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Wang X, Xu T, Ding S, Xu Y, Jin X, Guan F. Recombinase polymerase amplification combined with lateral flow dipstick assay for rapid visual detection of A.simplex (s. s.) and A.pegreffii in sea foods. Heliyon 2024; 10:e28943. [PMID: 38623257 PMCID: PMC11016599 DOI: 10.1016/j.heliyon.2024.e28943] [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: 02/20/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Anisakiasis is a food-borne parasitic disease mainly caused by the third stage of Anisakis simplex (s. s.) and Anisakis pegreffii. Traditional methods for detecting of Anisakis involve morphology identification such as visual inspection, enzyme digestion, and molecular methods based on PCR, but they have certain limitations. In this study, the internal transcribed spacer 1 (ITS 1) regions of Anisakis were targeted to develop a visual screening method for detecting A. simplex (s. s.) and A. pegreffii in fish meat based on recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD). Specific primers and probes were designed and optimized for temperature, reaction time, and detection threshold. LFD produced clear visual results that were easily identifiable after a consistent incubation of 10-20 min at 37 °C. The whole process of DNA amplification by RPA and readout by LFD did not exceed 30 min. In addition, the detection limit is up to 9.5 × 10-4 ng/μL, and the detection of the artificially contaminated samples showed that the developed assay can effectively and specifically detect A. simplex (s. s.) and A. pegreffii, which fully meet the market's requirements for fish food safety supervision.
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Affiliation(s)
- Xiaoming Wang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Zhejiang Museum of Natural History, Hangzhou 310018, China
| | - Ting Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Siling Ding
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Ye Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xingsheng Jin
- Zhejiang Museum of Natural History, Hangzhou 310018, China
| | - Feng Guan
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Zhou Y, Zhang J, Sun H, Tao D, Xu B, Han X, Ren R, Ruan J, Steinaa L, Hemmink JD, Han J, Li X, Xu J, Zhao S, Xie S, Zhao C. Sensitive and Specific Exonuclease III-Assisted Recombinase-Aided Amplification Colorimetric Assay for Rapid Detection of Nucleic Acids. ACS Synth Biol 2023; 12:2877-2886. [PMID: 37729559 DOI: 10.1021/acssynbio.3c00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The development of a contamination-free and on-site nucleic acid detection platform with high sensitivity and specificity but low-cost for the detection of pathogenic nucleic acids is critical for infectious disease diagnosis and surveillance. In this study, we combined the recombinase-aided amplification (RAA) with the exonuclease III (Exo III)-assisted signal amplification into a platform for sensitive and specific detection of nucleic acids of African swine fever virus (ASFV). We found that this platform enabled a naked eye visual detection of ASFV at a detection limit as low as 2 copies/μL in 30 min. As expected, no cross-reactivity was observed with other porcine viruses. In addition, to avoid aerosol contamination, a one-tube RAA-Exo III colorimetric assay was also established for the accurate detection of ASFV in clinical samples. Taken together, we developed a rapid, instrument-free, and low-cost Exo III-assisted RAA colorimetric-assay-based nucleic acid detection platform.
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Affiliation(s)
- Yuan Zhou
- 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, P. R. China
| | - Jinfu Zhang
- 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, P. R. China
| | - Haowen Sun
- 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, P. R. 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, P. R. China
| | - Bingrong Xu
- 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, P. R. China
| | - Xiaosong Han
- 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, P. R. China
| | - Ruimin Ren
- 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, P. R. China
| | - Jinxue Ruan
- 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, P. R. China
| | - Lucilla Steinaa
- Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Johanneke D Hemmink
- Animal and Human Health Program, Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Biosciences, International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Xinyun Li
- 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, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, P. R. China
| | - Jing Xu
- 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, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shuhong Zhao
- 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, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, P. R. 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, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, P. R. China
| | - Changzhi Zhao
- 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, P. R. China
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3
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Recent advances in diagnostic approaches for orf virus. Appl Microbiol Biotechnol 2023; 107:1515-1523. [PMID: 36723701 DOI: 10.1007/s00253-023-12412-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023]
Abstract
Orf virus (ORFV), the prototype species of the Parapoxvirus genus, is an important zoonotic virus, causing great economic losses in livestock production. At present, there are no effective drugs for orf treatment. Therefore, it is crucial to develop accurate and rapid diagnostic approaches for ORFV. Over decades, various diagnostic methods have been established, including conventional methods such as virus isolation and electron microscopy; serological methods such as virus neutralization test (VNT), immunohistochemistry (IHC) assay, immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA); and molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and recombinase-aided amplification (RAA) assay. This review provides an overview of currently available diagnostic approaches for ORFV and discusses their advantages and limitations and future perspectives, which would be significantly helpful for ORFV early diagnosis and surveillance to prevent outbreak of orf. KEY POINTS: • Orf virus emerged and reemerged in past years • Rapid and efficient diagnostic approaches are needed and critical for ORFV detection • Novel and sensitive diagnostic methods are required for ORFV detection.
