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CN110760620A - Classical swine fever virus and African classical swine fever virus dual-fluorescence PCR detection reagent, kit and detection method - Google Patents

Classical swine fever virus and African classical swine fever virus dual-fluorescence PCR detection reagent, kit and detection method Download PDF

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CN110760620A
CN110760620A CN201911276696.XA CN201911276696A CN110760620A CN 110760620 A CN110760620 A CN 110760620A CN 201911276696 A CN201911276696 A CN 201911276696A CN 110760620 A CN110760620 A CN 110760620A
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王金涛
孙东波
宋伟红
郑家三
李春秋
邢晓旭
陈国福
刘光前
师庆伟
佟玲
刁彩霞
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Heilongjiang Academy of Land Reclamation Sciences
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Abstract

一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂、试剂盒和检测方法,属于动物病原检测领域。本发明针对猪瘟病毒5’‑UTR基因和非洲猪瘟病毒P72基因,分别设计并筛选出能覆盖所有毒株,又适合双重检测的引物和探针,包括二对特异性引物和二条特异性探针;本发明还记载了包含该引物和探针的试剂盒以及利用该引物和探针的PCR检测方法;本发明通过引物设计和PCR各组分的调整,在敏感性和特异性均不降低的前提下,实现一次分析,同时检测和区分猪瘟病毒与非洲猪瘟病毒的目的,不仅减少了检测的工作量和成本,且能大大节省检测的时间,为疫病防治赢得宝贵时间。

A swine fever virus and African swine fever virus double fluorescent PCR detection reagent, kit and detection method belong to the field of animal pathogen detection. The invention aims at the 5'-UTR gene of swine fever virus and the P72 gene of African swine fever virus, respectively designs and screens out primers and probes that can cover all strains and are suitable for double detection, including two pairs of specific primers and two specific primers. The present invention also describes a kit comprising the primers and probes and a PCR detection method using the primers and probes; the present invention, through the design of primers and the adjustment of each component of PCR, has different sensitivity and specificity. Under the premise of reducing the cost, the purpose of simultaneously detecting and distinguishing between swine fever virus and African swine fever virus can be realized in one analysis, which not only reduces the workload and cost of detection, but also greatly saves the time of detection and wins valuable time for epidemic prevention and control.

Description

一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂、试剂盒 和检测方法A kind of swine fever virus and African swine fever virus double fluorescent PCR detection reagent and kit and detection methods

技术领域technical field

本发明属于动物病原检测领域,具体涉及一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂、试剂盒和检测方法。The invention belongs to the field of animal pathogen detection, and in particular relates to a swine fever virus and African swine fever virus double fluorescent PCR detection reagent, a kit and a detection method.

背景技术Background technique

猪瘟病毒(Classical Swine Fever Virus,CSFV)属于黄病毒科,瘟病毒属,是单股正链RNA病毒,是猪瘟的病原,危害家猪和野猪,其他动物不发病。猪瘟是一种急性、热性、高度接触性传染病,主要特征是高温、微血管变性而引起全身出血、坏死、梗塞。猪瘟对猪危害极为严重,会造成养猪业重大损失。非洲猪瘟(African swine fever,ASF)是由非洲猪瘟病毒(African swine fever virus,ASFV)感染引起的疣猪、豪猪、野猪以及家养猪的一种烈性传染病。该病毒属于非洲猪瘟病毒科,非洲猪瘟病毒属,是线状双链DNA病毒。猪感染该病毒后,主要临床症状表现为高热、食欲废绝、皮肤发绀,剖检后会发现淋巴结、肾、胃肠黏膜等出血,毒力强的毒株感染猪后,造成的病死率可高达100%。世界动物卫生组织(OIE)将猪瘟和非洲猪瘟列为法定上报的动物疫病,在我国2008年修订的《一、二、三类动物疫病病种名录》将猪瘟和非洲猪瘟列为一类动物疾病。Swine fever virus (Classical Swine Fever Virus, CSFV) belongs to Flaviviridae, Pestivirus genus. Swine fever is an acute, febrile, and highly contagious infectious disease characterized by systemic hemorrhage, necrosis, and infarction caused by high temperature and microvascular degeneration. Swine fever is extremely harmful to pigs and will cause heavy losses to the pig industry. African swine fever (ASF) is a severe infectious disease of warthogs, porcupines, wild boars and domestic pigs caused by African swine fever virus (ASFV). The virus belongs to the African swine fever virus family, the genus African swine fever virus, and is a linear double-stranded DNA virus. After pigs are infected with the virus, the main clinical symptoms are high fever, loss of appetite, skin cyanosis, and bleeding in lymph nodes, kidneys, and gastrointestinal mucosa after autopsy. up to 100%. The World Organization for Animal Health (OIE) lists swine fever and African swine fever as notifiable animal diseases. A class of animal diseases.

目前,非洲猪瘟常用的实验室检测方法主要为病原学检测。在病原学诊断方面,病毒的分离鉴定是诊断动物疫病的金标准,但由于非洲猪瘟的分离培养对实验室的水平要求较高,多数地方不具备这个条件,因而该方法很难普及推广。荧光PCR是一种用于放大扩增特定的DNA片段的分子生物学技术,具有灵敏度高、特异性强、简便快速、对标本的纯度要求低等特点,是目前应用最为广泛的病原学检测技术,2019年1月4日,中国动物疫病预防控制中心公布了第一批非洲猪瘟现场快速检测试剂评价结果,共3类11个品种,其中有8个为荧光PCR产品。At present, the commonly used laboratory detection methods for African swine fever are mainly pathogenic detection. In terms of etiological diagnosis, virus isolation and identification is the gold standard for diagnosing animal diseases. However, because the isolation and culture of African swine fever requires a high level of laboratory, most places do not have this condition, so this method is difficult to popularize. Fluorescent PCR is a molecular biology technique used to amplify specific DNA fragments. It has the characteristics of high sensitivity, strong specificity, simplicity and rapidity, and low requirements for the purity of the specimen. It is currently the most widely used pathogenic detection technology. , On January 4, 2019, the China Center for Animal Disease Control and Prevention announced the evaluation results of the first batch of rapid detection reagents for African swine fever on-site. There are 11 varieties in 3 categories, of which 8 are fluorescent PCR products.

