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Ding L, Wang X, Chen X, Xu X, Wei W, Yang L, Ji Y, Wu J, Xu J, Peng C. Development of a novel Cas13a/Cas12a-mediated 'one-pot' dual detection assay for genetically modified crops. J Adv Res 2024:S2090-1232(24)00311-4. [PMID: 39084403 DOI: 10.1016/j.jare.2024.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/10/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024] Open
Abstract
INTRODUCTION Genetically modified (GM) crops have been widely cultivated across the world and the development of rapid, ultrasensitive, visual multiplex detection platforms that are suitable for field deployment is critical for GM organism regulation. OBJECTIVE In this study, we developed a novel one-pot system, termed MR-DCA (Multiplex RPA and Dual CRISPR assay), for the simultaneous detection of CaMV35S and NOS genetic targets in GM crops. This innovative approach combined Multiplex RPA (recombinase polymerase amplification) with the Dual CRISPR (clustered regularly interspaced short palindromic repeat) assay technique, to provide a streamlined and efficient method for GM crop detection. METHODS The RPA reaction used for amplification CaMV35S and NOS targets was contained in the tube base, while the dual CRISPR enzymes were placed in the tube cap. Following centrifugation, the dual CRISPR (Cas13a/Cas12a) detection system was initiated. Fluorescence visualization was used to measure CaMV35S through the FAM channel and NOS through the HEX channel. When using lateral flow strips, CaMV35S was detected using rabbit anti-digoxin (blue line), whilst NOS was identified using anti-mouse FITC (red line). Line intensity was quantified using Image J and depicted graphically. RESULTS Detection of the targets was completed in 35 min, with a limit of detection as low as 20 copies. In addition, two analysis systems were developed and they performed well in the MR-DCA assay. In an analysis of 24 blind samples from GM crops with a wide genomic range, MR-DCA gave consistent results with the quantitative PCR method, which indicated high accuracy, applicability and semi-quantitative ability. CONCLUSION The development of MR-DCA represents a significant advancement in the field of GM detection, offering a rapid, sensitive and portable method for multiple target detection that can be used in resource-limited environments.
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Affiliation(s)
- Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Pan J, Zeng M, Zhao M, Huang L. Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus. Front Microbiol 2023; 14:1097905. [PMID: 36970703 PMCID: PMC10033578 DOI: 10.3389/fmicb.2023.1097905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.
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Affiliation(s)
- Jinghua Pan
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengyi Zeng
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengmeng Zhao
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- *Correspondence: Mengmeng Zhao,
| | - Liangzong Huang
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- Liangzong Huang,
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Development of a Multiplex Crystal Digital RT-PCR for Differential Detection of Classical, Highly Pathogenic, and NADC30-like Porcine Reproductive and Respiratory Syndrome Virus. Animals (Basel) 2023; 13:ani13040594. [PMID: 36830384 PMCID: PMC9951750 DOI: 10.3390/ani13040594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) type 1 (European genotype) and PRRSV type 2 (North American genotype) are prevalent all over the world. Nowadays, the North American genotype PRRSV (NA-PRRSV) has been widely circulating in China and has caused huge economic losses to the pig industry. In recent years, classical PRRSV (C-PRRSV), highly pathogenic PRRSV (HP-PRRSV), and NADC30-like PRRSV (NL-PRRSV) have been the most common circulating strains in China. In order to accurately differentiate the circulating strains of NA-PRRSV, three pairs of specific primers and corresponding probes were designed for the Nsp2 region of C-PRRSV, HP-PRRSV, and NL-PRRSV. After optimizing the annealing temperature, primer concentration, and probe concentration, a multiplex real-time quantitative RT-PCR (qRT-PCR) and a multiplex Crystal digital RT-PCR (cdRT-PCR) for the differential detection of C-PRRSV, HP-PRRSV, and NL-PRRSV were developed. The results showed that the two assays illustrated high sensitivity, with a limit of detection (LOD) of 3.20 × 100 copies/μL for the multiplex qRT-PCR and 3.20 × 10-1 copies/μL for the multiplex cdRT-PCR. Both assays specifically detected the targeted viruses, without cross-reaction with other swine viruses, and indicated excellent repeatability, with coefficients of variation (CVs) of less than 1.26% for the multiplex qRT-PCR and 2.68% for the multiplex cdRT-PCR. Then, a total of 320 clinical samples were used to evaluate the application of these assays, and the positive rates of C-PRRSV, HP-PRRSV, and NL-PRRSV by the multiplex qRT-PCR were 1.88%, 21.56%, and 9.69%, respectively, while the positive rates by the multiplex cdRT-PCR were 2.19%, 25.31%, and 11.56%, respectively. The high sensitivity, strong specificity, excellent repeatability, and reliability of these assays indicate that they could provide useful tools for the simultaneous and differential detection of the circulating strains of C-PRRSV, HP-PRRSV, and NL-PRRSV in the field.