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Cui H, Guan J, Lu H, Liu J, Tu F, Zhang C, Su K, Guo Z, Zhao K. Rapid Onsite Visual Detection of Orf Virus Using a Recombinase-Aided Amplification Assay. Life (Basel) 2023; 13:life13020494. [PMID: 36836851 PMCID: PMC9968157 DOI: 10.3390/life13020494] [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: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Orf is an important zoonotic disease caused by the Orf virus (ORFV) which can cause contagious pustular dermatitis in goats and sheep. Orf is widespread in most sheep-raising countries in the world, causing huge economic losses. Although diagnostic methods for ORFV infection already exist, it is still necessary to develop a time-saving, labor-saving, specific, low-cost and visual diagnostic method for rapid detection of ORFV in the field and application in grassroots laboratories. This study establishes a DNA extraction-free, real-time, visual recombinase-aided amplification (RAA) method for the rapid detection of ORFV. This method is specific to ORFV and does not cross-react with other common DNA viruses. The detection limits of the real-time RAA and visual judgment of the RAA assay at 95% probability were 13 and 21 copies per reaction for ORFV, respectively. Compared with qPCR, the sensitivity and specificity of the real-time RAA assay were 100%, and those of the visual RAA assay were 92.31% and 100.0%, respectively. The DNA extraction-free visual detection method of RAA established in this study can meet the needs of rapid onsite detection and grassroots laboratories and has important reference value and significance for the early diagnosis of diseased animals.
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Affiliation(s)
- Huan Cui
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jiyu Guan
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Huijun Lu
- Key Laboratory of Zoonosis, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun 130062, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Fei Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Cheng Zhang
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lucky South Street, Baoding 071000, China
| | - Kai Su
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lucky South Street, Baoding 071000, China
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- Correspondence: (Z.G.); (K.Z.)
| | - Kui Zhao
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
- Correspondence: (Z.G.); (K.Z.)
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5
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Qiao M, Zhang L, Chang J, Li H, Li J, Wang W, Yuan G, Su J. Rapid and sensitive detection of pathogenic Elizabethkingia miricola in black spotted frog by RPA-LFD and fluorescent probe-based RPA. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2022; 3:100059. [PMID: 36419595 PMCID: PMC9680066 DOI: 10.1016/j.fsirep.2022.100059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Established fluorescent probe-based RPA (exo RPA) and RPA-LFD methods for fast and sensitive detection of E. miricola. Exo RPA and RPA-LFD could detect E. miricola genomic DNA at 38 °C in 30 min. The detection sensitivity of exo RPA and RPA-LFD were 102 copies/μL. The exo RPA and RPA-LFD achieved rapid detection of E. miricola without bulky lab equipment.
Elizabethkingia miricola is a highly infectious pathogen, which causes high mortality rate in frog farming. Therefore, it is urgent to develop a rapid and sensitive detection method. In this study, two rapid and specific methods including recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) and fluorescent probe-based recombinase polymerase amplification (exo RPA) were established to effectively detect E. miricola, which can accomplish the examination at 38 °C within 30 min. The limiting sensitivity of RPA-LFD and exo RPA (102 copies/μL) was ten-fold higher than that in generic PCR assay. The specificities of the two methods were verified by detecting multiple DNA samples (E. miricola, Staphylococcus aureus, Aeromonas hydrophila, Aeromonas veronii, CyHV-2 and Edwardsiella ictaluri), and the result showed that the single band was displayed in E. miricola DNA only. By tissue bacterial load and qRT-PCR assays, brain is the most sensitive tissue. Random 24 black spotted frog brain samples from farms were tested by generic PCR, basic RPA, RPA-LFD and exo RPA assays, and the results showed that RPA-LFD and exo RPA methods were able to detect E. miricola accurately and rapidly. In summary, the methods of RPA-LFD and exo RPA were able to detect E. miricola conveniently, rapidly, accurately and sensitively. This study provides prospective methods to detect E. miricola infection in frog culture.
