences in detection limits were recorded. Furthermore, the competitiveness of the primers in the assay was tested by serial RNA dilutions of samples with mixed and single infections. The least competitive was the internal control nad5 gene primer pair; therefore, there is a reduced risk of false negatives as all the other primers tend to be more efficient in the given primer cocktail than in the primers for internal control.     

Genetic diversity of apricot revealed by a set of SSR markers from linkage group G1

Eight polymorphic simple sequence repeat (SSR) markers located in the G1 linkage group of apricot (Prunus armeniaca L.) were previously developed and evaluated in a small set of cultivars. Those primers were used for studying variability in 77 apricot cultivars belonging to five different geographical groups, such as Chinese, Asian (Irano-Caucasian and Central Asian), North American, Mediterranean and Western European as well as Middle European cultivars. Six of the markers were polymorphic and revealed a total of 71 alleles ranging from 5 (aprigms11) to 20 (aprigms1) alleles per locus with a mean value of 11.83 alleles per locus. In conclusion, the SSR loci located in the G1 linkage group show a level of polymorphism which is similar to loci dispersed throughout the entire genome. The total number of alleles and the number of unique alleles were the highest in Chinese apricots and the lowest in Middle European cultivars. Heterozygosity also showed a decrease from Asia and China to Middle Europe. No association could have been observed between any SSR markers tested and plum pox virus (PPV) resistant phenotype of cultivars. PPV resistant cultivars did not form a separate clade on the dendrogram obtained by UPGMA cluster analysis. Middle European and Chinese cultivars formed separate clusters while other genotypes formed smaller multiple sub-groups or scattered among different clusters. Our results support previous hypotheses on the origin of PPV resistance in North American apricots. The allele data was also presented in a form that allowed the easy observation of allele frequencies in each geographical group at each locus. Using this data field, differences and similarities between cultivar groups can be easily assessed. The analysis demonstrated the links between the North American and Mediterranean apricot germplasm and confirmed that the Chinese and Eastern European cultivars are distantly related.     

Evaluation of apricot resistance to Plum pox virus (Sharka) in controlled greenhouse and natural field conditions

In this study we compare the evaluation of Plum pox virus (Sharka) resistance of 29 apricot genotypes in controlled greenhouse conditions by grafting onto infected ‘GF305’ peach seedlings growing in pots, and in natural conditions by grafting onto infected 5-year-old apricot trees growing in the orchard. Apricot genotypes evaluated were initially classified into three groups: susceptible to PPV (presence of PPV symptoms and ELISA positive in greenhouse and field assays), resistant (absence of PPV symptoms and ELISA negative in both assays) and undetermined (evaluated differently in both assays). Results showed a similar behavior against Plum pox virus in both assays in 20 out of the 29 apricot genotypes studied (69%). However, in the other nine genotypes results were different (31%). Evaluation in field was more accurate, detecting a higher number of susceptible genotypes, probably due to the higher inoculation pressure in the old trees in comparison with the GF305 rootstocks in pots. However, greenhouse evaluation let to work in controlled isolated conditions with a higher number of genotypes. This situation is greatly required in areas where Sharka is not widely spread. Greenhouse evaluation could be then the first screening method to evaluate Plum pox virus resistance of apricot genotypes, and could be complemented with the evaluation onto infected trees in natural conditions in insect-proof quarantine shelter.     

Analysis of the main factors involved in the evaluation of Prunus resistance to Plum pox virus (Sharka) in controlled greenhouse conditions

In countries like Spain or France, quarantine rules force researchers to evaluate the resistance to Sharka (Plum pox virus, PPV) in controlled, isolated conditions. This evaluation method shows important limitations resulting from the management of plants in the controlled conditions, grown in pots with artificial cycles of growth in the greenhouse and cold chamber, alternately. The objective of this study is to analyse different factors that affect the efficiency of the method of evaluation of PPV resistance in controlled greenhouse conditions. The cultivars evaluated as model genotypes were the resistant ‘Stark Early Orange’ and the susceptible ‘Real Fino’ apricot. Furthermore the ‘GF305’ peach was used as a susceptible control. The different studied factors were the inoculation protocol (rootstock or variety inoculation), the grafting success (depending on inoculation method, rootstock–variety combination and date of grafting), and the efficiency of the process in each artificial cycle of growth. Results showed that rootstock inoculation was more effective than inoculation of the variety. As rootstock, the ‘GF305’ seedlings were slightly better than the ‘Real Fino’ seedlings in the inoculation process, but they were quite similar in terms of effectiveness in the evaluation and grafting process. Grafting can be carried out in spring or autumn without having important differences. The global efficiency of the evaluation process was much higher with rootstock inoculation.     

