JP2012125220A - Method for prompt and simultaneous detection of group a bovine rotavirus and bovine coronavirus - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide a method for clearly identifying and detecting group A bovine rotavirus (BRV) and bovine coronavirus (BCoV) with high specificity and high sensitivity.SOLUTION: The method in which group A bovine rotavirus (BRV) and bovine coronavirus (BCoV) are simultaneously detected using the following primer sets including: a primer set for detection of BRV which is composed of oligonucleotides designed based on the base sequence of a highly conserved region of the VP6 gene of BRV and a primer set for detection of BCoV composed of oligonucleotides designed based on the base sequence of highly conserved region of the N gene of BCoV; the primer sets; and a kit including the primer sets are provided.

Description

  The present invention is to detect a bovine group A rotavirus and a bovine coronavirus primer set which are causative viruses of calf diarrhea and simultaneously detect bovine group A rotavirus and bovine coronavirus using the primer set with high sensitivity. It relates to a method that can do.

  Bovine Group A rotavirus (hereinafter sometimes referred to as “BRV”) and bovine coronavirus (hereinafter also referred to as “BCoV”) are the most important viruses as pathogens causing diarrhea, particularly in newborn calves. It is. Both BRV and BCoV not only infect cattle and cause economic losses, but have also been pointed out that humans may be infectious, and because they cause infectious diseases common to humans and animals, they are also closely watched for public health. Is an animal virus. However, diarrhea symptoms caused by BRV and BCoV cannot be clinically distinguished. BRV and BCoV are considered to be preventable by vaccination, so if both can be identified and specifically detected as pathogens of diarrhea, measures to prevent BRV and BCoV infection can be taken. Is useful.

  Currently, a BRV detection kit by immunochromatography (Orion diagnostic) is commercially available, but there is no information on sensitivity. The virus content in the stool specimen may be very small, and high detection sensitivity is required from the viewpoint of a false reaction due to non-specific aggregates. As for BCoV, there is a report on detection by semi-nested RT-PCR (Non-Patent Document 1), but it requires complicated operations and equipment compared to the BRV detection kit, and there are few opportunities to carry it out. The reality of BCoV infection is not well understood. In addition, in the semi-nested RT-PCR method for detecting BCoV, BRV infection is missed when BRV and BCoV are mixed.

Trop Anim Health Prod. 41: 1563-1567, 2009

  Accordingly, an object of the present invention is to provide means for clearly distinguishing bovine group A rotavirus (BRV) and bovine coronavirus (BCoV) and detecting them specifically and with high sensitivity.

  As a result of intensive studies to solve the above problems, the present inventors have found that the genes encoding the proteins constituting each virus particle of bovine group A rotavirus (BRV) and bovine coronavirus (BCoV). When a primer was designed in a highly conserved region and PCR was performed using the primer, both BRV and BCoV were clearly identified and successfully detected with specific and high sensitivity. It came to complete.

The present invention includes the following inventions.
[1] A bovine group A rotavirus (BRV) detection primer set comprising the following oligonucleotide (a) and oligonucleotide (b):
(a) An oligonucleotide consisting of the base sequence shown in SEQ ID NO: 1 or a primer for detecting bovine group A rotavirus consisting of a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 1 Oligonucleotides that can function as
(b) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 2 or a primer for detecting bovine group A rotavirus consisting of a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 2 Oligonucleotides that can function as
[2] A bovine coronavirus (BCoV) detection primer set comprising the following oligonucleotide (c) and oligonucleotide (d):
(c) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 3 or a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 3 and functioning as a bovine coronavirus detection primer Possible oligonucleotides
(d) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 4 or a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 4 and functioning as a primer for detecting bovine coronavirus Possible oligonucleotides
[3] A kit for simultaneous detection of bovine group A rotavirus (BRV) and bovine coronavirus (BCoV), comprising the primer set according to [1] and the primer set according to [2].
[4] A bovine group A rotavirus (BRV) comprising a step of performing RT-PCR amplification using RNA extracted from a specimen as a template, using the primer set described in [1], and detecting the obtained amplification product Detection method.
[5] Detection of bovine coronavirus (BCoV) including the step of performing RT-PCR amplification using the RNA extracted from the specimen as a template and the primer set described in [2] and detecting the resulting amplification product Method.
[6] Using the RNA extracted from the sample as a template, performing PCR amplification using both the primer set described in [1] and the primer set described in [2], and detecting each obtained amplification product A method for simultaneously detecting bovine group A rotavirus (BRV) and bovine coronavirus (BCoV).
[7] The method according to any one of [4] to [6], wherein the specimen is feces.