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Affiliation(s)
- Meihua Qiao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Liqiang Zhang
- Wuhan Academy of Agricultural Science, Wuhan 430070, China
| | - Jiao Chang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoxuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingkang Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Weicheng Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gailing Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Corresponding author at: Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Toldrà A, Ainla A, Khaliliazar S, Landin R, Chondrogiannis G, Hanze M, Réu P, Hamedi MM. Portable electroanalytical nucleic acid amplification tests using printed circuit boards and open-source electronics. Analyst 2022; 147:4249-4256. [PMID: 35993403 PMCID: PMC9511072 DOI: 10.1039/d2an00923d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 09/19/2023]
Abstract
The realization of electrochemical nucleic acid amplification tests (NAATs) at the point of care (POC) is highly desirable, but it remains a challenge given their high cost and lack of true portability/miniaturization. Here we show that mass-produced, industrial standardized, printed circuit boards (PCBs) can be repurposed to act as near-zero cost electrodes for self-assembled monolayer-based DNA biosensing, and further integration with a custom-designed and low-cost portable potentiostat. To show the analytical capability of this system, we developed a NAAT using isothermal recombinase polymerase amplification, bypassing the need of thermal cyclers, followed by an electrochemical readout relying on a sandwich hybridization assay. We used our sensor and device for analytical detection of the toxic microalgae Ostreopsis cf. ovata as a proof of concept. This work shows the potential of PCBs and open-source electronics to be used as powerful POC DNA biosensors at a low-cost.
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Affiliation(s)
- Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Alar Ainla
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Roman Landin
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Martin Hanze
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
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Qu G, Li Y, Zhao Z, Miao L, Wei F, Tang N, Xu Q, Nair V, Yao Y, Shen Z. Establishment and Application of a Real-Time Recombinase Polymerase Amplification Assay for the Detection of Avian Leukosis Virus Subgroup J. Front Vet Sci 2022; 9:847194. [PMID: 35873679 PMCID: PMC9301284 DOI: 10.3389/fvets.2022.847194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Avian leukosis caused by avian leukosis virus (ALV), belonging to the genus Alpharetrovirus of the family Retroviridae, is associated with benign and malignant tumors in hemopoietic cells in poultry. Although several methods have been developed for ALV detection, most of them are not suitable for rapid on-site testing due to instrument limitations, professional operators, or the low sensitivity of the method. Herein, we described the real-time recombinase polymerase amplification (RPA) assay for rapid detection of ALV subgroup J (ALV-J). The major viral structural glycoprotein gp85, highly specific for the subgroup, was used as the molecular target for the real-time RPA assay. The results were obtained at 38°C within 20 min, with the detection sensitivity of 10 copies/μl of standard plasmid pMD18-T-gp85 as the template per reaction. Real-time RPA was capable of ALV-J-specific detection without cross-reaction with other non-targeted avian pathogens. Of the 62 clinical samples tested, the ALV-positive rates of real-time RPA, PCR, and real-time PCR were 66.13% (41/62), 59.68% (37/62), and 67.74% (42/62), respectively. The diagnostic agreement between real-time RPA and real-time PCR was 98.39% (61/62), and the kappa value was 0.9636. The developed real-time ALV-J assay seems promising for rapid and sensitive detection of ALV-J in diagnostic laboratories. It is suitable for on-site detection, especially in a poor resource environment, thus facilitating the prevention and control of ALV-J.
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Affiliation(s)
- Guanggang Qu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- *Correspondence: Guanggang Qu
| | - Yun Li
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Zhongwei Zhao
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
| | - Lizhong Miao
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Feng Wei
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Na Tang
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Qingqing Xu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
- Yongxiu Yao
| | - Zhiqiang Shen
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
- Zhiqiang Shen
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Zhu P, Huang Z, Xiong Z, Guo S, Zhang S, Cai T. Development and evaluation of real-time recombinase polymerase amplification assay for rapid and sensitive detection of Vibro mimicus in human plasma samples. J Appl Microbiol 2022; 133:1650-1659. [PMID: 35702884 DOI: 10.1111/jam.15666] [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: 12/09/2021] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
AIM We aimed at developing a fast and accurate method to detect Vibrio mimicus using real-time recombinase polymerase amplification assay. METHODS AND RESULTS Specific primers and probe were designed to target V. mimicus haemolysin (vmh) gene. Target DNA was successfully amplified at 41°C within 20 min. The method exhibited a high level of specificity and the sensitivity was 2.1 × 102 copies/25 μl or 8.4 copies/μl, which is in line with real-time polymerase chain reaction (PCR). The calibration curve plotted by the second-order polynomial regression showed better than the linear curve, as the correlation coefficient was raised to 0.9907, which suggested that the second-order polynomial regressions might be considered to apply to the quantification of real-time recombinase polymerase amplification (RPA). The limit of detection (LOD) was predicted to be 77 copies/25 μl or 3 copies/μl by a probit model. The limit of quantification (LOQ) was calculated to be 28 copies /25 μl or 1 copies/μl by a receiver operating characteristic (ROC) curve, which firstly make LOQ could be available to real-time RPA. For the performance of the real-time RPA in plasma samples, the detection sensitivity of real-time RPA was as good as the real-time PCR. For pretreatment of plasma samples, the boiling method was better than using kits, as it further shortened the time of the real-time RPA in detecting V. mimicus. CONCLUSIONS The real-time RPA assay developed in our study shows multiple advantages over currently available DNA diagnostic method, including a quicker time-to-result for a single sample, requiring minimal infrastructure and technical support and being tolerant to inhibitors in plasma samples. SIGNIFICANCE AND IMPACT OF THE STUDY The real-time RPA assay developed here is a potentially valuable tool for point-of-care (POC) diagnosis of V. mimicus infection in endemic field, especially in the resources-limited settings, as combined with portable devices.