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Development of CRISPR-Mediated Nucleic Acid Detection Technologies and Their Applications in the Livestock Industry. Genes (Basel) 2022; 13:genes13112007. [PMID: 36360244 PMCID: PMC9690124 DOI: 10.3390/genes13112007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
The rapid rate of virus transmission and pathogen mutation and evolution highlight the necessity for innovative approaches to the diagnosis and prevention of infectious diseases. Traditional technologies for pathogen detection, mostly PCR-based, involve costly/advanced equipment and skilled personnel and are therefore not feasible in resource-limited areas. Over the years, many promising methods based on clustered regularly interspaced short palindromic repeats and the associated protein systems (CRISPR/Cas), i.e., orthologues of Cas9, Cas12, Cas13 and Cas14, have been reported for nucleic acid detection. CRISPR/Cas effectors can provide one-tube reaction systems, amplification-free strategies, simultaneous multiplex pathogen detection, visual colorimetric detection, and quantitative identification as alternatives to quantitative PCR (qPCR). This review summarizes the current development of CRISPR/Cas-mediated molecular diagnostics, as well as their design software and readout methods, highlighting technical improvements for integrating CRISPR/Cas technologies into on-site applications. It further highlights recent applications of CRISPR/Cas-based nucleic acid detection in livestock industry, including emerging infectious diseases, authenticity and composition of meat/milk products, as well as sex determination of early embryos.
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Rapid and Visual Detection of Heterodera schachtii Using Recombinase Polymerase Amplification Combined with Cas12a-Mediated Technology. Int J Mol Sci 2021; 22:ijms222212577. [PMID: 34830457 PMCID: PMC8618885 DOI: 10.3390/ijms222212577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Heterodera schachtii is a well-known cyst nematode that causes serious economic losses in sugar beet production every year. Rapid and visual detection of H. schachtii is essential for more effective prevention and control. In this study, a species-specific recombinase polymerase amplification (RPA) primer was designed from a specific H. schachtii sequence-characterized amplified region (SCAR) marker. A band was obtained in reactions with DNA from H. schachtii, but absent from nontarget cyst nematodes. The RPA results could be observed by the naked eye, using a lateral flow dipstick (LFD). Moreover, we combined CRISPR technology with RPA to identify positive samples by fluorescence detection. Sensitivity analysis indicated that 10−4 single cysts and single females, 4−3 single second-stage juveniles, and a 0.001 ng genomic DNA template could be detected. The sensitivity of the RPA method for H. schachtii detection is not only higher than that of PCR and qPCR, but can also provide results in <1 h. Consequently, the RPA assay is a practical and useful diagnostic tool for early diagnosis of plant tissues infested by H. schachtii. Sugar beet nematodes were successfully detected in seven of 15 field sugar beet root samples using the RPA assay. These results were consistent with those achieved by conventional PCR, indicating 100% accuracy of the RPA assay in field samples. The RPA assay developed in the present study has the potential for use in the direct detection of H. schachtii infestation in the field.
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Liu S, Tao D, Liao Y, Yang Y, Sun S, Zhao Y, Yang P, Tang Y, Chen B, Liu Y, Xie S, Tang Z. Highly Sensitive CRISPR/Cas12a-Based Fluorescence Detection of Porcine Reproductive and Respiratory Syndrome Virus. ACS Synth Biol 2021; 10:2499-2507. [PMID: 34543570 DOI: 10.1021/acssynbio.1c00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is an economically important disease of swine that is caused by PRRS virus (PRRSV). In this study, we established a fluorescence assay for highly sensitive detection of PRRSV through integration of the reverse transcription-recombinase polymerase amplification (RT-RPA)-coupled Cas12a system with an optical property of single stranded DNA-fluorescently quenched (ssDNA-FQ) reporter. This technique can achieve isothermal and visual detection of PRRSV in 25 min. In particular, the assay reaction can be completed in a single tube. The limit of sensitivity for PRRSV detection was single copy without cross-reactivity of other porcine viruses. Correlation between 11 PRRSV clinical samples measured by the quantitative reverse transcription polymerase chain reaction (RT-qPCR) and CRISPR/Cas12a assay was determined; the result showed that our results were highly accurate. To sum up, this study developed a visual, sensitive, and specific method of nucleic acid detection based on a CRISPR-Cas12a technique for the on-site detection of PRRSV.
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Affiliation(s)
- Siyuan Liu
- College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128, PR China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
| | - Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Nanning 530001, PR China
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
| | - Shouzhang Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Yunnan 650201, PR China
| | - Yulan Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
| | - Peng Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
- School of Life Sciences, Henan University, Kaifeng 475004, PR China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
| | - Bin Chen
- College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128, PR China
| | - Yonggang Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Yunnan 650201, PR China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, PR China
- GuangXi Engineering Research Center for Resource Development of Bama Xiang Pig, Bama 547500, PR China
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Liu H, Wang J, Zeng H, Liu X, Jiang W, Wang Y, Ouyang W, Tang X. RPA-Cas12a-FS: A frontline nucleic acid rapid detection system for food safety based on CRISPR-Cas12a combined with recombinase polymerase amplification. Food Chem 2021; 334:127608. [PMID: 32711280 DOI: 10.1016/j.foodchem.2020.127608] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/12/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022]
Abstract
Food analysis to ensure food safety and quality are relevant to all countries. This study aimed to develop a detection technique by combining recombinase polymerase amplification with CRISPR-Cas12a for food safety (termed RPA-Cas12a-FS). Our data showed that this novel method could be detected via fluorescence intensity for the molecular identification of foodborne pathogenic bacteria, genetically modified crops, and meat adulteration. After optimization, the sensitivity and stability of RPA-Cas12a-FS was further enhanced. The RPA-Cas12a-FS system could specifically detect target gene levels as low as 10 copies in 45 min at 37 °C. The RPA-Cas12a-FS system was sensitive both using standard samples in the lab and using samples from the field, which indicated that this detection method was practical. In conclusion, a simple, rapid, and highly sensitive detection method based on CRISPR-Cas12a was developed for molecular identification in the food safety field without requiring technical expertise or ancillary equipment.