  According to the primer set of the present invention and the method using the same, simultaneous detection of bovine group A rotavirus (BRV) and bovine coronavirus (BCoV) can be performed quickly and easily.

FIG. 1A shows an electrophoretogram of a PCR amplification product of BRV (6505 strain) VP6 gene using a BRV detection primer set. FIG. 1B shows an electrophoretogram of the PCR amplification product of the N gene of BCoV (Kakegawa strain) using the BCoV detection primer set. FIG. 1C shows an electrophoretogram of PCR amplification products of the VP6 gene of BRV (6505 strain) and the N gene of BCoV (Kakegawa strain) by the primer set for BRV detection and the primer set for BCoV detection. FIG. 2 shows simultaneous detection of BRV and BCoV using bovine clinical specimens (N: negative control, P: positive control, M: molecular weight marker, 1-28: fecal specimen of cattle with diarrhea symptoms).

  The primer sets of the present invention are two primer sets: a bovine group A rotavirus (BRV) primer set and a bovine coronavirus (BCoV) primer set.

  The primer set for bovine group A rotavirus (BRV) is a primer set composed of a pair of oligonucleotides designed based on the base sequence of a highly conserved region in the gene encoding the inner core capsid protein VP6 of BRV. The primer set for bovine coronavirus (BCoV) is a primer composed of a pair of oligonucleotides designed based on the nucleotide sequence of a highly conserved region in the gene encoding nucleocapsid protein N of bovine coronavirus (BCoV) Is a set.

  In order to design the primer of the present invention, first, base sequences of BRV VP6 gene and BCoV N gene including a highly conserved region are obtained. The base sequence information may be obtained from a gene database such as GenBank or a paper, or may be obtained by directly analyzing the base sequence. The base sequence of the above highly conserved region can be identified by aligning and comparing a plurality of obtained base sequences. For alignment of base sequences, alignment software (for example, CLUSTALW, URL: http://www.ddbj.nig.ac.jp/) published on the Internet can be used.

  Next, a primer is designed based on the specified base sequence. Primers are designed in consideration of oligonucleotide length, GC content, Tm value, complementarity between oligonucleotides, secondary structure within the oligonucleotide, etc. "Applications" (Protein / Nucleic Acid / Enzyme Special Issue 1996 Kyoritsu Shuppan Co., Ltd.) and "Bio-Experiment Illustrated 3 Really Renewable PCR: A Cellular Engineering Experiment Notebook Series" by Hiroki Nakayama ), “PCR Technology-Principles and Applications of DNA Amplification” (edited by Henry A Erlich, supervised by Kuniyuki Kato, Takara Shuzo Co., Ltd.).

The specific design criteria adopted are as follows.
(a) When the PCR amplification products of BRV VP6 gene and BCoV N gene are electrophoresed, the size of the PCR amplification products is different to such an extent that the difference in the migration distance becomes clear.
(b) The number of bases in the amplified region should be 370 to 390 bp for BRV and 590 to 610 bp for BCoV.
(c) The primer length should be in the range of 15-25 bp to allow specific annealing with the template DNA.
(d) Since the annealing temperature depends on Tm (melting temperature), in order to obtain highly specific PCR amplification products, select primers that are close to each other with a Tm value of 55 to 65 ° C.
(e) High homology between the base sequence at the 3 ′ end of the primer and the template DNA sequence.
(f) Avoid complementary sequences between both primers so that they do not form dimers or conformations.
(g) In order to ensure stable binding to the template DNA, the GC content should be about 50% so that GC-rich or AT-rich is not unevenly distributed in the primer.

