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Flores-Contreras EA, Carrasco-González JA, Linhares DCL, Corzo CA, Campos-Villalobos JI, Henao-Díaz A, Melchor-Martínez EM, Iqbal HMN, González-González RB, Parra-Saldívar R, González-González E. Emergent Molecular Techniques Applied to the Detection of Porcine Viruses. Vet Sci 2023; 10:609. [PMID: 37888561 PMCID: PMC10610968 DOI: 10.3390/vetsci10100609] [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: 07/28/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | | | - Daniel C. L. Linhares
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Cesar A. Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA;
| | | | | | - Elda M. Melchor-Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Reyna Berenice González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Everardo González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
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Gu H, Luo B, Wu S, Shi S, Zou X, Dai Q, Zhao M, Zhang L. Novel optical fiber Vernier immunosensor based on cascading Sagnac loops embedded with excessively tilted fiber grating for specific detection of canine distemper virus. JOURNAL OF BIOPHOTONICS 2023; 16:e202200294. [PMID: 36527446 DOI: 10.1002/jbio.202200294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
A novel optical fiber Vernier effect (VE) biosensor based on cascading Sagnac loops embedded with excessively tilted fiber grating (ExTFG) is proposed for the label free and specific detection of canine distemper virus (CDV). The VE was realized by cascading two different Sagnac loops with similar free spectrum range (FSR), one of which was integrated with panda-type polarization maintaining fiber (PMF) as the reference loop, and the other was embedded with ExTFG as the sensing loop. Owning to the amplified function of the VE, the refractive index (RI) sensitivity of the proposed sensing structure reached -1914.89 nm/RIU, which is approximately 12 times higher than that of the single ExTFG based RI sensor. Furthermore, the ExTFG in sensing loop was modified by graphene oxide (GO) and bio-functionalized by the CDV monoclonal antibodies (anti-CDV MAbs) for the specific detection of the CDV. Experimental results show that the proposed optical fiber Vernier sensor could detect the CDV in buffer solution with concentration as low as 1 pg/mL, and the sensitivity was about -1.18 nm/[log(mg/ml)] in the concentration range of 1 pg/mL ~ 50 ng/mL. The excellent specific and clinical properties of the biosensor were verified by immunoassays for fetal bovine serum, Toxoplasma gondii, rabies virus and CDV serum in sequence. Due to the sensitivity amplification function of VE, dense comb spectrum of the Sagnac loop and the stable interference spectra maintained by the polarized light, the proposed biosensor possesses the combined advantages of high sensitivity, high Q-factor and high stability, which may have potential applications in biosensing fields.
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Affiliation(s)
- Hong Gu
- Chongqing Key Laboratory of Optical Fiber Sensor and Photoelectric Detection, Chongqing University of Technology, Chongqing, China
| | - Binbin Luo
- Chongqing Key Laboratory of Optical Fiber Sensor and Photoelectric Detection, Chongqing University of Technology, Chongqing, China
| | - Shengxi Wu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Shenghui Shi
- Chongqing Key Laboratory of Optical Fiber Sensor and Photoelectric Detection, Chongqing University of Technology, Chongqing, China
| | - Xue Zou
- Chongqing Key Laboratory of Optical Fiber Sensor and Photoelectric Detection, Chongqing University of Technology, Chongqing, China
| | - Qin Dai
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Mingfu Zhao
- Chongqing Key Laboratory of Optical Fiber Sensor and Photoelectric Detection, Chongqing University of Technology, Chongqing, China
| | - Lin Zhang
- Aston Institute of Photonic Technologies, Aston University, Birmingham, UK
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3
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Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
