CN110894553A - Primer, probe, kit and RT-iPCR method for detecting Zika virus - Google Patents
Primer, probe, kit and RT-iPCR method for detecting Zika virus Download PDFInfo
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- CN110894553A CN110894553A CN201911086867.2A CN201911086867A CN110894553A CN 110894553 A CN110894553 A CN 110894553A CN 201911086867 A CN201911086867 A CN 201911086867A CN 110894553 A CN110894553 A CN 110894553A
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
- C12Q1/701—Specific hybridization probes
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
Abstract
The invention belongs to the field of molecular biology detection, and discloses a primer, a probe, a kit and an RT-iPCR method for detecting Zika virus. The sequences of the primer and the probe are SEQ ID NO. 1-3. The kit comprises the primer and the probe, and also comprises four nucleotides, a positive quality control substance, a negative quality control substance, a magnesium ion buffer solution, a reverse transcriptase and taq DNA polymerase, wherein the four nucleotides are dATP, dGTP, dCTP and dUTP. The detection method comprises the following steps: extracting sample RNA; and adding the sample RNA into a thermal convection PCR tube and using the kit to detect by a thermal convection PCR detection device. The detection method has the characteristics of good specificity, high sensitivity, simplicity, convenience, rapidness and practicability, and meets the detection requirements of the Zika virus in field and field environments.
Description
Technical Field
The invention belongs to the field of molecular biological detection, and particularly relates to a primer, a probe, a kit and an RT-iPCR method for detecting Zika virus.
Background
Zika Virus (ZIKV) belongs to the flavivirus genus of the family Flaviviridae, a positive-strand RNA Virus caused by mosquito-borne transmission.
Zika virus infection causes Zika fever, which is called Zika virus disease. Following ZIKV infection in adults, which appear asymptomatic or cause mild, influenza-like symptoms, there have also been recent studies reporting visual impairment and infertility. Pregnant women are infected with Zika virus and spread vertically, and ZIKV can cause fetal death, or Guillain-Barre syndrome, a neuroinflammatory disease of the peripheral nervous system, and can also cause neonatal microcephaly. Since 2014, cases of Zika virus infection occurred in a plurality of countries in America, specifically, Zika fever was prevalent in over ten countries and regions such as Brazil, Columbia and Salvador, and countries such as Europe, Asia and oceania also had input case reports, and China also had confirmed input Zika virus infection cases.
The frequent movement of international personnel makes the spreading of Zika virus more extensive, and puts a lot of pressure on infectious disease monitoring and prevention and control in disease control and quarantine departments.
Therefore, it is necessary to establish a nucleic acid detection method for Zika virus which can be applied to the field and even the field, and the method has important significance for pathogen detection and improvement of epidemic situation coping capability.
Disclosure of Invention
The present invention is directed to solving at least one of the problems of the prior art described above. Therefore, the invention provides a primer, a probe, a kit and an RT-iPCR method for detecting Zika virus. The detection method has the characteristics of good specificity, high sensitivity, simplicity, convenience, rapidness and practicability, and meets the detection requirements of the Zika virus in field and field environments.
A primer and a probe for detecting Zika virus, comprising:
two primers for detecting Zika virus, the sequences of which are
A forward primer: 5 '-GTTCACACGGCYCTYGCTGGAGC-3', (SEQ ID NO.1)
Reverse primer: 5 '-GCGRCATTTCAARTGGCCRGAG-3'; (SEQ ID NO.2)
A probe for detecting Zika virus, the sequence of which is
And (3) probe: 5 '-TCCYTTTGCACCATCCATCTCAGCCTC-3'; (SEQ ID NO.3)
The 5 'end of the probe is marked with a fluorescent group, and the 3' end of the probe is marked with a quenching group.
The meaning of Y, R, K, D and W in the primers and probes is: r is A/G, Y is C/T, K is G/T, W is A/T, and D is A/G/T.
Preferably, the fluorophore is FAM, TET, HEX, CY3, or JOE.
Preferably, the quencher group is BHQ1, BHQ2, TAMRA, DABCYL, MGB or Eclipse.
A kit for detecting Zika virus comprises the primer and the probe.
Preferably, the kit further comprises four nucleotides, a positive quality control material, a negative quality control material, a magnesium ion buffer, a reverse transcriptase and a taq DNA polymerase, wherein the four nucleotides are dATP, dGTP, dCTP and dUTP.
More preferably, the negative quality control substance is TE buffer solution or ultrapure water. The TE buffer solution is prepared from Tris and EDTA, and the prepared water is ultrapure water without ribonuclease.
More preferably, the positive quality control substance is pGEM-T vector plasmid containing SEQ ID NO.4 sequence. The SEQ ID NO.4 sequence includes a specific conserved sequence for detecting Zika virus.