  Also, commercially available software for primer design such as Oligo ™ [manufactured by National Bioscience Inc. (USA)], GENETYX [manufactured by Software Development Co., Ltd. (Japan)], etc. can be used.

  The bovine A type rotavirus (BRV) primer set and bovine coronavirus (BCoV) primer set of the present invention composed of oligonucleotides designed based on the above criteria are shown below.

[BRV detection primer set]
BRVF: 5'-ATGGGTACGATGTGGCTCAA-3 '(SEQ ID NO: 1)
BRVR: 5'-ACCGCTGGTGTCATGTTTGG-3 '(SEQ ID NO: 2)

[Primer set for BCoV detection]
BCoVF: 5'-CGATCAGTCCGACCAATCTA-3 '(SEQ ID NO: 3)
BCoVR: 5'-GAGGTAGGGGTTCTGTTGCC-3 '(SEQ ID NO: 4)

  By performing PCR using the above-mentioned primer set for detecting BRV, a region sandwiched between two types of primers, BRVF and BRVR, can be amplified. In this case, the size of the PCR amplification product is 383 bp.

  By performing PCR using the above-described primer set for detecting BCoV, a region sandwiched between two types of primers, BCoVF and BCoVR, can be amplified. In this case, the size of the PCR amplification product is 597 bp.

  In addition, the oligonucleotide consisting of the base sequence of SEQ ID NO: 1 to 4 constituting the primer set is modified to the base sequence within the range having substantially the same function as the oligonucleotide consisting of the base sequence of SEQ ID NO: 1-4 May be an oligonucleotide to which is added.

  Such a modified oligonucleotide comprises a nucleotide sequence having 90% or more, preferably 95% or more identity to the nucleotide sequences of SEQ ID NOs: 1 to 4, and functions as a BRV or BCoV detection primer. Possible oligonucleotides. Modification includes deletion, substitution, insertion, or addition, and the number of bases to be modified is 3 or less, preferably 2 or less, more preferably 1. The base may be added on the 3 ′ side or the 5 ′ side.

  The oligonucleotide may be deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). In the case of ribonucleic acid, the thymidine residue (T) may be read as uridine residue (U). Further, in the synthesis, DNA containing uridine residue may be obtained by synthesizing by changing T at any position to U. Similarly, RNA containing a thymidine residue in which any U is changed to T may be used. There may also be modified nucleotides in the oligonucleotide.

  Each oligonucleotide of the above primer set is prepared by a DNA / RNA automatic synthesizer (for example, Applied Biosystems) commonly used in the art by methods known in the art, for example, phosphotriethyl method, phosphodiester method, etc. It is possible to synthesize using Model 394 manufactured by the company.

  The present invention also provides a BRV detection method, a BCoV detection method, and a simultaneous detection method of BRV and BCoV using either or both of the above primer sets.

  The BRV and / or BCoV detection method of the present invention is obtained by PCR using a process in which RT-PCR amplification is performed using RNA extracted from a specimen as a template and using one or both of the above primer sets. Detecting the amplified product.

  In the amplification reaction, BRV and / or BCoV can be easily detected by incorporating a radioactively-labeled nucleotide such as a radioactive substance during the reaction, or by fractionating the amplified product by electrophoresis and detecting specific bands. can do. In particular, when the primer set for BRV detection and the primer set for BCoV detection of the present invention are used, due to the size difference between the PCR amplification product of BRV VP6 gene and the PCR amplification product of BCoV N gene, Based on the difference in migration distance, these two PCR amplification products can be easily distinguished. In addition, PCR amplified products can be directly detected by using the above-described labeled oligonucleotide as a primer.