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Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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Chen H, Sun C, Wang Y, Gao X, You J, Yu W, Sun N, Yang Y, Li X. Rapid Detection of SARS-CoV-2 Using Duplex Reverse Transcription-Multienzyme Isothermal Rapid Amplification in a Point-of-Care Testing. Front Cell Infect Microbiol 2021; 11:678703. [PMID: 34746020 PMCID: PMC8569318 DOI: 10.3389/fcimb.2021.678703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In December 2019, a severe acute respiratory syndrome caused by SARS-CoV-2 spread rapidly worldwide. Portable nucleic acid tests of SARS-CoV-2 are critically important for diagnostics. In this study, we used an isothermal amplification method-Multienzyme Isothermal Rapid Amplification (MIRA)-for rapid detection of SARS-CoV-2. We designed the primers and probes in ORF1ab and N gene of SARS-CoV-2. The amplicons could be monitored by lateral flow dipsticks (LFDs). The reaction temperature, time, concentrations of primers and probes, and working volume were optimized. Four commercial swab collection buffers were used to test the amplification efficacy of our assay without RNA extraction. Our assay was able to amplify duplex targets of SARS-CoV-2 in one single reaction using one-step RT-MIRA. The assay worked well in a low volume of 10 μl at 38°C for 20 min. Using three collection buffers without guanidinium, our assay was able to amplify efficaciously without RNA extraction. The 95% limit of detection (LoD) of the RT-MIRA assay was 49.5 (95% CI, 46.8-52.7) copies/ml for ORF1ab gene and 48.8 (95% CI, 46.5-52.6) copies/ml for N gene. There is no cross-reaction with other human respiratory pathogens, such as SARS-CoV, MERS-CoV, influenza A virus, influenza B virus, human adenovirus, respiratory syncytial virus, human parainfluenza virus, and coronavirus 229E in our assay. The precision evaluation revealed that the C50-20% to C50+20% range bounds the C5-C95 interval. This assay also showed high anti-interference ability. The extraction-free RT-MIRA and qPCR detection results of 243 nucleic acid specimens from suspected patients or national references showed a 100.0% (95% confidence interval, 94.2%-100.0%) positive predictive value and a 100.0% (95% confidence interval, 92.7%-100.0%) negative predictive value. Compared with qPCR, the kappa value of the two assays was 1.00 (P < 0.0001). In conclusion, we provide a portable and visualized method for detection of SARS-CoV-2 without RNA extraction, allowing its application in SARS-CoV-2 on-site detection.
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Affiliation(s)
- Hui Chen
- Department of Medicine, JiangSu University, Zhenjiang, China.,Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Chang Sun
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Wang
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojiao Gao
- Department of Clinical Laboratory, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Jinwei You
- Department of Laboratory Animal, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Wanwan Yu
- Department of Emergency, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Ning Sun
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Yang
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojun Li
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, China
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Wang W, Zhang Y, Huang Y, Chen G, Shi M, Qiao Y, Huang T, Wei T, Mo M, He X, Wei P. Rapid and visual detection of the emerging novel duck reovirus by using a specific and sensitive reverse transcription recombinase polymerase amplification method. J Virol Methods 2021; 291:114098. [PMID: 33621643 DOI: 10.1016/j.jviromet.2021.114098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Duck spleen necrosis disease (DSND) caused by Novel Duck Reovirus (NDRV), is an emerging infectious disease that causes severely threaten to duck industry. Currently, the popular conventional RT-PCR technique for detecting NDRV is time consuming. So, it is essential to develop a rapid and accurate molecular diagnosis techniques of the pathogen for the purpose to effective control of the disease. In our study, a simple, rapid and reliable detection method was developed by an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA). The RT-RPA primers were designed targeting the S3 gene of NDRV, and its specificity was verified by testing a series of other waterfowl pathogens. A total of 20 field and experimental samples from infected ducklings were tested by the RT-RPA and compared with the results of the conventional RT-PCR and the quantitative RT-PCR simultaneously. The RT-RPA method could detect as little as 4.14 × 102 copies/μl of the target gene in the sensitivity analysis, which was 10×higher sensitive than the conventional RT-PCR. The major advantage of the RT-RPA method is that it could be performed as an isothermal reaction at 37 ℃ and completed within 20 min. In addition, no cross-reactivity was detected with other waterfowl-origin viruses. Also, the amplified products could be visualized faster, without the gel electrophoresis, by adding the SYBR Green I and observing them under an ultraviolet light. The newly developed RT-RPA method offers a simple, rapid and accurate for rapid detection of NDRV, which especially useful in on-site facilities and resource-limited areas.