Wherein the specific conserved sequences for detecting Zika virus are: TCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAA are provided. (SEQ ID NO.4)
The invention adopts a reverse transcription thermal convection PCR (RT-iPCR) method to detect the Zika virus. Among them, constant temperature thermal isolation PCR (insulated isothermal PCR, iPCR) is also called thermal convection PCR, and is developed by a novel simple PCR amplification technology established by Krishnan M et al in 2002. The iPCR utilizes the principle of thermal convection of the solution, i.e., when heating the bottom of a container containing liquid, the liquid moves downward due to gravity because of the cooler upper surface and higher specific gravity; the liquid heated at the lower part is extruded to move upwards because of the lower specific gravity, and therefore, the circulation of the liquid is naturally formed. This cycle continues as the warmer liquid flows to the surface, cooling due to heat dissipation from the environment, and the cooler liquid flows to the bottom, heating due to heat, thus creating a steady temperature gradient. If the shape and material of the heated container are specially designed, the optimal pipe diameter and height are found, for example, the R-Tube PCR Tube with the lower part being thin and the upper part being thick on the market can skillfully control the convection time and the heat dissipation rate, and a local environment suitable for the denaturation-annealing-extension and other reactions of PCR can be formed.
An RT-iPCR method for detecting Zika virus comprises the following steps:
extracting sample RNA; and adding the sample RNA into a thermal convection PCR tube and using the kit to detect by a thermal convection PCR detection device.
Preferably, in the thermal convection PCR tube, the final concentration of the primer is 0.3-0.8 mu mol/L, and the final concentration of the probe is 0.2-0.4 mu mol/L. Wherein the final concentration of the primers indicates the final concentration of each primer.
Preferably, the reaction procedure of the RT-iPCR method is as follows: reverse transcription is carried out for 8-10 min at 50 ℃; and carrying out thermal convection PCR reaction at 95 ℃ for 45-50 min.
POCKIT is preferably adopted in the inventionTMOn-site nucleic acid detection equipment (Taiwan Ruiki ocean)Biotechnology, ltd) for detection of RT-iiPCR. After the reaction is finished, the POCKIT equipment automatically converts the signal-to-noise ratio (S/N) of the change of the fluorescence signal into 3 types of results of positive, negative or questionable according to a built-in algorithm and a default S/N threshold, wherein the results are respectively expressed as "+", "-" and "? "is displayed on the touch screen of the instrument. "+" indicates a positive result, "-" indicates a negative result, "? "indicates that the result is ambiguous and needs to be retested.
Compared with the prior art, the invention has the following beneficial effects:
(1) the detection method has the advantages that the specificity is strong and the sensitivity is good through the designed specific primers and probes;
(2) according to the invention, the RT-iPCR detection method is adopted, the reverse transcription and the PCR amplification are integrated, the method belongs to a one-step method, the operation is simple, the sample can be added without opening a cover, and the sample can be effectively prevented from being polluted;
(3) the thermal convection PCR method adopted by the invention has the advantages of simplicity, convenience, practicability and low cost, and the detection instrument is easy to carry and is suitable for field or even field rapid detection;
(4) the detection method is short in time, and the detection result can be obtained by detecting on a computer for 50-60 min.
Drawings
FIG. 1 shows the results of the specificity test in example 4.
Detailed Description
In order to make the technical solutions of the present invention more apparent to those skilled in the art, the following examples are given for illustration. It should be noted that the following examples are not intended to limit the scope of the claimed invention.
Example 1
A primer and a probe for detecting Zika virus, comprising:
two primers for detecting Zika virus, the sequences of which are
A forward primer: 5'-GTTCACACGGCCCTTGCTGGAGC-3' the flow of the air in the air conditioner,
reverse primer: 5'-GCGACATTTCAAGTGGCCAGAG-3', respectively;
a probe for detecting Zika virus, the sequence of which is
And (3) probe: 5'-TCCCTTTGCACCATCCATCTCAGCCTC-3', respectively;
the 5 'end of the probe for detecting the Zika virus is labeled with a fluorescent group FAM, and the 3' end of the probe is labeled with a quenching group BHQ 1.
Example 2
A kit for detecting Zika virus, which comprises the primers and probes in example 1, and also comprises four nucleotides of dATP, dGTP, dCTP and dUTP, a positive quality control substance, a negative quality control substance, a magnesium ion buffer solution, MMLV RTase reverse transcriptase and taq DNA polymerase.
The negative quality control substance is TE buffer solution, the TE buffer solution is prepared from Tris and EDTA, and the prepared water is ultrapure water without ribonuclease.
Wherein the positive quality control substance is pGEM-T carrier plasmid containing SEQ ID NO.4 sequence.
Example 3
An RT-iPCR method for detecting Zika virus comprises the following steps:
sample RNA was extracted, and 5. mu.L of sample RNA, 2.5. mu.L of a mixture of MMLVRTase reverse transcriptase and taq DNA polymerase, 17.5. mu.L of ultrapure water, and 25. mu.L of a reaction mixture were added to a PCR Tube (R-Tube) for thermal convection. The reaction mixture contains four nucleotides dATP, dGTP, dCTP and dUTP, the primers and probes in example 1, and magnesium buffer. The final concentration of each primer was 0.5. mu. mol/L, and the final concentration of the probe was 0.3. mu. mol/L.
Sealing cap with R-Tube reaction Tube, centrifuging in special centrifuge, and placing in POCKITTMDetection was performed in a nucleic acid analyzer (taiwan ruiji ocean biotechnology limited).