  Specimens include biological samples such as feces, rectal swabs, spinal fluid, sputum, nasal discharge, and throat swabs obtained from animals including cattle suspected of being infected with BRV and / or BCoV. Feces are preferred. In addition, cells used in infection experiments, culture solutions thereof, specimens containing viruses isolated from biological specimens, cultured cells, and the like are also samples. These samples may be subjected to pretreatment such as separation, extraction, concentration, and purification.

  As a method for extracting RNA from a specimen, a method known in the art, for example, an RNA extraction method using guanidine isothiocyanate, phenol and chloroform can be used. Alternatively, a commercially available RNA extraction reagent may be used.

  Methods for synthesizing cDNA using RNA as a template are also well known in the art. A commercially available random primer is used as a primer, and cDNA is synthesized using reverse transcriptase in the presence of dNTPs. As the reverse transcriptase, for example, SuperScript II (manufactured by Invitrogen), Thermoscript RT, AMV reverse transcriptase, MMLV reverse transcriptase, and the like can be used.

  Next, using the synthesized cDNA as a template, PCR amplification is performed using either the bovine A type rotavirus (BRV) primer set, the bovine coronavirus (BCoV) primer set, or both. PCR amplification is not particularly limited except that the above primer set is used, and may be performed according to a conventional method. Specifically, a cycle including denaturation of template DNA, annealing of the primer to the template, and primer extension reaction using a thermostable enzyme (DNA polymerase such as Taq polymerase or Tth DNA polymerase from Thermus themophilis) is repeated. Thus, a fragment containing specific gene sequences of the VP6 gene of BRV and the N gene of BCoV is amplified. The composition of the PCR reaction solution and the PCR reaction conditions (temperature cycle, number of cycles, etc.) should be determined by a person skilled in the art based on preliminary experiments, etc. under conditions such that a PCR amplification product can be obtained with high sensitivity in PCR using the above primer set. Can be selected and set appropriately. Methods for selecting appropriate PCR reaction conditions based on the Tm of the primer are well known in the art, for example, first a denaturation reaction at 94 ° C. for 5 minutes and then at 94 ° C. for 50 seconds (denaturation). The extension reaction can be carried out at 55 ° C. for 50 seconds (annealing), 72 ° C. for 1 minute (extension) for 30 cycles, and finally 72 ° C. for 1 minute. However, the conditions shown here are only examples, and the enzyme used, the reaction temperature, the reaction time, the number of cycles, etc. can be appropriately changed. Such a series of PCR operations can be performed using a commercially available PCR kit or PCR apparatus according to the operating instructions. For example, GeneAmp PCR System 9700 (Applied Biosystems), GeneAmp PCR System 9600 (Applied Biosystems) or the like can be used as the PCR apparatus. In the method of the present invention, RNA is converted to cDNA and PCR is performed (RT -PCR) The Takara One Step RT-PCR Kit AMV (manufactured by TAKARA), which can be carried out continuously in one tube, can be suitably used.

  Further, in order to facilitate the detection of PCR amplification products, PCR can be performed using an oligonucleotide with a labeling substance. As a labeling substance, a fluorescent substance, a radioactive substance, a chemiluminescent substance, an enzyme substrate, a biotin / avidin-based label, and the like well known in the art can be used. The labeling method may be end labeling or labeling in the middle of the sequence. Moreover, the label | marker to any of the sugar of a nucleotide, a phosphate group, and a base part may be sufficient.

  PCR amplification products are detected using conventional methods such as agarose gel electrophoresis and capillary electrophoresis, methods such as DNA hybridization and real-time PCR. For example, in agarose gel electrophoresis, staining is performed with ethidium bromide, SYBR Green solution, etc., and the amplification product is detected as a single band, and BRV and / or BCoV is determined based on the size. Alternatively, the amplification product can be detected by performing the PCR using a primer previously labeled with a fluorescent dye or the like. In DNA hybridization, a PCR amplification product is bound to an immobilization carrier such as a microarray, and the PCR amplification product is confirmed by fluorescence or enzymatic reaction. The immobilization carrier for detection is a support on which a DNA fragment having a sequence capable of hybridizing with the sequence of the BRV gene or BcoV gene to be detected is immobilized. As the support, for example, a nylon film, a nitrocellulose film, glass, a silicon chip, or the like can be used.