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Affiliation(s)
- Hua Liu
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences; Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, P.R.C., 2901 Beidi Road, Shanghai 201106, China
| | - Jinbin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences; Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, P.R.C., 2901 Beidi Road, Shanghai 201106, China.
| | - Haijuan Zeng
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences; Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, P.R.C., 2901 Beidi Road, Shanghai 201106, China
| | - Xiaofeng Liu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Wei Jiang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences; Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, P.R.C., 2901 Beidi Road, Shanghai 201106, China
| | - Yu Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Wanbao Ouyang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xueming Tang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences; Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, P.R.C., 2901 Beidi Road, Shanghai 201106, China.
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Zhang D, Bai C, Ge K, Li Y, Gao W, Jiang S, Wang Y. Establishment of an SYBR Green-based real-time PCR assay for porcine circovirus type 4 detection. J Virol Methods 2020; 285:113963. [PMID: 32882322 DOI: 10.1016/j.jviromet.2020.113963] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/25/2022]
Abstract
Porcine circovirus 4 (PCV4) is a novel circovirus first discovered in China in April 2019. Here, we established an SYBR Green I-based real-time PCR for quantitative detection of PCV4. A pair of specific primers was designed based on the conserved region of Cap of PCV4. The standard curve of the established real-time PCR. assay showed a good linear relationship. The sensitivity of the established real-time PCR was 100 times greater than that of conventional PCR, and the detection limit of the assay was 3 × 101 copies. There was no cross-reactivity with other swine DNA viruses, showing good specificity. The intra-group variation coefficient was 0.37-0.78 %, and the inter-group variation coefficient was 0.57-0.94%, indicating that the assay has good repeatability. Moreover, the analysis of clinical samples showed that the positive detection rate of PCV4 was 10.71% (18/168), while that of conventional PCR was 8.93% (15/168). Interestingly, co-infection with PCV2 or PCV3, or both PCV2 and PCV3, was also detected. In conclusion, the established SYBR Green I-based real-time PCR may be a cost-effective and rapid method for PCV4 clinical diagnosis.
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Affiliation(s)
- Da Zhang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Caixia Bai
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Kai Ge
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, PR China
| | - Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Wenhui Gao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Shudong Jiang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Yong Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:2697230. [PMID: 32184908 PMCID: PMC7061119 DOI: 10.1155/2020/2697230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 01/23/2023]
Abstract
Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.
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Chang Y, Deng Y, Li T, Wang J, Wang T, Tan F, Li X, Tian K. Visual detection of porcine reproductive and respiratory syndrome virus using CRISPR-Cas13a. Transbound Emerg Dis 2019; 67:564-571. [PMID: 31541593 DOI: 10.1111/tbed.13368] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 12/26/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has varied constantly and circulated in the pig industry worldwide. The prevention and control of porcine reproductive and respiratory syndrome (PRRS) is complicated. A visual, sensitive and specific diagnostic method is advantageous to the control of PRRS. The collateral cleavage activity of LwCas13a is activated to degrade non-targeted RNA, when crRNA of LwCas13a bond to target RNA. The enhanced Cas13a detection is the combination of collateral cleavage activity of LwCas13a and recombinase polymerase amplification (RPA). In this study, the enhanced Cas13a detection for PRRSV was established. The novel method was an isothermal detection at 37°C, and the detection can be used for real-time analysis or visual readout. The detection limit of the enhanced Cas13a detection was 172 copies/μl, and there were no cross-reactions with porcine circovirus 2, porcine parvovirus, classical swine fever virus and pseudorabies virus. The enhanced Cas13a detection can work well in clinical samples. In summary, a visual, sensitive and specific nucleic acid detection method based on CRISPR-Cas13a was developed for PRRSV.
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Affiliation(s)
- Yafei Chang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yue Deng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tianyu Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Juan Wang
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Tongyan Wang
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Feifei Tan
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Xiangdong Li
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Kegong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,National Research Center for Veterinary Medicine, Luoyang, China.,OIE Reference Laboratory for PRRS in China, Beijing, China
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Fluorescence resonance energy transfer combined with asymmetric PCR for broad and sensitive detection of porcine reproductive and respiratory syndrome virus 2. J Virol Methods 2019; 272:113710. [PMID: 31351984 DOI: 10.1016/j.jviromet.2019.113710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 11/21/2022]
Abstract
With its ever-increasing viral genetic diversity, accurate diagnosis of porcine reproductive and respiratory syndrome virus (PRRSV) infection is indispensable for PRRSV control. Here, a sensitive graphene oxide (GO)-based FRET method was developed to detect PRRSV-2 based on the ability of GO to quench fluorophore by fluorescence resonance energy transfer (FRET). Using primers and a fluorophore-labeled ssDNA probe targeting a conserved region between the PRRSV M gene and 3'UTR, asymmetric PCR specifically amplified viral ssDNA that could anneal with probe to generate dsDNA only in the presence of virus. Upon exonuclease III treatment to release the probe fluorophore, which degrades dsDNA with blunt ends or recessed 3´-termini, the ssDNA annealed with other probe to generate enhanced fluorescence. This GO-based FRET assay specifically detected both classical and highly pathogenic PRRSV, with analytical sensitivity approaching 10 copies/μL, similar to that of real-time PCR but greater than that of conventional reverse transcription PCR (RT-PCR). Consistent with real-time RT-PCR detection, the assay developed here exhibited high diagnostic sensitivity for virus detection of sera from experimentally and naturally infected pigs. Thus, this novel GO-based FRET assay combined with asymmetric PCR detection is sensitive and specific and will be valuable for future PRRSV diagnosis.