尽管非洲猪瘟具有典型的临床症状和病理变化,但由于临床感染日趋复杂,多种病原混合感染,因而很难依据临床症状和病理变化对非洲猪瘟作出确诊,尤其与对养猪业危害较大的猪瘟更加无法区分。此外,目前在世界范围内尚无可以有效预防非洲猪瘟的疫苗,因而对于非洲猪瘟只能是尽早做出准确地诊断,从而及时采取相应的扑杀、消毒等措施。如果能够建立一种既方便、快捷,又能区分猪瘟病毒和非洲猪瘟病毒的鉴别诊断方法,从而为临床上猪瘟与非洲猪瘟的快速确诊提供科学、准确的依据,进而为相应防控措施的制定提供指导方向,这将具有巨大的市场应用前景。Although African swine fever has typical clinical symptoms and pathological changes, due to the increasingly complex clinical infection and mixed infection of various pathogens, it is difficult to diagnose African swine fever based on clinical symptoms and pathological changes. Large swine fever is even more indistinguishable. In addition, there is currently no vaccine that can effectively prevent African swine fever in the world. Therefore, for African swine fever, an accurate diagnosis can only be made as soon as possible, so that corresponding measures such as culling and disinfection can be taken in a timely manner. If a convenient and fast differential diagnosis method can be established, which can distinguish between swine fever virus and African swine fever virus, it will provide a scientific and accurate basis for the rapid diagnosis of swine fever and African swine fever in clinical practice, and then provide corresponding preventive measures. The formulation of control measures provides guidance, which will have huge market application prospects.

目前检测单一猪瘟病毒和非洲猪瘟病毒的荧光RT-PCR和荧光PCR方法和专利均有报道,而能够同时检测猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测试剂及其制备方法与应用,还罕见报道。At present, fluorescent RT-PCR and fluorescent PCR methods and patents for detecting single swine fever virus and African swine fever virus have been reported, and dual fluorescent PCR detection reagents that can simultaneously detect swine fever virus and African swine fever virus, and their preparation method and application , also rarely reported.

发明内容SUMMARY OF THE INVENTION

本发明的第一个目的是提供分别用于检测猪瘟病毒和非洲猪瘟病毒的荧光PCR引物和探针。The first object of the present invention is to provide fluorescent PCR primers and probes for detecting swine fever virus and African swine fever virus, respectively.

本发明的第二个目的是提供用于检测和鉴别猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测试剂盒。The second object of the present invention is to provide a double fluorescent PCR detection kit for detecting and identifying swine fever virus and African swine fever virus.

本发明的第三个目的是提供一种鉴别猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测方法。The third object of the present invention is to provide a double fluorescent PCR detection method for identifying swine fever virus and African swine fever virus.

与单重荧光PCR相比,本发明通过引物设计和PCR各组分的调整,在敏感性和特异性均不降低的前提下,实现一次分析,同时检测和区分猪瘟病毒与非洲猪瘟病毒的目的,不仅减少了检测的工作量和成本,且能大大节省检测的时间,为疫病防治赢得宝贵时间;Compared with single-plex fluorescent PCR, the present invention realizes one analysis through primer design and adjustment of each component of PCR under the premise of not reducing sensitivity and specificity, and simultaneously detects and distinguishes swine fever virus and African swine fever virus. The purpose is not only to reduce the workload and cost of testing, but also to greatly save the time of testing and gain valuable time for epidemic prevention and control;

为实现上述目的,本发明采取的技术方案如下:To achieve the above object, the technical scheme adopted by the present invention is as follows:

一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂,针对猪瘟病毒5’-UTR基因和非洲猪瘟病毒P72基因,分别设计并筛选出能覆盖所有毒株,又适合双重检测的引物和探针,包括二对特异性引物和二条特异性探针,扩增目的片段长度分别为94bp和249bp,引物和探针序列为:A swine fever virus and African swine fever virus dual fluorescent PCR detection reagent, for the 5'-UTR gene of swine fever virus and the African swine fever virus P72 gene, respectively design and screen out primers that can cover all strains and are suitable for dual detection and probes, including two pairs of specific primers and two specific probes, the lengths of the amplified target fragments are 94bp and 249bp respectively, and the primer and probe sequences are:

猪瘟病毒:Swine fever virus:

上游引物CSFV-F:5’-TGCCCAYAGTAGGACTAG-3’SEQ ID NO.1Upstream primer CSFV-F: 5'-TGCCCAYAGTAGGACTAG-3'SEQ ID NO.1

下游引物CSFV-R:5’-CTACTGACGACTGTCCTG-3’SEQ ID NO.2Downstream primer CSFV-R: 5'-CTACTGACGACTGTCCTG-3'SEQ ID NO.2

探针CSFV-P:5’-TGGCGAGCTCCCTGGGTGGTCTA-3’SEQ ID NO.3Probe CSFV-P: 5'-TGGCGAGCTCCCCTGGGTGGTCTA-3'SEQ ID NO.3

非洲猪瘟病毒:African swine fever virus:

上游引物ASFV-F:5’-GATACCACAAGATCTGCCGT-3’SEQ ID NO.4Upstream primer ASFV-F: 5'-GATACCACAAGATCTGCCGT-3'SEQ ID NO.4

下游引物ASFV-R:5’-CTGCTCATGGTATCAATCTTATCG-3’SEQ ID NO.5Downstream primer ASFV-R: 5'-CTGCTCATGGTATCAATCTTATCG-3'SEQ ID NO.5

探针ASFV-P:5’-CCACGGGAGGAATACCAACCCAGTG-3’SEQ ID NO.6Probe ASFV-P: 5'-CCACGGGAGGAATACCAACCCAGTG-3'SEQ ID NO.6

所述探针CSFV-P和探针ASFV-P在5’端分别标记不同的荧光报告基团,所述探针CSFV-P和探针ASFV-P在3’端均标记相同或不同的荧光淬灭基团,所述上游引物CSFV-F中的Y为简并碱基,Y=C/T。The probe CSFV-P and the probe ASFV-P are respectively labeled with different fluorescent reporter groups at the 5' end, and the probe CSFV-P and the probe ASFV-P are labeled with the same or different fluorescence at the 3' end Quenching group, Y in the upstream primer CSFV-F is a degenerate base, Y=C/T.

