CN105176979A - Method for detecting infectious pancreatic necrosis virus - Google Patents

Method for detecting infectious pancreatic necrosis virus Download PDF

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CN105176979A
CN105176979A CN201510548476.3A CN201510548476A CN105176979A CN 105176979 A CN105176979 A CN 105176979A CN 201510548476 A CN201510548476 A CN 201510548476A CN 105176979 A CN105176979 A CN 105176979A
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necrosis virus
primer
primer pair
infectious
seqidno
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CN105176979B (en
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孙翠言
张培
类延乐
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Zhejiang Hengyu Biotechnology Co., Ltd
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孙翠言
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Abstract

The invention provides a method for detecting an infectious pancreatic necrosis virus. The sequences of upstream and downstream primers adopted by the method are respectively shown as SEQ ID NO:1 and SEQ ID NO:2. According to the invention, a large number of primers are designed according to the genomic sequences of the infectious pancreatic necrosis virus, and the primers capable of rapidly and effectively detecting are screened. The primers used by the method disclosed by the invention have the characteristics of high specificity, high sensitivity, high practicability and high convenience, and can carry out highly-sensitive detection on the infectious pancreatic necrosis virus.

Description

A kind of method detecting infectious pancreas necrosis virus
Technical field
The invention belongs to aquatic products disease technical field of microbial detection, be specifically related to a kind of method detecting infectious pancreas necrosis virus.
Background technology
Along with socioeconomic fast development, culture fishery also presents the unprecedented raising of cultivation scale and cultural technique, and especially in intensive culture and industrialized culture, development is rapid, and this brings nutrition and health to the life of the people.But in the breeding process of marine fish, breaking out of virus disease often carrys out huge harm to cultivation industrial belt.Infectious pancreatic necrosis is the fish transmissible disease caused by infectious pancreatic necrosis virus (infectiouspancreaticnecrosisvirus, IPNV), and the son of main harm salmon fishes, juvenile fish, mortality ratio reaches more than 90%.One of feature of morbidity fish is seed sudden death, and sick fish is first slowly travelling, asynergia, or following current levitating, and normal to do vertical revolution travelling, just sinks under water soon and dead.Sick fish body colour blackout, ophthalmoptosis, belly expands, belly and fin ray portion congested, the gill is incarnadine, and anus place often holds in the palm a long and thicker white mucus ight soil.Dissect disease fish and check there is ascites as seen, sick fish pancreas is congested, and pylorospasm is hemorrhage, histocyte severe necrosis; The pale anaemia of liver,spleen,kidney, also has necrotic lesion, gastrorrhagia, without food in enteron aisle, and has milky or faint yellow mucus.Therefore, detect whether aquaculture water, apparatus and feed are subject to infectious pancreatic necrosis virus in time just extremely important.But detection method mainly histopathology technology, electron microscopy, cell culture technology, immunoassay technology and the molecular detection technology etc. of IPNV at present.These detection methods have respective advantage in accuracy, susceptibility and cost etc., but they are subject to the restriction needing professional and complex instrument in varying degrees.
Summary of the invention
The object of this invention is to provide a kind of method detecting infectious pancreas necrosis virus, thus make up the deficiencies in the prior art.
First the present invention provides a kind of primer detecting infectious pancreas necrosis virus, and the sequence of its upstream and downstream primer is respectively SEQIDNO:1 and SEQIDNO:2;
As preferably, the sequence of its downstream primer is SEQIDNO:3.
The present invention also provides a kind of test kit detecting infectious pancreas necrosis virus, and this test kit includes above-mentioned primer pair.
The present invention also provides a kind of method detecting infectious pancreas necrosis virus, is whether to have infected the method for infectious pancreas necrosis virus for detecting in water body or feed, and the method comprises following step:
1) nucleic acid of detected sample is extracted as the template detected;
2) RNA of extraction is carried out reverse transcription and prepare cDNA;
3) carry out the pcr amplification detecting sample, reaction system 50 μ L, includes the Taq enzyme of 0.05U/ μ L, Mg 2+concentration is the primer of the dNTPs of the 10 × PCRBuffer of 2mmol/L, 0.25mmol/L, 0.36 μm of ol/L; Step 2) cDNA for preparing is as amplification template;
The response procedures of pcr amplification is as follows: 94 DEG C of 5min; 94 DEG C of 15s, 56 DEG C of 15s, 72 DEG C 15s, 25-40 circulation; 4 DEG C of termination reactions;
4) product carries out electrophoresis detection, has determined whether target fragment.
Wherein step 3) in carry out simultaneously positive control and negative control amplification; Positive control is the plasmid carrying infectious pancreas necrosis virus nucleic acid fragment, and negative control is deionized water.
The present invention devises a large amount of primer according to infectious pancreas necrosis virus genome sequence, therefrom filters out the primer that can effectively detect fast.Primer used in the present invention has higher specificity, sensitivity, practicality and convenience, effectively can carry out high-sensitive detection to infectious pancreas necrosis virus.
Embodiment
Below in conjunction with embodiment, the present invention is described in detail.
Embodiment 1: the design of primer