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Liu J, Li LM, Han JQ, Sun TR, Zhao X, Xu RT, Song QY. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains. Mol Cell Probes 2019; 45:37-42. [PMID: 31004698 DOI: 10.1016/j.mcp.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an important pathogen causing severe watery diarrhea, vomiting, dehydration, and death in sucking piglets. Attenuated vaccines have been used widely in sows in order to protect piglets through passive lactogenic immunity. Rapid and sensitive detection methods for differentiating attenuated vaccine strains from virulent ones are essential and practical in PEDV prevention and control. Based on the deletion mutation in ORF3 gene sequence, a TaqMan probe-based real-time quantitative PCR (TaqMan qPCR) was developed to distinguish PEDV virulent strains from attenuated vaccine ones in this study. The TaqMan qPCR could specifically detect PEDV virulent strain but not attenuated vaccine strain and other viruses. At least 37 DNA copies and PEDV of 0.995 TCID50 could be detected by TaqMan qPCR. The reproducibility was evaluated using various dilution of plasmids carrying PEDV ORF3 gene and virulent PEDV, and the inter-assay coefficient of variation (CV) was less than 0.44%. The TaqMan qPCR was further applied to detect 38 samples including intestines and their contents, fecal swabs, and mesenteric lymph nodes. Meanwhile, indirect immunofluorescence assay (IFA) was employed to detect PEDV-specific antigen. PEDV positive rates were 31.58% (12/38) and 26.32% (10/38) by TaqMan PCR and IFA, respectively, which suggested that the former was more sensitive than the latter. The TaqMan qPCR based on PEDV ORF3 gene could be a valuable tool in diagnose of porcine epidemic diarrhea and in molecular epidemiological study of the virulent PEDV.
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Affiliation(s)
- Jing Liu
- College of Animal Medicine, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Li-Min Li
- College of Animal Medicine, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Jiu-Qaun Han
- College of Foreign Languages, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Tai-Ran Sun
- Baoding Animal Disease Control and Prevention Center, Baoding, Hebei, 071000, China.
| | - Xue Zhao
- College of Animal Medicine, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Rui-Tao Xu
- College of Animal Medicine, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Qin-Ye Song
- College of Animal Medicine, Hebei Agricultural University, Baoding, Hebei, 071000, China.
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Aloisio M, Morelli M, Elicio V, Saldarelli P, Ura B, Bortot B, Severini G, Minafra A. Detection of four regulated grapevine viruses in a qualitative, single tube real-time PCR with melting curve analysis. J Virol Methods 2018; 257:42-47. [DOI: 10.1016/j.jviromet.2018.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 10/17/2022]
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14
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A novel HRM assay for differentiating classical strains and highly pathogenic strains of type 2 porcine reproductive and respiratory syndrome virus. Mol Cell Probes 2018; 39:25-32. [PMID: 29609038 DOI: 10.1016/j.mcp.2018.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/13/2018] [Accepted: 03/29/2018] [Indexed: 12/31/2022]
Abstract
Differentiation of classical strains and highly pathogenic strains of porcine reproductive and respiratory syndrome virus is crucial for effective vaccination programs and epidemiological studies. We used nested PCR and high resolution melting curve analysis with unlabeled probe to distinguish between the classical and the highly pathogenic strains of this virus. Two sets of primers and a 20 bp unlabeled probe were designed from the NSP3 gene. The unlabeled probe included two mutations specific for the classical and highly pathogenic strains of the virus. An additional primer set from the NSP2 gene of the highly pathogenic vaccine strain JXA1-R was used to detect its exclusive single nucleotide polymorphism. We tested 107 clinical samples, 21 clinical samples were positive for PRRSV (consistent with conventional PCR assay), among them four were positive for the classical strain with the remainder 17 for the highly pathogenic strain. Around 10 °C difference between probe melting temperatures showed the high discriminatory power of this method. Among highly pathogenic positive samples, three samples were determined as positive for JXA1-R vaccine-related strain with a 95% genotype confidence percentage. All these genotyping results using the high resolution melting curve assay were confirmed with DNA sequencing. This unlabeled probe method provides an alternative means to differentiate the classical strains from the highly pathogenic porcine reproductive and respiratory syndrome virus strains rapidly and accurately.
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Yang Q, Xi J, Chen X, Hu S, Chen N, Qiao S, Wan S, Bao D. The development of a sensitive droplet digital PCR for quantitative detection of porcine reproductive and respiratory syndrome virus. Int J Biol Macromol 2017; 104:1223-1228. [DOI: 10.1016/j.ijbiomac.2017.06.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 11/29/2022]
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16
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Yang K, Tian Y, Zhou D, Duan Z, Guo R, Liu Z, Yuan F, Liu W. A Multiplex RT-PCR Assay to Detect and Discriminate Porcine Reproductive and Respiratory Syndrome Viruses in Clinical Specimens. Viruses 2017; 9:v9080205. [PMID: 28763016 PMCID: PMC5580462 DOI: 10.3390/v9080205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 11/25/2022] Open
Abstract
Outbreaks of highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) have led to large economic losses in China. The attenuated vaccine (HP-PRRSV JXA1-R) was used to control HP-PRRSV. However, in recent years, co-infection with classical PRRSV (C-PRRSV), HP-PRRSV, and/or HP-PRRSV JXA1-R has been increasing in China, resulting in a significant impact on PRRSV diagnostics and management. To facilitate rapid discrimination of HP-PRRSV JXA1-R from HP-PRRSV and C-PRRSV, a multiplex RT-PCR assay for the visual detection of HP-PRRSV JXA1-R, HP-PRRSV, and C-PRRSV was established and evaluated with reference PRRSV strains and clinical samples. Primer specificities were evaluated with RNA/DNA extracted from 10 viral strains, and our results revealed that the primers had a high specificity for PRRSV. The assay sensitivity was 24 copies/μL for PRRSVs. A total of 516 serum samples were identified, of which 12.21% (63/516) were HP-PRRSV-positive, 2.33% (12/516) were HP-PRRSV JXA1-R-positive, and 1.16% (6/516) were C-PRRSV-positive, respectively, which was completely consistent with the sequencing method. The high specificity, sensitivity, and reliability of the multiplex RT-PCR assay described in this study indicate that it is useful for the rapid and differential diagnosis of HP-PRRSV JXA1-R, HP-PRRSV, and C-PRRSV.