进一步的,所述荧光报告基团为FAM或VIC,所述荧光淬灭基团为TAMRA或BHQ。Further, the fluorescent reporter group is FAM or VIC, and the fluorescence quenching group is TAMRA or BHQ.

进一步的,所述探针CSFV-P在5’端标记FAM,在3’端标记TAMRA;所述探针ASFV-P在5’端标记VIC,在3’端标记BHQ。Further, the probe CSFV-P is labeled with FAM at the 5' end and TAMRA at the 3' end; the probe ASFV-P is labeled with VIC at the 5' end and BHQ at the 3' end.

一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂盒,包括所述的二对特异性引物和二条特异性探针。A double fluorescent PCR detection kit for swine fever virus and African swine fever virus includes the two pairs of specific primers and two specific probes.

进一步的,所述试剂盒还包括反应缓冲液、酶、阳性对照和阴性对照。Further, the kit also includes reaction buffer, enzyme, positive control and negative control.

进一步的,所述反应缓冲液为One Step RT-PCRbuffer;所述酶为Ex Taq和PrimeScript RT Enzyme;所述阳性对照为猪瘟病毒和非洲猪瘟病毒合成片段的体外重组质粒;所述阴性对照为灭菌去离子水。Further, the reaction buffer is One Step RT-PCRbuffer; the enzymes are Ex Taq and PrimeScript RT Enzyme; the positive control is an in vitro recombinant plasmid of swine fever virus and African swine fever virus synthetic fragments; the negative control Deionized water for sterilization.

一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测方法,包括以下步骤:A double fluorescent PCR detection method for swine fever virus and African swine fever virus, comprising the following steps:

步骤一、提取待测样本的DNA和RNA,将RNA反转录成cDNA;Step 1: Extract the DNA and RNA of the sample to be tested, and reverse-transcribe the RNA into cDNA;

步骤二、以步骤一中所述的DNA和cDNA为模板,利用权利要求4所述的试剂盒进行双重荧光PCR扩增;Step 2, take the DNA and cDNA described in step 1 as templates, utilize the test kit of claim 4 to carry out double fluorescent PCR amplification;

步骤三、分析PCR产物,根据扩增反应结果判定待测样本中是否含有猪瘟病毒和/或非洲猪瘟病毒。Step 3: Analyze the PCR product, and determine whether the sample to be tested contains swine fever virus and/or African swine fever virus according to the results of the amplification reaction.

进一步的,步骤二中,猪瘟病毒5’-UTR基因最适上游引物CSFV-F和下游引物CSFV-R的终浓度均为0.4μmol/L,最适探针CSFV-P的终浓度为0.6μmol/L;检测非洲猪瘟病毒P72基因最适上游引物ASFV-F、下游引物ASFV-R的终浓度均为0.6μmol/L,最适探针ASFV-P的终浓度为0.6μmol/L。Further, in step 2, the final concentration of the optimal upstream primer CSFV-F and the downstream primer CSFV-R of the 5'-UTR gene of swine fever virus are both 0.4 μmol/L, and the final concentration of the optimal probe CSFV-P is 0.6 μmol/L; the final concentration of the optimal upstream primer ASFV-F and downstream primer ASFV-R for detection of African swine fever virus P72 gene was 0.6 μmol/L, and the final concentration of the optimal probe ASFV-P was 0.6 μmol/L.

进一步的,步骤二中,双重荧光PCR扩增的反应程序为:42℃5min,95℃10s;95℃5s,60℃30s,共45个循环。Further, in step 2, the reaction procedure of the double fluorescent PCR amplification is: 42°C for 5 min, 95°C for 10s; 95°C for 5s, 60°C for 30s, a total of 45 cycles.

本发明相对于现有技术的有益效果是:The beneficial effects of the present invention relative to the prior art are:

(1)覆盖性和通用性好:本发明中涉及的引物和探针都分别针对猪瘟病毒和非洲猪瘟病毒最保守的基因设计,覆盖了Genebank中现有该种病毒的所有序列,不会存在漏检的情况。另外,本发明的引物和探针形成的扩增条件与其它几种猪重要传染病的扩增条件相同,可以与其它疫病在同一平台同时开展实验,通用性较好,这是目前医学诊断已经开始的研发方向,目的是让诊断更快捷、更方便;这是本发明的主要创新点。(1) Good coverage and versatility: The primers and probes involved in the present invention are designed for the most conserved genes of swine fever virus and African swine fever virus, respectively, covering all sequences of the existing virus in Genebank, not There will be missed inspections. In addition, the amplification conditions formed by the primers and probes of the present invention are the same as the amplification conditions of other important swine infectious diseases, and experiments can be carried out on the same platform with other diseases at the same time, and the versatility is good. The purpose of the initial research and development direction is to make diagnosis faster and more convenient; this is the main innovation of the present invention.

(2)多重性和高通量:该双重荧光PCR体系可实现在一个反应中同时对猪瘟病毒和非洲猪瘟病毒进行快速鉴别检测,65分钟内即可完成检测,节约了检测时间和成本。能满足大批量检测的要求,有利于疫病特别是混合感染的及时确诊,为疫病防治赢得宝贵时间。(2) Multiplex and high-throughput: The dual fluorescent PCR system can realize rapid identification and detection of swine fever virus and African swine fever virus in one reaction, and the detection can be completed within 65 minutes, saving detection time and cost . It can meet the requirements of large-scale testing, which is conducive to the timely diagnosis of epidemic diseases, especially mixed infections, and wins precious time for epidemic prevention and control.

(3)灵敏度高:该双重荧光PCR检测方法的灵敏性与相应的单重荧光PCR检测方法相当,克服了目前国产商品化的多重荧光PCR试剂盒敏感性下降的弱点。(3) High sensitivity: The sensitivity of the dual fluorescence PCR detection method is equivalent to the corresponding single-plex fluorescence PCR detection method, which overcomes the weakness of the current domestic commercialized multiple fluorescence PCR kits that reduce the sensitivity.