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Affiliation(s)
- Weiwei Wang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yan Zhang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yu Huang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Guo Chen
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Mengya Shi
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yuanzheng Qiao
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Teng Huang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Tianchao Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Meilan Mo
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Xiumiao He
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory Cultivation Base for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, Guangxi, 530006, China.
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China.
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Yang K, Jiao Z, Zhou D, Guo R, Duan Z, Tian Y. Development of a multiplex PCR to detect and discriminate porcine circoviruses in clinical specimens. BMC Infect Dis 2019; 19:778. [PMID: 31488066 PMCID: PMC6727504 DOI: 10.1186/s12879-019-4398-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/23/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A diagnostic method to simultaneously detect and discriminate porcine circovirus type 1 (PCV1), porcine circovirus type 2 (PCV2) and porcine circovirus type 3 (PCV3) in clinical specimens is imperative for the differential diagnosis and monitoring and control of PCVs in the field. METHODS Three primer pairs were designed and used to develop a multiplex PCR assay. And 286 samples from 8 farms in Hubei province were tested by the developed multiplex PCR assay to demonstrate the accuracy. RESULTS Each of target genes of PCV1, PCV2 and PCV3 was amplified using the designed primers, while no other porcine viruses genes were detected. The limit of detection of the assay was 10 copies/μL of PCV1, PCV2 OR PCV3. The results of the tissue samples detection showed that PCV1, PCV2 and PCV3 are co-circulating in central China. The PCV1, PCV2 and PCV3 singular infection rate was 52.4% (150/286), 61.2% (175/286) and 45.1% (129/286), respectively, while the PCV1 and PCV2 co-infection rate was 11.2% (32/286), the PCV1 and PCV3 co-infection rate was 5.9% (17/286), the PCV2 and PCV3 co-infection rate was 23.4% (67/286), and the PCV1, PCV2 and PCV3 co-infection rate was 1.7% (5/286), respectively, which were 100% consistent with the sequencing method and real-time PCR methods. CONCLUSIONS The multiplex PCR assay could be used as a differential diagnostic tool for monitoring and control of PCVs in the field. The results also indicate that the PCVs infection and their co-infection are severe in Hubei province, Central China.
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Affiliation(s)
- Keli Yang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China. .,Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, 430064, People's Republic of China.
| | - Zuwu Jiao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Danna Zhou
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Rui Guo
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Zhengying Duan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Yongxiang Tian
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China. .,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Wuhan, 430064, People's Republic of China.
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Sun N, Wang Y, Yao X, Chen F, Gao D, Wang W, Li X. Visual signal generation for the detection of influenza viruses by duplex recombinase polymerase amplification with lateral flow dipsticks. Anal Bioanal Chem 2019; 411:3591-3602. [PMID: 31079175 DOI: 10.1007/s00216-019-01840-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
We present a detailed study on visual detection of influenza viruses by duplex recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFDs). The LFD consisted of two test lines and a control line, on which anti-fluorescein isothiocyanate antibodies, anti-digoxigenin antibodies, and biotinylated bovine serum albumin were immobilized, respectively. The performance of the LFD was evaluated with dual-labeled DNA amplicons. The results indicate that the detection of DNA amplicons by LFDs is specific and sensitive, with detection limits of 5.80 fmol for fluorescein isothiocyanate-labeled amplicons and 8.39 fmol for digoxigenin-labeled amplicons. We next developed a duplex RPA-LFD assay for simultaneous detection of influenza A virus and influenza B virus, and then optimized the parameters, including the reaction temperature, reaction time, and concentrations of primers and probes. Assessment of the specificity and sensitivity indicated that this assay is sensitive and specific for simultaneous detection of influenza viruses, with detection limits of 50 copies per reaction for influenza B virus and 500 copies per reaction for influenza A virus, without cross-reactivity with other pathogens. Compared with real-time PCR as a reference method to detect influenza viruses in clinical samples, the clinical sensitivity of the duplex RPA-LFD assay was 78.57% for influenza A virus and 87.50% for influenza B virus, with 100% specificity. In conclusion, the duplex RPA-LFD assay is a rapid, cost-effective, and sensitive method for the identification of influenza viruses.