  The above primer set can be made into a kit in order to more easily perform simultaneous detection of BRV and BCoV. The kit of this invention should just contain said 2 sets of primer sets. If necessary, the kit of the present invention includes RNA extraction reagents, PCR reagents such as PCR buffers and DNA polymerase, DNA solutions containing PCR amplification regions that serve as positive controls for reactions, staining agents, and electrophoresis. It may contain detection reagents such as gels, instructions and the like. The reagent in the kit may be a solution or a lyophilized product.

  EXAMPLES Hereinafter, the present invention will be described more specifically with reference to examples, but these examples do not limit the present invention.

(Example 1) Establishment of primer set
Download the VP6 gene of 46 bovine group A rotavirus (BRV) registered in GenBank and the base sequence of N gene of 17 bovine coronavirus (BCoV) from GenBank, and use alignment software (DNASTAR) The virus strains were aligned with each other, and a sequence (highly conserved sequence) highly conserved between the virus strains in the above target sequence was searched. In addition, Oligo 6.31 (http://www.oligo.net/) was used to search for regions that could be optimal primers. In addition, highly conserved sequences of the BCoV N gene were found at positions 29477-29496 and 30054-30073. For BRV, a forward primer complementary to the highly conserved sequence at positions 552 to 571 and a reverse primer complementary to the highly conserved sequence at positions 915 to 934 were designed as candidate primers. For BCoV, a plurality of forward primers complementary to the highly conserved sequences at positions 29477-29496 and reverse primers complementary to the highly conserved sequences at positions 30054-30073 were designed as candidate primers. Finally, the following two primer sets were established.

[BRV detection primer set]
BRVF: 5'-ATGGGTACGATGTGGCTCAA-3 (SEQ ID NO: 1)
BRVR: 5'-ACCGCTGGTGTCATGTTTGG-3 '(SEQ ID NO: 2)

[Primer set for BCoV detection]
BCoVF: 5'-CGATCAGTCCGACCAATCTA-3 '(SEQ ID NO: 3)
BCoVR: 5'-GAGGTAGGGGTTCTGTTGCC-3 '(SEQ ID NO: 4)

(Example 2) Primer performance evaluation test BRV (6505 strain) and BCoV (Kakegawa strain) culture supernatants were used as specimens. RNA was extracted from 100 μl of culture supernatant using QIAamp Viral RNA Mini Kit (QIAGEN) to obtain 50 μl of RNA extract. Using 5 μl of the obtained RNA extract (RNA sample) as a template for PCR, using the BRV detection primer set and BCoV detection primer set established in Example 1, one-step RT-PCR (Takara One Step RT-PCR Kit AMV (TAKARA) was performed with 50 μl of reaction solution per tube.

  As a result of the examination of the conditions, the optimum annealing temperature was 55 ° C., so RT-PCR was performed with the reaction solution composition and reaction conditions.

(RT-PCR reaction solution composition)
RNA sample 5μl
Each primer (20mM) 1μl X 4
RT-PCR buffer 5 μl
AMV Reverse Transciptase XL (5U / μl) 1μl
RNase inhibitor (40U / μl) 1μl
MgCl ₂ (25mM) 10μl
dNTP mixture (10mM each) 5μl
DNA polymerase (AMV-Optimized Taq: 5U / μl) 1μl
RNase Free dH ₂ O 18μl

(RT-PCR conditions)
After 30 minutes reverse transcription (RT) reaction at 50 ° C, first heat denaturation reaction at 94 ° C for 5 minutes, then heat denaturation reaction at 94 ° C for 50 seconds, annealing at 55 ° C for 50 seconds, 60 at 72 ° C A total of 30 cycles were carried out, with an extension reaction of seconds as one cycle, and finally, an extension reaction was carried out at 72 ° C. for 10 minutes.