(4)特异性强:设计引物和探针时充分考虑了病原之间可能存在的干扰,经实验证明该双重荧光PCR与猪只常见的其它重要传染病,如猪繁殖与呼吸综合征病毒、猪伪狂犬病毒、猪口蹄疫病毒、猪圆环病毒2型、猪细小病毒、猪乙型脑炎病毒、猪流行性腹泻病毒、猪传染性胃肠炎病毒之间无交叉反应。(4) Strong specificity: When designing primers and probes, the possible interference between pathogens has been fully considered. It has been proved by experiments that this dual fluorescent PCR is compatible with other important infectious diseases common to pigs, such as porcine reproductive and respiratory syndrome virus, There was no cross-reaction among porcine pseudorabies virus, porcine foot-and-mouth disease virus, porcine circovirus type 2, porcine parvovirus, porcine Japanese encephalitis virus, porcine epidemic diarrhea virus, and porcine transmissible gastroenteritis virus.

(5)本发明的扩增循环数由目前国产试剂盒常用的40循环增加到进口试剂盒常用的45个循环,结果判定标准由常用的35个循环增加到38个循环,使试剂盒的整体水平有了进一步的提升;这也是本发明的创新点之一。(5) The number of amplification cycles of the present invention is increased from 40 cycles commonly used in domestic kits to 45 cycles commonly used in imported kits, and the result determination standard is increased from 35 cycles commonly used to 38 cycles, so that the overall performance of the kit is increased. The level has been further improved; this is also one of the innovative points of the present invention.

附图说明Description of drawings

图1为本发明中猪瘟病毒和非洲猪瘟病毒基因特异性扩增曲线。其中,1为猪瘟病毒阳性对照扩增曲线;2为非洲猪瘟病毒阳性对照扩增曲线;3-11为阴性对照、猪繁殖与呼吸综合征病毒、猪伪狂犬病毒、猪口蹄疫病毒、猪圆环病毒2型、猪细小病毒、猪乙型脑炎病毒、猪流行性腹泻病毒、猪传染性胃肠炎病毒扩增曲线。Fig. 1 is the gene-specific amplification curve of swine fever virus and African swine fever virus in the present invention. Among them, 1 is the amplification curve of swine fever virus positive control; 2 is the amplification curve of African swine fever virus positive control; 3-11 are negative control, porcine reproductive and respiratory syndrome virus, porcine pseudorabies virus, swine foot-and-mouth disease virus, pig Amplification curves of circovirus type 2, porcine parvovirus, porcine Japanese encephalitis virus, porcine epidemic diarrhea virus, and porcine transmissible gastroenteritis virus.

图2为本发明中猪瘟病毒基因扩增曲线。Fig. 2 is the gene amplification curve of swine fever virus in the present invention.

图3为本发明中猪瘟病毒基因标准曲线。Figure 3 is the standard curve of the swine fever virus gene in the present invention.

图4为本发明中非洲猪瘟病毒基因扩增曲线。Fig. 4 is the gene amplification curve of African swine fever virus in the present invention.

图5为本发明中非洲猪瘟病毒基因标准曲线。Figure 5 is the standard curve of African swine fever virus gene in the present invention.

图6为本发明中猪瘟病毒基因单重与双重荧光PCR扩增曲线的比较。其中,1为猪瘟病毒单重荧光PCR扩增曲线;2为猪瘟病毒与非洲猪瘟病毒双重荧光PCR中猪瘟病毒扩增曲线。Figure 6 is a comparison of the single-plex and double-fluorescence PCR amplification curves of the swine fever virus gene in the present invention. Among them, 1 is the amplification curve of swine fever virus single-plex fluorescence PCR; 2 is the amplification curve of swine fever virus in double fluorescence PCR of swine fever virus and African swine fever virus.

图7为本发明中非洲猪瘟病毒基因单重与双重荧光PCR扩增曲线的比较。其中,1为非洲猪瘟病毒单重荧光PCR扩增曲线;2为猪瘟病毒与非洲猪瘟病毒双重荧光PCR中非洲猪瘟病毒扩增曲线。Figure 7 is a comparison of the single-plex and double-fluorescence PCR amplification curves of the African swine fever virus gene in the present invention. Among them, 1 is the amplification curve of ASFV single-plex fluorescence PCR; 2 is the amplification curve of ASFV in double fluorescence PCR of swine fever virus and ASFV.

具体实施方式Detailed ways

下面结合附图和实施例对本发明的技术方案作进一步的说明,但并不局限于此,凡是对本发明技术方案进行修改或者等同替换,而不脱离本发明技术方案的精神和范围,均应涵盖在本发明的保护范围中。下述实施例中所用方法如无特别说明均为常规方法,所用的试验材料如无特殊说明均为常规生化试剂。The technical solutions of the present invention will be further described below in conjunction with the accompanying drawings and embodiments, but are not limited thereto. Any modification or equivalent replacement of the technical solutions of the present invention without departing from the spirit and scope of the technical solutions of the present invention shall cover within the scope of the present invention. The methods used in the following examples are conventional methods unless otherwise specified, and the test materials used are conventional biochemical reagents unless otherwise specified.

实施例1:Example 1:

用于检测和鉴别猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测方法的建立。Development of a dual fluorescent PCR assay for detection and identification of swine fever virus and African swine fever virus.

第一步骤是猪瘟病毒和非洲猪瘟病毒引物、探针的设计与合成:The first step is the design and synthesis of swine fever virus and African swine fever virus primers and probes:

在NCBI序列比对分析的基础上,针对猪瘟病毒5’-UTR基因和非洲猪瘟病毒P72基因,分别设计并筛选出能覆盖所有毒株,又适合双重检测的引物和探针,包括二对特异性引物和二条特异性探针,扩增目的片段长度分别为94bp和249bp,引物和探针序列如下:On the basis of NCBI sequence alignment analysis, for the 5'-UTR gene of swine fever virus and the P72 gene of African swine fever virus, primers and probes that can cover all strains and are suitable for double detection were designed and screened respectively, including two For specific primers and two specific probes, the lengths of the amplified target fragments are 94bp and 249bp, respectively. The sequences of the primers and probes are as follows:

猪瘟病毒:Swine fever virus:

上游引物:F:5’-TGCCCAYAGTAGGACTAG-3’SEQ ID NO.1Upstream primer: F: 5'-TGCCCAYAGTAGGACTAG-3'SEQ ID NO.1

下游引物:R:5’-CTACTGACGACTGTCCTG-3’SEQ ID NO.2Downstream primer: R: 5'-CTACTGACGACTGTCCTG-3'SEQ ID NO.2

探针:P:5’-TGGCGAGCTCCCTGGGTGGTCTA-3’SEQ ID NO.3Probe: P: 5'-TGGCGAGCTCCCCTGGGTGGTCTA-3'SEQ ID NO.3

探针在5’端标记FAM,3’端标记TAMRA。The probe is labeled with FAM at the 5' end and TAMRA at the 3' end.