US National biology information technology center (NCBI) is logged in by Internet, the infectious pancreas necrosis virus gene nucleotide series that query and search has been announced, do not comprise not clear base content sequence, to the diseased plant of homology nearer same time with place, edit with the N gene nucleotide series of Editseq and the MegAlign software in DNAStar7.1 software package to selected sample, comparison one by one, with ClustalWMethod (software) default parameters, tetraploid rice is carried out to selected N nucleotide sequence, find the specific nucleotide sequence (target detection sequence) characterizing this virus.
Pcr amplification design of primers is undertaken by AssayDesignSW software, one group of higher primer of score is used to test, according to the homology analysis result of DNASTAR, choose sequence area comparatively conservative in sample gene, design of amplification primers, so that amplify the single band of specificity, for follow-up order-checking lays the foundation.And adopt primer-design software Primer_Premier_5.0 to analyze to the primer of design, comprise the design of primers indexs such as G value, primer length and GC content, select the conduct primer pair used in the present invention that mark is the highest, wherein the sequence of upstream primer is 5 '-CAAACAAAGCAACCGCAAC-3 ' (SEQIDNO:1), the sequence of downstream primer is 5 '-GTCCCATTCAGGGCATAGAG-3 ' (SEQIDNO:2), the annealing temperature of primer is preferably 54 DEG C, and expanding fragment length is 352bp.
Embodiment 2: the specific detection of primer
In order to verify the specificity of primer of the present invention, choose and carry lymphocystis disease virus LCDV, Megalocytivirus belongs to irido virus (Megalocytivirus, Mega), red-spotted grouper nervous necrosis virus (red-spottedgroupernervousnecrosisvirus, RGNNV), infectious hematopoietic necrosis's poison (infectioushaematopoieticnecrosisvirus, IHNV), viral hemorrhagic septicemia, VHS virus (viralhemorrhagicsepticemiavirus, and Infectious Salmonia Anemia virus (infectioussalmonanaemiavirus VHSV), ISAV) plasmid of nucleic acid fragment is as template.
The step detected is as follows:
(1) extraction of sample tissue nucleic acid.Sample thief about 0.02 ~ 1g is placed in 1.5ml plastic, with disposable grinding rod, sample is milled to pulpous state fast, then DNA extraction kit (Tian Gen biochemical technology company limited is used, Beijing) and TRizol (precious biotinylated biomolecule Engineering Co., Ltd, Dalian) extract DNA and RNA respectively.Concrete operation step carries out according to the specification sheets of test kit or reagent.If the viral sample plasmid bought, then omit this step
(2) cDNA is prepared in reverse transcription.When detecting the RNA viruses such as RGNNV, IHNV, IPNV, VHSV, ISAV, need to carry out reverse transcription to RNA template, use the single stage method gDNA of Beijing Quan Shijin biotech firm removal and cDNA synthetic agent box to carry out.Concrete grammar is: in the Eppendorf tube of 200 μ l, adds 5 ~ 500ngRNA sample, 1 μ l random primer (0.1 μ g/ μ l), 10 μ l reverse transcription buffer (2 × TSReactionMix), 1 μ l ThermoScript II ( rT/RIEnzymeMix), 1 μ l genomic dna degrading enzyme (gDNARemover), DEPC process water complements to 20 μ l.Above-mentioned reaction system is placed in 25 DEG C of 10min, then 42 DEG C of 30min, then 85 DEG C of 5min, last 4 DEG C save backup.Detect the DNA virus such as IPNV, Mega, TRBIV and do not need reverse transcription, directly use the DNA masterplate extracted.
(3) pcr amplification
In the PCR reaction tubes of single 200 μ l, containing 2.5U/ μ LTaqDNA polysaccharase 0.6 μ L, 10 × PCRBuffer (Mg 2+plus) 5 μ L, 2.5mmol/LdNTPs5 μ L, 2 μm of ol/LPrimer5 μ L, the DNA profiling of extraction and the cDNA masterplate of preparation each 1 μ L, ddH 2o is supplemented to 50 μ L.Amplified reaction program: 94 DEG C of 5min; 94 DEG C of 15s, 54 DEG C of 15s, 72 DEG C of 15s, 15 circulations; 94 DEG C of 15s, 70 DEG C of 15s, 6 circulations; 72 DEG C of 3min; 4 DEG C of preservations.
Product is carried out agarose gel electrophoresis, and adopt 2.0% sepharose to be separated PCR primer, 4SRed nucleic acid dye is added in the gel of thawing to specifications.To take pictures under gel imaging system after 90V constant voltage electrophoresis 35min observation.
Electrophoresis result proves to only have the swimming lane of the sample of infectious pancreas necrosis virus to have amplified production, thus proves that primer of the present invention has good specific amplification.
Embodiment 3: the mensuration of primer detection sensitivity
Get 1 μ L10 times gradient dilution (10 4~ 10 1, 5copies/ μ L) containing the plasmid of infectious pancreas necrosis virus nucleic acid as template, carry out the mensuration of sensitivity by the method for embodiment 2.Result shows, primer of the present invention just can can detect the plasmid of 10 copies 27 amplification cycles; But for 5 copy, need 38 circulations to show amplified band.
In order to improve sensitivity during detection, downstream primer being modified optimization, obtains new primer sequence 5 '-GTCCGATTCAGTGCATAGAG-3 ' (SEQIDNO:3); Be analyzed according to above-mentioned specificity and susceptibility detecting step, found that: compared to the primer amplification 10ng template before not optimizing, amplified band is more obviously clear under same cycle index condition.And, under similarity condition, primer before optimization 35 circulation times can not from 5 copy plasmid template sample amplify can be visual in gel electrophoresis product, and the primer after optimizing can go out at 32 cyclic amplifications the plasmid template sample that minimum concentration is 5 copies, and there is no the appearance of primer dimer.Illustrate that the primer after optimizing can significantly improve sensitivity, and specificity does not receive any impact.
The detection of embodiment 4 aquaculture water
The water body adopting primer pair of the present invention to there occurs infectious pancreas necrosis virus detects, and has carried out synchronous detection to the sick fish sample of 30 tails collected simultaneously.Result shows, and use the upstream primer that sequence is SEQIDNO:1, and the downstream primer of SEQIDNO:2 increases, and whole sick fish sample just detects object band at 25 circulation times; And water body just can will detect 39 circulations.Adopt sequence to be that the downstream primer of SEQIDNO:3 and the upstream primer of SEQIDNO:1 increase, obtain positive band 35 circulations with regard to obtaining to increase; Thus avoid the generation of false negative result.