香蕉3种病毒的多重PCR检测体系

根据GenBank中已发表的香蕉束顶病毒（Banana bunchy top virus,BBTV）﹑黄瓜花叶病毒（Cucumber mosaic virus,CMV）和香蕉线条病毒（Banana streak virus,BSV）的基因序列,找出保守序列分别设计出特异引物,在建立各种病毒单项PCR技术的基础上,通过优化多重PCR反应条件,建立了能同时检测3种病毒的多重PCR检测体系。该体系可同时扩增BBTV的615 bp、CMV的480 bp和BSV的945 bp的特异片段。这些片段克隆测序结果表明,多重PCR扩增的不同病毒片段是特异和专化的,其核苷酸序列与相应的病毒基因片段的相似性都达91%以上。该体系的灵敏度测定结果表明,从相当于或大于10-2 mg感病植物组织中均能检测到这3种病毒。     

新疆哈密瓜病毒的DAS-ELISA检测和分子鉴定

为了明确当前新疆哈密瓜病毒病的主要毒原种类及其遗传分化,为哈密瓜病毒病害的防治提供科学依据,对吐鲁番、鄯善、昌吉等哈密瓜主产区的病毒病调查、采样,采用双抗体夹心酶联免疫吸附法（DAS–ELISA）和RT-PCR技术对侵染哈密瓜的7种主要病毒及瓜类重要检疫性病毒--黄瓜绿斑驳花叶病毒（Cucumber green mottle mosaic virus,CGMMV）进行检测和分子鉴定。结果表明：在所检测的121个样品中,黄瓜花叶病毒（Cucumber mosaic virus,CMV）的检出率最高,为70.2%;西瓜花叶病毒（Watermelon mosaic virus,WMV）和小西葫芦黄花叶病毒（Zucchini yellow mosaic virus,ZYMV）次之,分别为62.0%和37.2%,甜瓜坏死斑点病毒（Melon necrotic spot virus,MNSV）的检出率仅为2.5%,CGMMV、南瓜花叶病毒（Squash mosaic virus,SqMV）、番木瓜环斑病毒（Papaya ring spot virus W,PRSV-W）和烟草坏死病毒（Tobacco necrosis virus,TNV）未检测到。CMV、WMV、ZYMV在田间分布广泛,2种及3种病毒的复合侵染发生普遍（60.19%）。对各病毒分离物进行CP基因扩增、序列测定和系统发育分析,确定了CMV新疆哈密瓜分离物归属于CMV亚组ⅠB。ZYMV、WMV和MNSV与已报道的病毒株系CP基因核苷酸序列具有较高的同源性,但存在一定的变异,ZYMV和WMV具有明显的地域分化现象。     

甘肃省河西地区辣(甜)椒病毒病毒原鉴定

2006～2009年用DAS-ELISA方法对采自甘肃省河西地区辣(甜)椒病毒病病株的27份样本进行了烟草花叶病毒(TMV)、黄瓜花叶病毒(CMV)、烟草蚀纹病毒(TEV)、辣椒轻微斑驳病毒(PMMoV)、番茄斑萎病毒(TSWV)、马铃薯X病毒(PVX)、马铃薯Y病毒(PVY)、苜蓿花叶病毒(AMV)和蚕豆萎蔫病毒(BBWV)共9种病毒的检测,同时采用反转录聚合酶链式反应对其中20份样本进行了前4种病毒的测定。结果表明,DAS-ELISA方法检测出的病毒种类有TMV、CMV、PMMoV、PVY和TEV,其中TMV和CMV是优势毒原种群,检出率分别为44.4%和33.3%;RT-PCR方法检测出TMV、CMV、TEV和PMMoV;未检出TSWV、PVX、AMV和BBWV。     

青海辣椒上番茄斑萎病毒检测及鉴定

在对青海辣椒上的病毒病进行调查时发现疑似番茄斑萎病毒（Tomato spotted wilt tospovirus，TSWV）病样，表现为环斑、坏死等症状。为明确其感染的病毒种类，对其进行了检测和鉴定。对Tospovirus的通用引物进行检测时发现采集的49份样品中有14份样品扩增到了目的条带，序列测定结果显示其与TSWV的同源性最高；同时利用TSWV特异性引物对阳性样品进行检测，结果全部为阳性；基于克隆的NSs基因序列聚类分析结果显示其属于TSWV的1个分离物，与中国云南、黑龙江等地分离物相对近缘，而与国外其他分离物相对远缘。在分子鉴定的基础上，利用TSWV的抗体通过Western blot进一步对样品进行了检测，结果也证明采集样品中存在TSWV的感染。这些结果表明青海辣椒上存在TSWV的感染。     

Establishment and evaluation of a TaqMan RT-qPCR method for tissue quantification of oncolytic virus M1 in vivo

AIMTo establish a TaqMan RT-qPCR method for surveiling the spread of oncolytic virus M1 in tissue, helping control the dosage and assessing the safety of virus. METHODSA TaqMan-based one-step RT-qP?CR method for the detection and quantification of oncolytic virus M1 in the tissues was established. The virus load and distribution in the tissues of SD rats, cynomolgus monkeys and nude mice were also investigated. RESULTSA pair of specif?ic primers (Q3) and the standard viral RNA for SYBR Green RT-qPCR were screened and selected with the best specificity and amplification efficiency. By optimizing the experiment conditions, we found that the annealing temperature above 62℃ reduced matrix effect but affected the amplification efficiency. So we established a one-step TaqMan RT-qPCR method and redesigned a pair of Q3 short primers (Q3S). Using the one-step TaqMan RT-qPCR and Q3S primer, the standard RNA with low copy numbers was specifically detected under the background of mixed matrix RNA of SD rats or cynomolgus monkeys. Furthermore, the method was verified to be suitable for detecting tissue distribution of M1 virus in the mice, SD rats and cynomolgus monkeys. CONCLUSION The TaqMan-based one-step RT-qPCR constructed with Q3S primer can be used for M1 virus quantification in various tissue samples of different animals with better specificity and sensitivity, and may be further applied to the detection of clinical samples.