非洲猪瘟病毒:African swine fever virus:

上游引物:F:5’-GATACCACAAGATCTGCCGT-3’SEQ ID NO.4Upstream primer: F: 5'-GATACCACAAGATCTGCCGT-3'SEQ ID NO.4

下游引物:R:5’-CTGCTCATGGTATCAATCTTATCG-3’SEQ ID NO.5Downstream primer: R: 5'-CTGCTCATGGTATCAATCTTATCG-3'SEQ ID NO.5

探针:P:5’-CCACGGGAGGAATACCAACCCAGTG-3’SEQ ID NO.6Probe: P: 5'-CCACGGGAGGAATACCAACCCAGTG-3'SEQ ID NO.6

探针在5’端标记VIC,3’端标记BHQ。The probe is labeled with VIC at the 5' end and BHQ at the 3' end.

第二步骤是猪瘟病毒和非洲猪瘟病毒阳性对照的制备:The second step is the preparation of swine fever virus and African swine fever virus positive controls:

(1)在NCBI网站中,对猪瘟病毒5’-UTR基因序列进行比对,选择一段序列保守、且包含上述引物的片段,将该片段送至生工生物工程(上海)股份有限公司进行合成;将合成的片段与克隆载体连接,转化至DH5α大肠杆菌基因工程菌,挑取、提取阳性克隆质粒;按公式换算成拷贝数,即得已知拷贝数浓度的猪瘟病毒阳性对照。(1) On the NCBI website, compare the 5'-UTR gene sequences of swine fever virus, select a fragment with a conservative sequence and include the above primers, and send the fragment to Sangon Bioengineering (Shanghai) Co., Ltd. for Synthesize; connect the synthesized fragment with the cloning vector, transform it into DH5α Escherichia coli genetically engineered bacteria, pick and extract the positive cloned plasmid; convert it into copy number according to the formula, and obtain the swine fever virus positive control with known copy number concentration.

(2)在NCBI网站中,对非洲猪瘟病毒P72基因序列进行比对,选择一段序列保守、且包含上述引物的片段,将该片段送至生工生物工程(上海)股份有限公司进行合成;将合成的片段与克隆载体连接,转化至DH5α大肠杆菌基因工程菌,挑取、提取阳性克隆质粒;按公式换算成拷贝数,即得已知拷贝数浓度的非洲猪瘟病毒阳性对照。(2) On the NCBI website, compare the gene sequences of African swine fever virus P72, select a fragment with a conservative sequence and include the above primers, and send the fragment to Sangon Bioengineering (Shanghai) Co., Ltd. for synthesis; Connect the synthesized fragment to the cloning vector, transform it into DH5α Escherichia coli genetically engineered bacteria, pick and extract the positive cloned plasmid; convert it into copy number according to the formula, and obtain the African swine fever virus positive control with known copy number concentration.

第三步骤是优化检测猪瘟病毒5’-UTR基因和非洲猪瘟病毒P72基因的双重荧光PCR反应体系与扩增条件:The third step is to optimize the double fluorescent PCR reaction system and amplification conditions for detecting the 5'-UTR gene of swine fever virus and the P72 gene of African swine fever virus:

(1)对第一步骤确定的引物和标记探针的浓度,用无菌水分别稀释至终浓度为0.2μmol/L、0.4μmol/L、0.6μmol/L、0.8μmol/L、1.0μmol/L和1.2μmol/L。(1) The concentrations of primers and labeled probes determined in the first step were diluted with sterile water to the final concentrations of 0.2 μmol/L, 0.4 μmol/L, 0.6 μmol/L, 0.8 μmol/L, 1.0 μmol/L, respectively. L and 1.2 μmol/L.

(2)采用One Step PrimeScript RT-PCR Kit试剂及推荐的反应扩增条件,在ABI7500PCR仪上对不同使用浓度组合的引物和标记探针进行荧光RT-PCR矩阵法筛选试验。(2) Using the One Step PrimeScript RT-PCR Kit reagent and the recommended reaction amplification conditions, the fluorescent RT-PCR matrix screening test was carried out on the ABI7500 PCR instrument for primers and labeled probes with different concentration combinations.

(3)以获得最小Ct值、较高的荧光强度增加值(ΔRn)以及典型的S型扩增曲线为综合判定依据,最终确定检测猪瘟病毒5’-UTR基因最适上游引物、下游引物的终浓度均为0.4μmol/L,最适探针的终浓度为0.6μmol/L;检测非洲猪瘟病毒P72基因最适上游引物、下游引物的终浓度均为0.6μmol/L,最适探针的终浓度为0.6μmol/L。(3) Obtain the minimum Ct value, the higher fluorescence intensity increase value (ΔRn) and the typical S-shaped amplification curve as the comprehensive judgment basis, and finally determine the optimal upstream primer and downstream primer for the detection of the 5'-UTR gene of swine fever virus The final concentration of the optimal probe is 0.4 μmol/L, and the final concentration of the optimal probe is 0.6 μmol/L; the final concentration of the optimal upstream and downstream primers for the detection of African swine fever virus P72 gene is 0.6 μmol/L, and the optimal probe concentration is 0.6 μmol/L. The final needle concentration was 0.6 μmol/L.

(4)在最适引物和探针浓度以及通用荧光RT-PCR反应扩增试剂条件下,扩增体系中反应缓冲液的添加量依次为6μL、8μL、10μL和12μL,对扩增反应液的使用量进行筛选,以获得最小Ct值、较高的荧光强度增加值(ΔRn)以及典型的S型扩增曲线为综合判定依据,最终确定反应缓冲液的添加量为10μL。(4) Under the conditions of the optimal primer and probe concentration and the general fluorescent RT-PCR reaction amplification reagent, the addition amount of the reaction buffer in the amplification system was 6 μL, 8 μL, 10 μL and 12 μL in turn. Screening was performed using the amount to obtain the minimum Ct value, higher fluorescence intensity increase value (ΔRn) and typical S-shaped amplification curve as the comprehensive judgment basis, and the final addition amount of reaction buffer was determined to be 10 μL.