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Affiliation(s)
- Keli Yang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Yongxiang Tian
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Danna Zhou
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Zhengying Duan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Rui Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Zewen Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Wei Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
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Wang JC, Yuan WZ, Han QA, Wang JF, Liu LB. Reverse transcription recombinase polymerase amplification assay for the rapid detection of type 2 porcine reproductive and respiratory syndrome virus. J Virol Methods 2017; 243:55-60. [PMID: 28122203 DOI: 10.1016/j.jviromet.2017.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 10/20/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens in pigs, and has tremendous negative economic impact on the swine industry worldwide. PRRSV is classified into the two distinct genotypes: type 1 and type 2, and most of the described PRRSV isolates in China are type 2. Rapid and sensitive detection of PRRSV is of great importance for the disease control and regional eradication programs. Recombinase polymerase amplification (RPA) has emerged as a novel isothermal amplification technology for the molecular diagnosis of infectious diseases. In this study, a fluorescence reverse transcription RPA (RT-RPA) assay was developed to detect the type 2 PRRSV using primers and exo probe specific for the viral nucleocapsid gene. The reaction was performed at 40°C within 20min. The RT-RPA assay could detect both the classical (C-PRRSV) and highly pathogenic PRRSV (HP-PRRSV), but there was no cross-reaction to other pathogens. Using the in vitro transcribed PRRSV RNA as template, the analytical sensitivity of RT-RPA was 690 copies. The assay performance was evaluated by testing 60 field samples and compared to real-time RT-PCR. The detection rate of RT-RPA was 86.6% (52/60), while the detection rate of real-time RT-PCR was 83.3% (50/60). This simple, rapid and reliable method could be potentially applied for rapid detection of PRRSV in point-of-care and rural areas.
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Affiliation(s)
- Jian-Chang Wang
- Inspection and Quarantine Technical Center of Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd., Shijiazhuang, Hebei 050051, China
| | - Wan-Zhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, No. 38 Lingyusi Street, Baoding, Hebei 071001, China.
| | - Qing-An Han
- Hebei Animal Disease Control Center, 219 Alishan Street, Shijiazhuang, Hebei 050050, China
| | - Jin-Feng Wang
- Inspection and Quarantine Technical Center of Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd., Shijiazhuang, Hebei 050051, China
| | - Li-Bing Liu
- Inspection and Quarantine Technical Center of Hebei Entry-Exit Inspection and Quarantine Bureau, 318 Heping West Rd., Shijiazhuang, Hebei 050051, China
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18
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Rapid detection of highly pathogenic porcine reproductive and respiratory syndrome virus by a fluorescent probe-based isothermal recombinase polymerase amplification assay. Virus Genes 2016; 52:883-886. [DOI: 10.1007/s11262-016-1378-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/06/2016] [Indexed: 01/22/2023]
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19
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Yang Q, Rui Y. Two Multiplex Real-Time PCR Assays to Detect and Differentiate Acinetobacter baumannii and Non- baumannii Acinetobacter spp. Carrying blaNDM, blaOXA-23-Like, blaOXA-40-Like, blaOXA-51-Like, and blaOXA-58-Like Genes. PLoS One 2016; 11:e0158958. [PMID: 27391234 PMCID: PMC4938629 DOI: 10.1371/journal.pone.0158958] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 06/26/2016] [Indexed: 01/01/2023] Open
Abstract
Nosocomial infections caused by Acinetobacter spp. resistant to carbapenems are increasingly reported worldwide. Carbapenem-resistant Acinetobacter (CRA) is becoming a serious concern with increasing patient morbidity, mortality, and lengths of hospital stay. Therefore, the rapid detection of CRA is essential for epidemiological surveillance. Polymerase chain reaction (PCR) has been extensively used for the rapid identification of most pathogens. In this study, we have developed two multiplex real-time PCR assays to detect and differentiate A. baumannii and non-A. baumannii Acinetobacter spp, and common carbapenemase genes, including blaNDM, blaOXA-23-like, blaOXA-40-like, blaOXA-51-like, and blaOXA-58-like. We demonstrate the potential utility of these assays for the direct detection of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA in clinical specimens. Primers were specifically designed, and two multiplex real-time PCR assays were developed: multiplex real-time PCR assay1 for the detection of Acinetobacter baumannii 16S–23S rRNA internal transcribed spacer sequence, the Acinetobacter recA gene, and class-B-metalloenzyme-encoding gene blaNDM; and multiplex real-time PCR assay2 to detect class-D-oxacillinase-encoding genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like,and blaOXA-58-like). The assays were performed on an ABI Prism 7500 FAST Real-Time PCR System. CRA isolates were used to compare the assays with conventional PCR and sequencing. Known amounts of CRA cells were added to sputum and fecal specimens and used to test the multiplex real-time PCR assays. The results for target and nontarget amplification showed that the multiplex real-time PCR assays were specific, the limit of detection for each target was 10 copies per 20 μL reaction volume, the assays were linear over six log dilutions of the target genes (r2 > 0.99), and the Ct values of the coefficients of variation for intra- and interassay reproducibility were less than 5%. The multiplex real-time PCR assays showed 100% concordance with conventional PCR when tested against 400 CRA isolates and their sensitivity for the target DNA in sputum and fecal specimens was 102 CFU/mL. Therefore, these novel multiplex real-time PCR assays allow the sensitive and specific characterization and differentiation of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA, making them potential tools for the direct detection of CRA in clinical specimens and the surveillance of nosocomial infections.