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Affiliation(s)
- Ning Sun
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Ying Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xinyue Yao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Fangfang Chen
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Deyu Gao
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Weiping Wang
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China
| | - Xiaojun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, School of Medicine, Nanjing University, Zhongshan East Road No. 305, Nanjing, 210002, Jiangsu, China. .,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, 210002, Jiangsu, China.
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Liu L, Wang J, Zhang R, Lin M, Shi R, Han Q, Wang J, Yuan W. Visual and equipment-free reverse transcription recombinase polymerase amplification method for rapid detection of foot-and-mouth disease virus. BMC Vet Res 2018; 14:263. [PMID: 30170587 PMCID: PMC6119248 DOI: 10.1186/s12917-018-1594-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/24/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Foot-and-mouth disease (FMD), which is caused by foot-and-mouth disease virus (FMDV), is a highly contagious tansboundary disease of cloven-hoofed animals and causes devastating economic damages. Accurate, rapid and simple detection of FMDV is critical to containing an FMD outbreak. Recombinase polymerase amplification (RPA) has been explored for detection of diverse pathogens because of its accuracy, rapidness and simplicity. A visible and equipment-free reverse-transcription recombinase polymerase amplification assay combined with lateral flow strip (LFS RT-RPA) was developed to detect the FMDV using primers and LF probe specific for the 3D gene. RESULTS The FMDV LFS RT-RPA assay was performed successfully in a closed fist using body heat for 15 min, and the products were visible on the LFS inspected by the naked eyes within 2 min. The assay could detect FMDV serotypes O, A and Asia1, and there were no cross-reactions with vesicular stomatitis virus (VSV), encephalomyocarditis virus (EMCV), classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV2) and pseudorabies virus (PRV). The analytical sensitivity was 1.0 × 102 copies in vitro transcribed FMDV RNA per reaction, which was the same as a real-time RT-PCR. For the 55 samples, FMDV RNA positive rate was 45.5% (25/55) by LFS RT-RPA and 52.7% (29/55) by real-time RT-PCR. For the LFS RT-RPA assay, the positive and negative predicative values were 100% and 80%, respectively. CONCLUSIONS The performance of the LFS RT-RPA assay was comparable to real-time RT-PCR, while the LFS RT-RPA assay was much faster and easier to be performed. The developed FMDV LFS RT-RPA assay provides an attractive and promising tool for rapid and reliable detection of FMDV in under-equipped laboratory and at point-of-need facility, which is of great significance in FMD control in low resource settings.
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Affiliation(s)
- Libing Liu
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China
| | - Jinfeng Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China
| | - Ruoxi Zhang
- Hebei Animal Disease Control Center, Shijiazhuang, 050050, People's Republic of China
| | - Mi Lin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Ruihan Shi
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China.,Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang, 050051, People's Republic of China
| | - Qingan Han
- Hebei Animal Disease Control Center, Shijiazhuang, 050050, People's Republic of China
| | - Jianchang Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China. .,Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang, 050051, People's Republic of China.
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, No.38 Lingyusi Street, Baoding, Hebei, 071001, People's Republic of China.