(5)在最适引物探针浓度和最佳反应缓冲液添加量以及通用荧光RT-PCR反应扩增试剂条件下,扩增体系中酶的添加量依次为0.6μL、0.8μL、1.0μL和1.2μL,对酶的使用量进行筛选,以获得最小Ct值、较高的荧光强度增加值(ΔRn)以及典型的S型扩增曲线为综合判定依据,最终确定酶的添加量为1.0μL。(5) Under the conditions of the optimal primer probe concentration and the optimal reaction buffer addition amount and the general fluorescent RT-PCR reaction amplification reagent, the addition amount of enzyme in the amplification system was 0.6 μL, 0.8 μL, 1.0 μL and 1.0 μL. 1.2μL, the amount of enzyme used was screened to obtain the minimum Ct value, higher fluorescence intensity increase value (ΔRn) and typical S-shaped amplification curve as the comprehensive judgment basis, and the final addition amount of enzyme was determined to be 1.0μL.

(6)在最适引物探针浓度和最佳反应缓冲液、酶添加量以及通用荧光RT-PCR反应扩增试剂条件下,对退火延伸温度在55℃--62℃范围内进行筛选试验,最终确定退火延伸温度为60℃。(6) Under the conditions of the optimal primer probe concentration, optimal reaction buffer, enzyme addition amount and general fluorescent RT-PCR reaction amplification reagent, the annealing extension temperature is in the range of 55℃--62℃. The annealing extension temperature was finally determined to be 60°C.

(7)优化的20μLPCR反应体系中,猪瘟病毒上、下游引物的终浓度均为0.4μmol/L,探针的终浓度为0.6μmol/L,非洲猪瘟病毒上、下游引物的终浓度均为0.6μmol/L,探针的终浓度为0.6μmol/L,反应缓冲液的使用量为10μL,酶的添加量为1.0μL,模板的添加量为2.0μL,去离子水补足至总体积20μL。优化的PCR扩增条件为:42℃5min,95℃10s;95℃5s,60℃30s,共45个循环。(7) In the optimized 20 μL PCR reaction system, the final concentrations of the upstream and downstream primers of swine fever virus were both 0.4 μmol/L, the final concentration of probes was 0.6 μmol/L, and the final concentrations of the upstream and downstream primers of African swine fever virus were both 0.4 μmol/L and 0.6 μmol/L. is 0.6 μmol/L, the final concentration of probe is 0.6 μmol/L, the amount of reaction buffer used is 10 μL, the amount of enzyme added is 1.0 μL, the amount of template added is 2.0 μL, and deionized water is added to the total volume of 20 μL . The optimized PCR amplification conditions were: 42°C for 5 min, 95°C for 10s; 95°C for 5s, 60°C for 30s, a total of 45 cycles.

(8)结果判定(8) Result judgment

1)质控标准:1) Quality control standard:

阳性对照出现特定的S形扩增曲线,且Ct值在20-25左右;阴性对照无扩增曲线,且无Ct值。The positive control showed a specific sigmoid amplification curve, and the Ct value was around 20-25; the negative control had no amplification curve and no Ct value.

满足此条件,判定检测结果成立。If this condition is satisfied, it is determined that the detection result is established.

2)结果判定:2) Result judgment:

A、待测样本在FAM和VIC通道均出现特定扩增曲线,且Ct值≤38,则判定待测样品中同时存在猪瘟病毒和非洲猪瘟核酸;A. The sample to be tested has specific amplification curves in both the FAM and VIC channels, and the Ct value is ≤38, it is determined that both swine fever virus and African swine fever nucleic acid exist in the sample to be tested;

B、待测样本在FAM或VIC某一通道出现特定扩增曲线,且Ct值≤38,则判定待测样品中存在猪瘟病毒或非洲猪瘟核酸;B. The sample to be tested has a specific amplification curve in a channel of FAM or VIC, and the Ct value is less than or equal to 38, it is determined that there is swine fever virus or African swine fever nucleic acid in the sample to be tested;

C、待测样本在FAM和/或VIC通道出现特定扩增曲线,且38<Ct值≤40,则需重复检验,重复结果为阳性则判定为阳性,否则判定为阴性;C. The sample to be tested has a specific amplification curve in the FAM and/or VIC channel, and 38 < Ct value ≤ 40, the test needs to be repeated, and the repeated result is positive, it is judged as positive, otherwise it is judged as negative;

D、待测样本在FAM和VIC通道均未出现特定扩增曲线,且Ct值>40或无Ct,则判定待测样品中无猪瘟病毒或非洲猪瘟核酸。D. There is no specific amplification curve in the FAM and VIC channels of the sample to be tested, and the Ct value is >40 or no Ct, it is determined that there is no swine fever virus or African swine fever nucleic acid in the sample to be tested.

第四步骤是猪瘟病毒和非洲猪瘟病毒双重荧光PCR特异性实验:The fourth step is the specificity experiment of swine fever virus and African swine fever virus double fluorescent PCR:

(1)猪繁殖与呼吸综合征病毒、猪伪狂犬病毒、猪口蹄疫病毒、猪圆环病毒2型、猪细小病毒、猪乙型脑炎病毒、猪流行性腹泻病毒、猪传染性胃肠炎病毒,均为购买的商品化疫苗。上述疫苗核酸的提取按照相应的商品化试剂盒说明书进行;(1) Porcine reproductive and respiratory syndrome virus, porcine pseudorabies virus, porcine foot-and-mouth disease virus, porcine circovirus type 2, porcine parvovirus, porcine Japanese encephalitis virus, porcine epidemic diarrhea virus, porcine infectious gastroenteritis Viruses are all commercially available vaccines. The extraction of the above-mentioned vaccine nucleic acid is carried out according to the instructions of the corresponding commercial kit;

(2)以第三步骤确定的最适反应体系与扩增条件进行荧光PCR扩增,结果表明猪瘟病毒与非洲猪瘟病毒阳性对照均出现特定的扩增曲线;猪繁殖与呼吸综合征病毒、猪伪狂犬病毒、猪口蹄疫病毒、猪圆环病毒2型、猪细小病毒、猪乙型脑炎病毒、猪流行性腹泻病毒、猪传染性胃肠炎病毒和阴性对照等均未出现特定的扩增曲线。实验结果见图1。(2) Fluorescent PCR amplification was carried out with the optimal reaction system and amplification conditions determined in the third step. The results showed that both swine fever virus and African swine fever virus positive control showed specific amplification curves; porcine reproductive and respiratory syndrome virus , porcine pseudorabies virus, porcine foot-and-mouth disease virus, porcine circovirus type 2, porcine parvovirus, porcine Japanese encephalitis virus, porcine epidemic diarrhea virus, porcine transmissible gastroenteritis virus, and negative controls did not appear to be specific. Amplification curve. The experimental results are shown in Figure 1.