Claims (7)

1. detect a primer pair for infectious pancreas necrosis virus, it is characterized in that, the sequence of the upstream and downstream primer of described primer pair is respectively SEQIDNO:1 and SEQIDNO:2.
2. primer pair as claimed in claim 1, it is characterized in that, the sequence of described downstream primer is SEQIDNO:3.
3. detect a test kit for infectious pancreas necrosis virus, it is characterized in that, described test kit includes the primer pair described in claim 1 or 2.
4. detect a method for infectious pancreas necrosis virus, be whether infected the method for infectious pancreas necrosis virus for detecting in water body or feed, the method comprises following step:
1) nucleic acid of detected sample is extracted as the template detected;
2) RNA of extraction is carried out reverse transcription and prepare cDNA;
3) carry out the pcr amplification detecting sample, reaction system 50 μ L, includes the Taq enzyme of 0.05U/ μ L, Mg 2+concentration is the dNTPs of the 10 × PCRBuffer of 2mmol/L, 0.25mmol/L, the primer pair described in the claim 1 or 2 of 0.36 μm of ol/L; Step 2) cDNA for preparing is as amplification template;
The response procedures of pcr amplification is as follows: 94 DEG C of 5min; 94 DEG C of 15s, 56 DEG C of 15s, 72 DEG C 15s, 25-35 circulation; 4 DEG C of termination reactions;
4) product carries out electrophoresis detection, has determined whether target fragment.
5. method as claimed in claim 4, is characterized in that, described step 3) in carry out positive control and negative control amplification simultaneously.
6. method as claimed in claim 5, it is characterized in that, described positive control is the plasmid carrying infectious pancreas necrosis virus nucleic acid fragment.
7. method as claimed in claim 5, it is characterized in that, described negative control is deionized water.
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Cited By (1)

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CN112176111A (en) * 2020-11-05 2021-01-05 北京市水产技术推广站 Primer, probe, kit and detection method for detecting infectious pancreatic necrosis virus

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CN112176111A (en) * 2020-11-05 2021-01-05 北京市水产技术推广站 Primer, probe, kit and detection method for detecting infectious pancreatic necrosis virus

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