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Affiliation(s)
- Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- * E-mail:
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20
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Miller LC, Crawford KK, Lager KM, Kellner SG, Brockmeier SL. Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs. J Vet Diagn Invest 2015; 28:20-9. [PMID: 26699519 DOI: 10.1177/1040638715621949] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In April 2013, a Porcine epidemic diarrhea virus (PEDV) epidemic began in the United States. As part of the response, real-time reverse transcription polymerase chain reaction (RT-PCR) assays to detect PEDV were developed by several veterinary diagnostic laboratories. Our study evaluated RT-PCR PEDV assays that detect the N gene (gN) and S gene (gS) for their ability to detect PEDV infection and the transmission potential of pigs experimentally exposed to PEDV. Detection limits and quantification cycle (Cq) values of real-time RT-PCR were assayed for PEDV samples and positive controls for both gN and gS. The limit of detection for the gN assay was 10(-6) (mean Cq: 39.82 ± 0.30) and 10(-5) (mean Cq: 39.39 ± 0.72) for the gS assay with PEDV strain USA/Colorado/2013. Following recommended guidelines, rectal swabs (n = 1,064) were tested; 354 samples were positive by gN assay and 349 samples were positive by gS assay (Cq ≤ 34.99), 710 samples were negative by gN assay and 715 were negative by gS assay (Cq > 34.99) of which 355 and 344 were "undetermined" (i.e., undetected within a threshold of 40 RT-PCR cycles, by gN and gS assays, respectively). The coefficient of variation (intra-assay variation) ranged from 0.00% to 2.65% and interassay variation had an average of 2.75%. PEDV could be detected in rectal swabs from all pigs for ~2 weeks postinfection at which time the prevalence began to decrease until all pigs were RT-PCR negative by 5 weeks postinfection. Our study demonstrated that RT-PCR assays functioned well to detect PEDV and that the gN assay was slightly better.
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Affiliation(s)
- Laura C Miller
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Kimberly K Crawford
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Kelly M Lager
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Steven G Kellner
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
| | - Susan L Brockmeier
- U.S. Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA
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21
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Yang HC, Haudenshield JS, Hartman GL. Multiplex Real-time PCR Detection and Differentiation of Colletotrichum Species Infecting Soybean. PLANT DISEASE 2015; 99:1559-1568. [PMID: 30695948 DOI: 10.1094/pdis-11-14-1189-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colletotrichum species are fungal plant pathogens of worldwide significance. Colletotrichum species were isolated from soybean with anthracnose symptoms in five states in the United States from 2009 to 2013. Among 240 isolates collected, four Colletotrichum species were initially identified by morphological and sequence analysis, including C. chlorophyti, C. incanum, C. truncatum, and Colletotrichum sp. (henceforth Glomerella glycines, the name of its sexual state). To increase diagnostic efficiency and accuracy, real-time multiplex PCR assays based on a double-stranded DNA-binding dye coupled with dissociation curve analysis were designed, using a region of the cytochrome c oxidase subunit 1 (cox1) gene to discern these four Colletotrichum species. Two sets of duplex, real-time PCR assays were established and species differentiation was based upon amplicon melting point temperatures (Tm) in the dissociation curve analysis. The Set 1 duplex assay distinguished C. chlorophyti and G. glycines, and the Set 2 duplex assay distinguished C. incanum and C. truncatum. Successful detection was achieved with as little as 1 pg DNA. The assays were especially useful for differentiating C. chlorophyti, C. incanum, and C. truncatum, which have similar morphological features. Colletotrichum gloeosporioides, another pathogen associated with soybean anthracnose, was not resolved from G. glycines by the melting curve analysis. The two duplex real-time PCR assays were used to screen more than 200 purified Colletotrichum isolates, showing that they were rapid and effective methods to detect and differentiate Colletotrichum species infecting soybean.