第五步骤是猪瘟病毒和非洲猪瘟病毒双重荧光PCR敏感性和标准曲线的建立:The fifth step is the establishment of double fluorescent PCR sensitivity and standard curve for swine fever virus and African swine fever virus:

(1)对猪瘟病毒5’-UTR基因阳性对照进行10倍系列稀释,以第三步骤确定的最适反应体系与扩增条件进行荧光PCR扩增,荧光PCR扩增的动力学曲线见图2;(1) Perform 10-fold serial dilution of the positive control of the 5'-UTR gene of CSFV, and perform fluorescence PCR amplification with the optimal reaction system and amplification conditions determined in the third step. The kinetic curve of fluorescence PCR amplification is shown in Fig. 2;

(2)根据扩增曲线结果绘制标准曲线,获得的标准曲线回归方程为:Y=-3.17X+39.73,相关系数(R2)为0.999,扩增效率为106.8%,见图3;表明所设计的引物及探针扩增效率和结合率高,优化的反应条件适宜,可检测到10个拷贝的猪瘟病毒5’-UTR基因阳性对照分子,可用于猪瘟病毒核酸的定性和定量检测;(2) Draw a standard curve according to the results of the amplification curve. The obtained regression equation of the standard curve is: Y=-3.17X+39.73, the correlation coefficient (R 2 ) is 0.999, and the amplification efficiency is 106.8%, as shown in Figure 3; The designed primers and probes have high amplification efficiency and binding rate, and the optimized reaction conditions are suitable. 10 copies of the 5'-UTR gene positive control molecule of swine fever virus can be detected, which can be used for qualitative and quantitative detection of swine fever virus nucleic acid. ;

(3)对非洲猪瘟病毒P72基因阳性对照进行10倍系列稀释,以第三步骤确定的最适反应体系与扩增条件进行荧光PCR扩增,荧光PCR扩增的动力学曲线见图4;(3) 10-fold serial dilution of the African swine fever virus P72 gene positive control was performed, and fluorescence PCR amplification was performed with the optimal reaction system and amplification conditions determined in the third step. The kinetic curve of fluorescence PCR amplification is shown in Figure 4;

(4)根据扩增曲线结果绘制标准曲线,获得的标准曲线回归方程为:Y=-3.256+38.05,相关系数(R2)为1,扩增效率为102.8%,见图5;表明所设计的引物及探针扩增效率和结合率高,优化的反应条件适宜,可检测到10个拷贝的非洲猪瘟病毒P72基因阳性对照分子,可用于非洲猪瘟瘟病毒核酸的定性和定量检测。(4) Draw a standard curve according to the results of the amplification curve, and the obtained regression equation of the standard curve is: Y=-3.256+38.05, the correlation coefficient (R 2 ) is 1, and the amplification efficiency is 102.8%, as shown in Figure 5; it shows that the designed The primers and probes have high amplification efficiency and binding rate, and the optimized reaction conditions are suitable. 10 copies of the positive control molecule of the African swine fever virus P72 gene can be detected, which can be used for qualitative and quantitative detection of African swine fever virus nucleic acid.

实施例2Example 2

用于检测和鉴别猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测方法的应用。Application of a dual fluorescent PCR assay for detection and identification of swine fever virus and African swine fever virus.

依据本发明建立的检测与鉴别猪瘟病毒和非洲猪瘟病毒双重荧光PCR方法和之前建立的猪瘟病毒和非洲猪瘟病毒单重荧光PCR检测方法进行比较,以两种病毒不同浓度的重组质粒组合作为临床样品(样品编号为:1-12),以灭菌水为阴性对照,分别采用本发明提供的方法和单重荧光PCR方法进行实验室检测,结果见表1、图6和图7。结果表明,猪瘟病毒单重荧光PCR的荧光强度高于猪瘟病毒与非洲猪瘟病毒双重荧光PCR中猪瘟病毒的荧光强度,结果见图6(为了更加清楚的比对,图6只展示了组合质粒7-12猪瘟病毒的扩增结果);12个质粒组合样品的平均Ct值二者相差0.05,几乎无差异。非洲猪瘟病毒单重荧光PCR的荧光强度和猪瘟病毒与非洲猪瘟病毒双重荧光PCR中非洲猪瘟病毒的荧光强度几乎没有差异,结果见图7(为了更加清楚的比对,图7只展示了组合质粒1-6非洲猪瘟病毒的扩增结果);12个质粒组合样品的平均Ct值二者相差0.32,也在正常差异范围内。这些结果表明采用本发明提供的检测和鉴别猪瘟病毒和非洲猪瘟病毒的双重荧光PCR检测方法与相应的单重荧光PCR检测方法相比,灵敏性和特性性并没出现差异,但反应时间大大缩短,进而为检测赢得了宝贵时间。The detection and identification of swine fever virus and African swine fever virus double fluorescent PCR method established according to the present invention was compared with the previously established single-plex fluorescent PCR detection method of swine fever virus and African swine fever virus, and the recombinant plasmids of the two viruses with different concentrations were compared The combination is used as a clinical sample (sample number is: 1-12), and sterile water is used as a negative control, and the method provided by the present invention and the single-plex fluorescence PCR method are respectively used for laboratory detection. The results are shown in Table 1, Figure 6 and Figure 7 . The results show that the fluorescence intensity of swine fever virus single-plex fluorescence PCR is higher than that of swine fever virus and African swine fever virus double fluorescence PCR, the results are shown in Figure 6 (for a clearer comparison, Figure 6 only shows The amplification results of the combination plasmid 7-12 swine fever virus); the average Ct value of the 12 plasmid combination samples differed by 0.05, and there was almost no difference. There is almost no difference between the fluorescence intensity of ASFV single-plex fluorescence PCR and the fluorescence intensity of ASFV in ASFV and ASFV double fluorescence PCR, the results are shown in Figure 7 (for a clearer comparison, Figure 7 The amplification results of the combination plasmids 1-6 of African swine fever virus are shown); the average Ct values of the 12 plasmid combination samples differ by 0.32, which is also within the normal range of difference. These results show that compared with the corresponding single-plex fluorescent PCR detection method using the dual fluorescent PCR detection method for detecting and identifying swine fever virus and African swine fever virus provided by the present invention, there is no difference in sensitivity and characteristic, but the reaction time This is greatly shortened, thereby gaining valuable time for detection.