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Evaluation of an incubation instrument-free reverse transcription recombinase polymerase amplification assay for rapid and point-of-need detection of canine distemper virus. J Virol Methods 2018; 260:56-61. [PMID: 30009850 PMCID: PMC7113680 DOI: 10.1016/j.jviromet.2018.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/20/2023]
Abstract
Visual, rapid molecular assay for detection of CDV was developed. Assay is based on RT-RPA and use of a lateral flow strip to visualize product. Assay was performed in closed fists using body heat for 15 min. Assay analytical sensitivity and specificity was similar to a real-time RT-PCR. Assay was demonstrated to be simple, convenient, rapid and reliable for detection of CDV.
Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Accurate, rapid and simple detection of CDV is critical to improve disease management and prevent outbreaks. In this study, a visible and incubation instrument-free reverse-transcription recombinase polymerase amplification assay combined with lateral flow strip (LFS RT-RPA) was developed to detect CDV using primers and lateral flow (LF) probe specific for the nucleocapsid (N) protein gene. The CDV LFS RT-RPA assay was performed in a closed fist using body heat for 15 min, and the products were visible to the naked eyes on the LFS within 5 min. The assay could detect CDV, and there was no cross-reaction with the other viruses tested. Using the in vitro transcribed CDV RNA as template, the analytical sensitivity was 9.4 × 101 copies per reaction, which was the same result as that of a real-time RT-PCR. The assay performance was further evaluated by testing 32 nasal/oropharyngeal swab samples, and CDV RNA positive rate was 62.0% (20/32) by LFS RT-RPA, which was the same result as that of the real-time RT-PCR assay. The performance of the LFS RT-RPA was comparable to real-time RT-PCR, while the LFS RT-RPA assay was much faster and easier to perform. The novel CDV LFS RT-RPA assay provides an attractive and promising tool for rapid and reliable detection of CDV in the underequipped laboratory and point-of-need facility, which is of great significance in CD control in low resource settings.
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Liu L, Wang J, Geng Y, Wang J, Li R, Shi R, Yuan W. Equipment-free recombinase polymerase amplification assay using body heat for visual and rapid point-of-need detection of canine parvovirus 2. Mol Cell Probes 2018; 39:41-46. [PMID: 29705183 PMCID: PMC7127419 DOI: 10.1016/j.mcp.2018.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/17/2018] [Accepted: 04/25/2018] [Indexed: 12/20/2022]
Abstract
A visible and equipment-free recombinase polymerase amplification assay combined with a lateral flow strip (LFS RPA) was developed to detect canine parvovirus type 2 (CPV-2), which is the etiological agent of canine parvovirus disease. The CPV-2 LFS RPA assay was developed based on the VP2 gene and is performed in a closed fist using body heat for 15 min; the products are visible to the naked eye on the LFS within 5 min. The assay could detect CPV-2a, CPV-2b and CPV-2c, and there was no cross-reaction with the other viruses tested. Using the standard CPV-2 DNA as a template, the analytical sensitivity was 1.0 × 102 copies per reaction, which was the same result as that of a real-time PCR. The assay performance was further evaluated by testing 60 canine fecal samples, and CPV-2 DNA was detected in 46 samples (76.7%, 46/60) by LFS RPA, which was the same result as that of the real-time PCR assay and higher than that of the SNAP method (48.3%, 29/60). The novel CPV-2 LFS RPA assay is an attractive and promising tool for rapid and convenient diagnosis of CPV disease, especially cage side and in underequipped laboratories. Visual and rapid molecular assay for detection of CPV-2 was developed. Assay was based on recombinase polymerase amplification and use of lateral flow strip to visualize product. Assay was incubated successfully in a closed fist using body heat. Assay showed high sensitivity and specificity for detection of CPV-2.
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Affiliation(s)
- Libing Liu
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China; Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China
| | - Jianchang Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China; Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China
| | - Yunyun Geng
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Jinfeng Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China; Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China
| | - Ruiwen Li
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Ruihan Shi
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China; Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China.