The reaction procedure for RT-iPCR detection is as follows:
the single wavelength mode of "520 nm" is selected, and the detection time is 58min which is the default of the system in the instrument. The built-in program is set as follows: first, reverse transcription was performed at 50 ℃ for 10min, and then a thermal convection PCR reaction was performed at 95 ℃ for about 48 min. And displaying the detection result of the Zika virus by an instrument.
Example 4
Specificity detection
This test selects as a reference for a specific test a sample of nucleic acids of a common pathogen with similar infection symptoms as Zika virus, the virus types including: yellow fever vaccine strains, chikungunya virus, hantavirus, norovirus type GII, avian influenza virus type H7N9 and group a rotavirus.
The virus sample and the positive quality control substance and the negative quality control substance in the kit of example 2 are used as test samples, the positive quality control substance is used as a positive control, the negative quality control substance is used as a negative control, and the RT-iPCR detection method in example 3 is adopted for detection.
The detection results are shown in fig. 1: no. 1-8 respectively correspond to detection results of yellow fever virus vaccine strain, chikungunya virus, hantavirus, norovirus GII, H7N9 avian influenza virus, group A rotavirus, negative control and positive control under the wavelength of 520 nm.
The experimental result shows that the detection result of each reference substance virus is reported as negative, namely "-"; the test result of the negative control was reported as negative, i.e. "-"; the test result of the positive control is reported as positive, i.e. "+", thus indicating that the kit has good specificity for testing.
Example 5
Sensitivity test
The positive control (plasmid) from example 2 was diluted in a 10-fold gradient to give a copy number of 107、106、105、104、103、102、101And 100The positive plasmid of (1) is detected by the detection method in example 3, each group is subjected to 3 times of repeated tests, and the result shows that the lowest copy number which can be effectively detected is 103The positive plasmid of (1).
Example 6
Repeatability test
The copy number of 10 in example 5 was used6And 104The positive plasmid of (1), each group was repeatedly tested 10 times, POCKITTMThe results reported by the apparatus are all positive, i.e.) "+ "shows that the RT-iPCR detection method used by the invention has good repeatability and stability.
SEQUENCE LISTING
<110> Zhuhai international travel health care center (Arch North customs port outpatient department)
<120> primers, probe, kit and RT-iPCR method for detecting Zika virus
<130>1
<160>4
<170>PatentIn version 3.5
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<213> Artificial sequence
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gttcacacgg cyctygctgg agc 23
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<213> Artificial sequence
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gcgrcatttc aartggccrg ag 22
<210>3
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<212>DNA
<213> Artificial sequence
<400>3
tccytttgca ccatccatct cagcctc 27
<210>4
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<212>DNA
<213> Artificial sequence
<400>4
tctagggagt caagaaggag cagttcacac ggcccttgct ggagctctgg aggctgagat 60
ggatggtgca aagggaaggc tgtcctctgg ccacttgaaa tgtcgcctga aaatggataa 120
Claims (10)
1. A primer and a probe for detecting Zika virus are characterized by comprising: two primers for detecting Zika virus, the sequences of which are forward primers: 5 '-GTTCACACGGCYCTYGCTGGAGC-3', reverse primer: 5 '-GCGRCATTTCAARTGGCCRGAG-3'; a probe for detecting Zika virus, the sequence of which is probe: 5 '-TCCYTTTGCACCATCCATCTCAGCCTC-3'; the 5 'end of the probe is marked with a fluorescent group, and the 3' end of the probe is marked with a quenching group.
2. The primers and probes as claimed in claim 1, wherein the fluorescent group is FAM, TET, HEX, CY3 or JOE.
3. The primers and probe of claim 1, wherein the quencher is BHQ1, BHQ2, TAMRA, DABCYL, MGB, or Eclipse.
4. A kit for detecting Zika virus, comprising the primer according to any one of claims 1 to 3 and a probe.
5. The kit of claim 4, further comprising four nucleotides, a positive quality control substance, a negative quality control substance, a magnesium ion buffer, a reverse transcriptase, and a taq DNA polymerase, wherein the four nucleotides are dATP, dGTP, dCTP, and dUTP.
6. The kit according to claim 5, wherein the negative quality control substance is TE buffer or ultrapure water.
7. The kit of claim 5, wherein the positive control is a pGEM-T vector plasmid having the sequence of SEQ ID No. 4.
8. An RT-iPCR method for detecting Zika virus is characterized by comprising the following steps:
extracting sample RNA, adding the sample RNA in a thermal convection PCR tube and detecting by a thermal convection PCR detection device using the kit of any one of claims 5 to 7.
9. The RT-iPCR method according to claim 8, wherein the final concentration of the primer is 0.3-0.8 μmol/L and the final concentration of the probe is 0.2-0.4 μmol/L in the thermal convection PCR tube.
10. The RT-iiPCR method according to claim 8, wherein the reaction sequence of the RT-iiPCR method is: reverse transcription is carried out for 8-10 min at 50 ℃; and carrying out thermal convection PCR reaction at 95 ℃ for 45-50 min.
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