表1本发明的检测方法与单重荧光PCR检测方法Ct值结果比较Table 1 The detection method of the present invention is compared with the Ct value result of the single-plex fluorescence PCR detection method

Figure BDA0002315749670000081
Figure BDA0002315749670000081

Figure BDA0002315749670000091
Figure BDA0002315749670000091

本发明的上述实施例仅是为清楚地说明本发明所作的举例,而并非是对本发明的实施方式的限定,对于所属领域的技术人员来说,在上述说明的基础上还可以做出其它不同形式的变化或变动,这里无法对所有的实施方式予以穷举,凡是属于本发明的技术方案所引伸出的显而易见的变化或变动仍处于本发明的保护范围之列。The above-mentioned embodiments of the present invention are only examples for clearly illustrating the present invention, rather than limiting the embodiments of the present invention. For those skilled in the art, other differences can also be made on the basis of the above-mentioned descriptions. Changes or changes in form cannot be exhaustively listed here, and all obvious changes or changes derived from the technical solutions of the present invention are still within the protection scope of the present invention.

序列表 sequence listing

<110> 黑龙江八一农垦大学<110> Heilongjiang Bayi Agricultural University

黑龙江省农垦科学院 Heilongjiang Academy of Agricultural Sciences

<120> 一种猪瘟病毒与非洲猪瘟病毒双重荧光PCR检测试剂、试剂盒和检测方法<120> A swine fever virus and African swine fever virus double fluorescent PCR detection reagent, kit and detection method

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Claims (9)

1. A dual fluorescence PCR detection reagent for swine fever virus and African swine fever virus is characterized in that: aiming at the swine fever virus 5' -UTR gene and the African swine fever virus P72 gene, primers and probes which can cover all strains and are suitable for double detection are respectively designed and screened, the primers and probes comprise two pairs of specific primers and two specific probes, the lengths of amplified target fragments are respectively 94bp and 249bp, and the sequences of the primers and the probes are as follows:
hog cholera virus:
an upstream primer CSFV-F: 5 '-TGCCCAYAGTAGGACTAG-3'
The downstream primer CSFV-R: 5'-CTACTGACGACTGTCCTG-3'
Probe CSFV-P: 5'-TGGCGAGCTCCCTGGGTGGTCTA-3'
African swine fever virus:
an upstream primer ASFV-F: 5'-GATACCACAAGATCTGCCGT-3'
A downstream primer ASFV-R: 5'-CTGCTCATGGTATCAATCTTATCG-3'
Probe ASFV-P: 5'-CCACGGGAGGAATACCAACCCAGTG-3'
The probe CSFV-P and the probe ASFV-P are respectively marked with different fluorescent reporter groups at the 5 'end, and the probe CSFV-P and the probe ASFV-P are both marked with the same or different fluorescent quencher groups at the 3' end.
2. The reagent for detecting classical swine fever virus and African swine fever virus dual fluorescence PCR according to claim 1, wherein: the fluorescence reporter group is FAM or VIC, and the fluorescence quencher group is TAMRA or BHQ.
3. The reagent for detecting classical swine fever virus and African swine fever virus dual-fluorescence PCR according to claim 1 or 2, wherein: the probe CSFV-P is marked with FAM at the 5 'end and TAMRA at the 3' end; the probe ASFV-P is labeled with VIC at the 5 'end and BHQ at the 3' end.
4. A dual fluorescence PCR detection kit for classical swine fever virus and African classical swine fever virus is characterized in that: comprising two pairs of specific primers according to claim 1 or 2 or 3 and two specific probes.
5. The hog cholera virus-African hog cholera virus dual-fluorescence PCR detection kit according to claim 4, wherein: the kit also comprises reaction buffer, enzyme, positive control and negative control.
6. The hog cholera virus-African hog cholera virus dual-fluorescence PCR detection kit according to claim 5, wherein: the reaction buffer solution is One Step RT-PCRbuffer; the enzyme is Ex Taq and PrimeScriptRTenzyme; the positive control is in vitro recombinant plasmid of a swine fever virus and African swine fever virus synthetic fragment; the negative control was sterilized deionized water.
7. A double fluorescence PCR detection method for classical swine fever virus and African classical swine fever virus is characterized by comprising the following steps:
step one, extracting DNA and RNA of a sample to be detected, and carrying out reverse transcription on the RNA into cDNA;
step two, using the DNA and the cDNA in the step one as templates, and carrying out double fluorescence PCR amplification by using the kit of claim 4;
and step three, analyzing the PCR product, and judging whether the sample to be detected contains the classical swine fever virus and/or the African classical swine fever virus according to the amplification reaction result.
8. The swine fever virus and African swine fever virus dual-fluorescence PCR detection method according to claim 7, wherein: in the second step, the final concentrations of the most suitable upstream primer CSFV-F and the most suitable downstream primer CSFV-R of the hog cholera virus 5' -UTR gene are both 0.4 mu mol/L, and the final concentration of the most suitable probe CSFV-P is 0.6 mu mol/L; the final concentrations of the most suitable upstream primer ASFV-F and the downstream primer ASFV-R for detecting the African swine fever virus P72 gene are both 0.6 mu mol/L, and the final concentration of the most suitable probe ASFV-P is 0.6 mu mol/L.
9. The swine fever virus and African swine fever virus dual-fluorescence PCR detection method according to claim 7, wherein: in the second step, the reaction procedure of the double fluorescence PCR amplification is as follows: 5min at 42 ℃ and 10s at 95 ℃; 5s at 95 ℃ and 30s at 60 ℃ for 45 cycles.
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