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Zhang Y, Wang J, Zhang Z, Mei L, Wang J, Wu S, Lin X. Development of recombinase polymerase amplification assays for the rapid detection of peste des petits ruminants virus. J Virol Methods 2018; 254:35-39. [DOI: 10.1016/j.jviromet.2018.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 01/17/2023]
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Fuller SL, Savory EA, Weisberg AJ, Buser JZ, Gordon MI, Putnam ML, Chang JH. Isothermal Amplification and Lateral-Flow Assay for Detecting Crown-Gall-Causing Agrobacterium spp. PHYTOPATHOLOGY 2017; 107:1062-1068. [PMID: 28569126 DOI: 10.1094/phyto-04-17-0144-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Agrobacterium is a genus of soilborne gram-negative bacteria. Members carrying oncogenic plasmids can cause crown gall disease, which has significant economic costs, especially for the orchard and nursery industries. Early and rapid detection of pathogenic Agrobacterium spp. is key to the management of crown gall disease. To this end, we designed oligonucleotide primers and probes to target virD2 for use in a molecular diagnostic tool that relies on isothermal amplification and lateral-flow-based detection. The oligonucleotide tools were tested in the assay and evaluated for detection limit and specificity in detecting alleles of virD2. One set of primers that successfully amplified virD2 when used with an isothermal recombinase was selected. Both tested probes had detection limits in picogram amounts of DNA. Probe 1 could detect all tested pathogenic isolates that represented most of the diversity of virD2. Finally, the coupling of lateral-flow detection to the use of these oligonucleotide primers in isothermal amplification helped to reduce the onerousness of the process, and alleviated reliance on specialized tools necessary for molecular diagnostics. The assay is an advancement for the rapid molecular detection of pathogenic Agrobacterium spp.
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Affiliation(s)
- Skylar L Fuller
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Elizabeth A Savory
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Alexandra J Weisberg
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Jessica Z Buser
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Michael I Gordon
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Melodie L Putnam
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
| | - Jeff H Chang
- All authors: Department of Botany and Plant Pathology; first and seventh authors: Molecular and Cellular Biology Program; and seventh author: Center for Genomic Research and Biocomputing, Oregon State University, Corvallis 97331
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Wang J, Wang J, Li R, Liu L, Yuan W. Rapid and sensitive detection of canine distemper virus by real-time reverse transcription recombinase polymerase amplification. BMC Vet Res 2017; 13:241. [PMID: 28810858 PMCID: PMC5558738 DOI: 10.1186/s12917-017-1180-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Recombinase polymerase amplification (RPA), as an isothermal gene amplification technique, has been explored for the molecular detection of diverse pathogens. METHODS A real-time reverse transcription RPA (RT-RPA) assay for the detection of canine distemper virus (CDV) using primers and exo probe targeting the CDV nucleocapsid protein gene was developed. A series of other viruses were tested by the RT-RPA.Thirty-two field samples were further tested by RT-RPA, and the resuts were compared with those obtained by the real-time RT-PCR. RESULTS The RT-RPA assay was performed successfully at 40 °C, and the results were obtained within 3 min-12 min. The assay could detect CDV, but did not show cross-detection of canine parvovirus-2 (CPV-2), canine coronavirus (CCoV), canine parainfluenza virus (CPIV), pseudorabies virus (PRV) or Newcastle disease virus (NDV), demonstrating high specificity. The analytical sensitivity of RT-RPA was 31.8 copies in vitro transcribed CDV RNA, which is 10 times lower than the real-time RT-PCR. The assay performance was validated by testing 32 field samples and compared to real-time RT-PCR. The results indicated an excellent correlation between RT-RPA and a reference real-time RT-PCR method. Both assays provided the same results, and R2 value of the positive results was 0.947. CONCLUSIONS The results demonstrated that the RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of CDV both in the laboratory and point-of-care facility, especially in the resource-limited settings.