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Affiliation(s)
- Hui-Ching Yang
- Department of Natural Resources and Environmental Sciences
| | | | - Glen L Hartman
- USDA Agricultural Research Service, Department of Crop Sciences, and Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
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22
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Development of a genome copy specific RT-qPCR assay for divergent strains of type 2 porcine reproductive and respiratory syndrome virus. J Virol Methods 2015; 218:1-6. [PMID: 25766790 DOI: 10.1016/j.jviromet.2015.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/10/2014] [Accepted: 02/08/2015] [Indexed: 11/21/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) became a significant pathogen of swine upon its emergence in the late 1980s and since then has exemplified a rapidly evolving, constantly re-emerging pathogen. In addition to the challenges faced in development of vaccines and diagnostics, research on the basic molecular pathogenesis of PRRSV is also restrained by the ability to accurately and comparatively quantitate levels of replication in different tissues and between strains. This is further complicated by the presence of non-genomic RNA within infected tissues which are generally detected with equivalent efficiency by RT-qPCR based techniques, thereby introducing inherent error in these measurements that may differ significantly by tissue and strain. To address this, an RT-qPCR based technique was developed which targets the viral RNA-dependent RNA polymerase gene (nsp9) which is unique to genomic RNA, being absent from all subgenomic and heteroclite RNAs. This assay targets a region of considerable sequence conservation, and based on sequence only, should be quantitative for approximately 40% of all Type 2 PRRSV strains in GenBank for which nsp9 sequence is available. The assay was demonstrated to be linear over nine orders of magnitude (10(10)-10(2) copies) and can be readily adapted for multiplex detection of additional divergent PRRSV strains. This assay will add significantly to the ability to assess and compare PRRSV replication in a variety of tissues and between divergent strains, including highly pathogenic strains of considerable concern to the global pork industry.
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Rao P, Wu H, Jiang Y, Opriessnig T, Zheng X, Mo Y, Yang Z. Development of an EvaGreen-based multiplex real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of six viral pathogens of porcine reproductive and respiratory disorder. J Virol Methods 2014; 208:56-62. [DOI: 10.1016/j.jviromet.2014.06.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/17/2014] [Accepted: 06/20/2014] [Indexed: 11/27/2022]
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24
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Kang K, Yang K, Zhong J, Tian Y, Zhang L, Zhai J, Zhang L, Song C, Gou CY, Luo J, Gou D. A direct real-time polymerase chain reaction assay for rapid high-throughput detection of highly pathogenic North American porcine reproductive and respiratory syndrome virus in China without RNA purification. J Anim Sci Biotechnol 2014; 5:45. [PMID: 25324970 PMCID: PMC4198619 DOI: 10.1186/2049-1891-5-45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/25/2014] [Indexed: 01/16/2023] Open
Abstract
Background Porcine reproductive and respiratory syndrome virus (PRRSV), and particularly its highly pathogenic genotype (HP-PRRSV), have caused massive economic losses to the global swine industry. Results To rapidly identify HP-PRRSV, we developed a direct real-time reverse transcription polymerase chain reaction method (dRT-PCR) that could detect the virus from serum specimen without the need of RNA purification. Our dRT-PCR assay can be completed in 1.5 h from when a sample is received to obtaining a result. Additionally, the sensitivity of dRT-PCR matched that of conventional reverse transcription PCR (cRT-PCR) that used purified RNA. The lowest detection limit of HP-PRRSV was 6.3 TCID50 using dRT-PCR. We applied dRT-PCR assay to 144 field samples and the results showed strong consistency with those obtained by cRT-PCR. Moreover, the dRT-PCR method was able to tolerate 5-20% (v/v) serum. Conclusions Our dRT-PCR assay allows for easier, faster, more cost-effective and higher throughput detection of HP-PRRSV compared with cRT-PCR methods. To the best of our knowledge, this is the first report to describe a real-time RT-PCR assay capable of detecting PRRSV in crude serum samples without the requirement for purifying RNA. We believe our approach has a great potential for application to other RNA viruses. Electronic supplementary material The online version of this article (doi:10.1186/2049-1891-5-45) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kang Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 China ; College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060 China
| | - Keli Yang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
| | - Jiasheng Zhong
- College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060 China
| | - Yongxiang Tian
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
| | - Limin Zhang
- College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060 China
| | - Jianxin Zhai
- Shenzhen Ao Dong Inspection and Testing Technology Co,. Ltd, Shenzhen, 518000 China
| | - Li Zhang
- Shenzhen Ao Dong Inspection and Testing Technology Co,. Ltd, Shenzhen, 518000 China
| | - Changxu Song
- Veterinary Medicine Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | | | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Deming Gou
- College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060 China
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25
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Zhao PD, Bai J, Jiang P, Tang TS, Li Y, Tan C, Shi X. Development of a multiplex TaqMan probe-based real-time PCR for discrimination of variant and classical porcine epidemic diarrhea virus. J Virol Methods 2014; 206:150-5. [PMID: 24928691 DOI: 10.1016/j.jviromet.2014.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/01/2014] [Accepted: 06/03/2014] [Indexed: 02/03/2023]
Abstract
Since October 2010, porcine diarrhea outbreaks have occurred widely, resulting in major losses in suckling piglets in China. A variant porcine epidemic diarrhea virus (PEDV), characterized by base deletion and insertion in the S gene, compared to classical PEDV CV777, was shown to be responsible for this outbreak. In this study, a multiplex TaqMan probe-based real-time PCR was developed for detecting PEDV and differentiating the variant from classical PEDV, by using two sets of primers and probes based on the S gene of PEDV. The limits of detection of both variant and classical PEDV were 5×10(2) DNA copies. Specificity was determined using eight other viral pathogens of swine. Reproducibility was evaluated using standard dilutions, with coefficients of variation <1.4%. Standard dilutions included in each test allowed quantification of the amount of PEDV. Among 42 intestinal samples from pigs with severe watery diarrhea, 36 variant PEDV and three classical PEDV samples were detected, with viral loads of 10(2)-10(8) copies/μl and 10(3)-10(5) copies/μl, respectively, which suggested that the variant PEDV was prevalent in China. The multiplex TaqMan probe-based real-time PCR should be a useful tool for quantifying viral load, detecting PEDV, and differentiating variant from classical PEDV.