  PCR amplification products were confirmed by 1.5% agarose gel electrophoresis containing 1 × GelRed (BIOTIUM, USA), and positive ones were confirmed when the target band was confirmed. Molecular weight markers were also electrophoresed at the same time, and the size of the detected amplification product was analyzed by comparing the relative mobility.

The detection limits of BRV single detection, BCoV single detection, and simultaneous detection of BRV and BCoV with the above primer set were examined based on the virus infectivity titer (PFU) (FIG. 1). From these results, it was shown that the detection limit of BRV is 10 ⁰ PFU and the detection limit of BCoV is 10 ¹ PFU, and the detection limit is the same in the simultaneous detection system of BRV and BCoV.

(Example 3) Simultaneous detection of BRV and BCoV using clinical samples of cattle Bovine fecal samples (28 samples) with diarrhea were diluted to 20% (v / v) with PBS (phosphate buffer) The supernatant was obtained by centrifugation (750 × g, 10 minutes). RNA was extracted from 100 μl of the supernatant in the same manner as in Example 2, and PCR was carried out under the same conditions as in Example 2 using the BRV detection primer set and BCoV detection primer set. Simultaneous detection was performed.

  For comparison, BRV is detected by a commercially available immunochromatography kit (Orion diagnostic), and BCoV is detected by the semi-nested PCR method already reported (Trop Anim Health Prod. 41: 1563-1567, 2009). Detection was performed.

  As shown in FIG. 2, all 19 specimens that were positive for BRV in the comparative kit (BRV Kit) were also positive for detection using the BRV detection primer set of the present invention, and the comparative kit (BRV Kit) was used. Among the 9 samples that were negative in), there were 6 samples that were positive in the detection with the primer set for detecting BRV of the present invention (Fig. 2, sample numbers 14, 17, 19, 21, 22, and 27). . In addition, for BCoV, the two samples that were positive by the comparative semi-nested method (BCoV SN-PCR) and the two samples that were positive by the detection using the BCoV detection primer set of the present invention were the same. 26 specimens were negative by either method.

  The present invention can be used in the field of manufacturing diagnostic agents and kits for bovine type A rotavirus and bovine coronavirus infections.

Claims (7)

A bovine group A rotavirus (BRV) detection primer set comprising the following oligonucleotide (a) and oligonucleotide (b):
(a) An oligonucleotide consisting of the base sequence shown in SEQ ID NO: 1 or a primer for detecting bovine group A rotavirus consisting of a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 1 Oligonucleotides that can function as
(b) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 2 or a primer for detecting bovine group A rotavirus consisting of a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 2 Oligonucleotides that can function as A bovine coronavirus (BCoV) detection primer set comprising the following oligonucleotide (c) and oligonucleotide (d):
(c) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 3 or a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 3 and functioning as a bovine coronavirus detection primer Possible oligonucleotides
(d) an oligonucleotide consisting of the base sequence shown in SEQ ID NO: 4 or a base sequence having 90% or more identity to the base sequence shown in SEQ ID NO: 4 and functioning as a primer for detecting bovine coronavirus Possible oligonucleotides   A kit for simultaneous detection of bovine group A rotavirus (BRV) and bovine coronavirus (BCoV), comprising the primer set according to claim 1 and the primer set according to claim 2.   A method for detecting bovine group A rotavirus (BRV), comprising a step of performing RT-PCR amplification using RNA extracted from a specimen as a template and using the primer set according to claim 1 and detecting the obtained amplification product. .   A method for detecting bovine coronavirus (BCoV) comprising a step of performing RT-PCR amplification using RNA extracted from a specimen as a template and using the primer set according to claim 2 and detecting the obtained amplification product.   A step of performing PCR amplification using RNA extracted from a specimen as a template and using both the primer set according to claim 1 and the primer set according to claim 2 and detecting each obtained amplification product; Simultaneous detection method of group A rotavirus (BRV) and bovine coronavirus (BCoV).   The method according to any one of claims 4 to 6, wherein the specimen is feces.

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