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Affiliation(s)
- Jianchang Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, No.318 Hepingxilu Road, Shijiazhuang, Hebei Province, 050051, People's Republic of China
| | - Jinfeng Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, No.318 Hepingxilu Road, Shijiazhuang, Hebei Province, 050051, People's Republic of China
| | - Ruiwen Li
- College of Veterinary Medicine, Agricultural University of Hebei, No.38 Lingyusi Street, Baoding, Hebei, 071001, People's Republic of China
| | - Libing Liu
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, No.318 Hepingxilu Road, Shijiazhuang, Hebei Province, 050051, People's Republic of China
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, No.38 Lingyusi Street, Baoding, Hebei, 071001, People's Republic of China.
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Development of a real-time recombinase polymerase amplification assay for rapid and sensitive detection of porcine circovirus 2. Arch Virol 2017; 162:2293-2296. [DOI: 10.1007/s00705-017-3368-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/17/2017] [Indexed: 10/19/2022]
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Denner J, Mankertz A. Porcine Circoviruses and Xenotransplantation. Viruses 2017; 9:v9040083. [PMID: 28425928 PMCID: PMC5408689 DOI: 10.3390/v9040083] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/06/2017] [Accepted: 04/12/2017] [Indexed: 02/07/2023] Open
Abstract
Allotransplantation and xenotransplantation may be associated with the transmission of pathogens from the donor to the recipient. Whereas in the case of allotransplantation the transmitted microorganisms and their pathogenic effect are well characterized, the possible influence of porcine microorganisms on humans is mostly unknown. Porcine circoviruses (PCVs) are common in pig breeds and they belong to porcine microorganisms that still have not been fully addressed in terms of evaluating the potential risk of xenotransplantation using pig cells, tissues, and organs. Two types of PCVs are known: porcine circovirus (PCV) 1 and PCV2. Whereas PCV1 is apathogenic in pigs, PCV2 may induce severe pig diseases. Although most pigs are subclinically infected, we do not know whether this infection impairs pig transplant functionality, particularly because PCV2 is immunosuppressive. In addition, vaccination against PCV2 is able to prevent diseases, but in most cases not transmission of the virus. Therefore, PCV2 has to be eliminated to obtain xenotransplants from uninfected healthy animals. Although there is evidence that PCV2 does not infect—at least immunocompetent—humans, animals should be screened using sensitive methods to ensure virus elimination by selection, Cesarean delivery, vaccination, or embryo transfer.
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Affiliation(s)
- Joachim Denner
- Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
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Development of Isothermal Recombinase Polymerase Amplification Assay for Rapid Detection of Porcine Circovirus Type 2. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8403642. [PMID: 28424790 PMCID: PMC5382309 DOI: 10.1155/2017/8403642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 11/17/2022]
Abstract
Porcine circovirus virus type II (PCV2) is the etiology of postweaning multisystemic wasting syndrome (PMWS), porcine dermatitis, nephropathy syndrome (PDNS), and necrotizing pneumonia. Rapid diagnosis tool for detection of PCV2 plays an important role in the disease control and eradication program. Recombinase polymerase amplification (RPA) assays using a real-time fluorescent detection (PCV2 real-time RPA assay) and RPA combined with lateral flow dipstick (PCV2 RPA LFD assay) were developed targeting the PCV2 ORF2 gene. The results showed that the sensitivity of the PCV2 real-time RPA assay was 102 copies per reaction within 20 min at 37°C and the PCV2 RPA LFD assay had a detection limit of 102 copies per reaction in less than 20 min at 37°C. Both assays were highly specific for PCV2, with no cross-reactions with porcine circovirus virus type 1, foot-and-mouth disease virus, pseudorabies virus, porcine parvovirus, porcine reproductive and respiratory syndrome virus, and classical swine fever virus. Therefore, the RPA assays provide a novel alternative for simple, sensitive, and specific identification of PCV2.
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