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Affiliation(s)
- Pan-deng Zhao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tai-shan Tang
- Jiangsu Entry-Exit Inspection and Quarantine Bureau, Nanjing 200001, China
| | - Yufeng Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Tan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Shi
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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26
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Drigo M, Franzo G, Gigli A, Martini M, Mondin A, Gracieux P, Ceglie L. The impact of porcine reproductive and respiratory syndrome virus genetic heterogeneity on molecular assay performances. J Virol Methods 2014; 202:79-86. [DOI: 10.1016/j.jviromet.2014.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 02/07/2014] [Accepted: 03/04/2014] [Indexed: 01/07/2023]
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27
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Drigo M, Franzo G, Belfanti I, Martini M, Mondin A, Ceglie L. Validation and comparison of different end point and real time RT-PCR assays for detection and genotyping of porcine reproductive and respiratory syndrome virus. J Virol Methods 2014; 201:79-85. [DOI: 10.1016/j.jviromet.2014.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 11/30/2022]
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28
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Chai Z, Zhang P, Fu F, Zhang X, Liu Y, Hu L, Li X. Oncolytic therapy of a recombinant Newcastle disease virus D90 strain for lung cancer. Virol J 2014; 11:84. [PMID: 24885546 PMCID: PMC4032357 DOI: 10.1186/1743-422x-11-84] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/30/2014] [Indexed: 01/31/2023] Open
Abstract
Background Lung cancer is one of the leading causes of deaths from cancer worldwide. Tumor virotherapy using naturally oncolytic Newcastle disease virus (NDV) has been shown to be safe and effective in preclinical studies and clinical trials. Previously, we have reported the NDV D90 strain that was isolated from natural source has an antiproliferative effect in human lung cancer cell line A549. Methods and results In this study, we constructed a reverse genetics system based on the oncolytic NDV D90 strain and generated a recombinant NDV carrying a gene encoding enhanced green fluorescent protein (rNDV-GFP). The rescued virus rNDV-D90 and rNDV-GFP showed the similar characteristics of replication and apoptotic ability in lung cancer A549 cells, which suggested that the recombinant viruses sustained the property of tumor-selective replication and induced apoptosis of tumor cells. The athymic mice bearing implanted lung cancer were treated with the parental D90 virus, the rescued rNDV-D90 and rNDV-GFP via intratumoral injections, respectively. The results showed that the recombinant viruses as well as the parental D90 virus significantly suppressed the loss of body weight and tumor growth. Conclusions The study provides a new platform to develop effective therapeutic agents for tumor treatment. The availability of the reverse genetics system for NDV D90 strain will make it possible to develop novel recombinant oncolytic viruses based on the NDV D90 strain for improving the efficacy of tumor treatment.
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Affiliation(s)
| | | | | | | | | | | | - Xi Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan St,, Nangang District, Harbin 150001, China.
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29
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Yang K, Li Y, Duan Z, Guo R, Liu Z, Zhou D, Yuan F, Tian Y. A one-step RT-PCR assay to detect and discriminate porcine reproductive and respiratory syndrome viruses in clinical specimens. Gene 2013; 531:199-204. [PMID: 24035936 DOI: 10.1016/j.gene.2013.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/28/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022]
Abstract
Outbreaks of highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) have led to large economic losses and, subsequently, have drawn great attention to its diagnosis and prevention. To facilitate rapid discrimination of HP-PRRSV from classical PRRSV (C-PRRSV), we developed a one-step RT-PCR assay. Primer specificities were evaluated with RNA extracted from 8 viral strains and our results revealed that the primers had a high specificity for PRRSV. The assay sensitivity was 25 copies/μL for both HP-PRRSV and C-PRRSV. A total of 929 serum samples were identified, of which 20.45% were HP-PRRSV-positive and 1.51% were C-PRRSV-positive, which was completely consistent with that of immunochromatochemistry and sequencing method. The proposed assay can detect the virus 2 days prior the onset of symptoms and it can be performed in 2h, thereby providing a rapid method to discriminate HP-PRRSV from C-PRRSV for the identification and prevention of PRRSV infections.
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Affiliation(s)
- Keli Yang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, PR China.
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30
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Pierce LR, Willey JC, Palsule VV, Yeo J, Shepherd BS, Crawford EL, Stepien CA. Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv) with a two-color fluorometric real-time PCR assay. PLoS One 2013; 8:e71851. [PMID: 23977162 PMCID: PMC3748128 DOI: 10.1371/journal.pone.0071851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/03/2013] [Indexed: 01/08/2023] Open
Abstract
Viral Hemorrhagic Septicemia virus (VHSv) is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR) assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02) and a linear dynamic range that spans seven orders of magnitude (R(2) = 0.99), ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6) actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.
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Affiliation(s)
- Lindsey R. Pierce
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, United States of America
| | - James C. Willey
- Department of Medicine, The University of Toledo, Toledo, Ohio, United States of America
| | - Vrushalee V. Palsule
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, United States of America
| | - Jiyoun Yeo
- Department of Medicine, The University of Toledo, Toledo, Ohio, United States of America
| | - Brian S. Shepherd
- ARS/USDA/University of Wisconsin at Milwaukee/School of Freshwater Sciences, Milwaukee, Wisconsin, United States of America
| | - Erin L. Crawford
- Department of Medicine, The University of Toledo, Toledo, Ohio, United States of America
| | - Carol A. Stepien
- Great Lakes Genetics/Genomics Laboratory, Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, Ohio, United States of America
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