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Affiliation(s)
- Peng Zhu
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zuoan Huang
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zi Xiong
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shiyu Guo
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Ting Cai
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.,Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
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9
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Development and Application of Recombinase Polymerase Amplification Assays for Rapid Detection of Escherichia coli O157 in Food. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Guaman-Bautista LP, Moreta-Urbano E, Oña-Arias CG, Torres-Arias M, Kyriakidis NC, Malcı K, Jonguitud-Borrego N, Rios-Solis L, Ramos-Martinez E, López-Cortés A, Barba-Ostria C. Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies. Diagnostics (Basel) 2021; 11:1981. [PMID: 34829328 PMCID: PMC8621220 DOI: 10.3390/diagnostics11111981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.
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Affiliation(s)
- Linda P. Guaman-Bautista
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Erick Moreta-Urbano
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Claudia G. Oña-Arias
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Marbel Torres-Arias
- Immunology and Virology Laboratory, Department of Life Science and Agriculture, Universidad de las Fuerzas Armadas, Quito 171103, Ecuador;
| | - Nikolaos C. Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas, Quito 170125, Ecuador;
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Espiridion Ramos-Martinez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 4510, Mexico;
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador;
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
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11
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Choi MH, Lee J, Seo YJ. Combined recombinase polymerase amplification/rkDNA-graphene oxide probing system for detection of SARS-CoV-2. Anal Chim Acta 2021; 1158:338390. [PMID: 33863409 PMCID: PMC7973912 DOI: 10.1016/j.aca.2021.338390] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 01/07/2023]
Abstract
The development of rapid, highly sensitive, and selective methods for the diagnosis of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should help to prevent the spread of this pandemic virus. In this study, we combined recombinase polymerase amplification (RPA), as a means of isothermal DNA amplification, with an rkDNA-graphene oxide (GO) probe system to allow the rapid detection of SARS-CoV-2 with high sensitivity and selectivity. We used in situ enzymatic synthesis to prepare an rkDNA probe that was complementary to an RPA-amplified sequence of the target N-gene of SARS-CoV-2. The fluorescence of this rkDNA was perfectly quenched in the presence of GO. When the quenched rkDNA-GO system was added to the RPA-amplified sequence of the target SARS-CoV-2, the fluorescence recovered dramatically. The combined RPA/rkDNA-GO system exhibited extremely high selectivity (discrimination factor: 17.2) and sensitivity (LOD = 6.0 aM) for the detection of SARS-CoV-2. The total processing time was only 1.6 h. This combined RPA/rkDNA-GO system appears to be a very efficient and simple method for the point-of-care detection of SARS-CoV-2.
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Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Jaehyeon Lee
- Department of Laborotory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54896, South Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea.
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12
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Fan J, Chen W, Zhang Y, Liu Z, Li X, Ding H, Yi L, Chen J, Zhao M. Development of a reverse-transcription recombinase polymerase amplification assay with a lateral flow assay for rapid detection of avian orthoavulavirus 1. J Vet Diagn Invest 2021; 33:308-312. [PMID: 33685333 DOI: 10.1177/1040638721990122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Newcastle disease is an avian infectious disease caused by avian orthoavulavirus 1, also known as Newcastle disease virus (NDV). This disease has caused significant economic losses to the poultry industry worldwide. The rapid and simple detection of NDV infection is crucial to inform the appropriate control measures. We developed a reverse-transcription recombinase polymerase amplification (RT-RPA) assay combined with a lateral flow assay (LFA) for NDV detection. The RPA assay can be completed at 37°C within 20 min, and the RPA result can be visualized by the LFA within 5 min. The NDV RT-RPA-LFA detected NDV specifically with no cross-reactivity with other pathogens. The detection limit of NDV cDNA with our RT-RPA-LFA was 3.34 × 10-3 ng/μL. Consequently, the RT-RPA-LFA showed good potential for the detection of NDV infection in the field, especially in resource-limited settings.
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Affiliation(s)
- Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhixiang Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoming Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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13
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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14
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Sensitively and quickly detecting Vibrio vulnificus by real time recombinase polymerase amplification targeted to vvhA gene. Mol Cell Probes 2021; 57:101726. [PMID: 33789126 DOI: 10.1016/j.mcp.2021.101726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/28/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022]
Abstract
Vibrio vulnificus (V. vulnificus) is a Gram-negative bacterium living in warm and salty water. This marine bacterium could produce hemolysin (VVH), which often causes serious gastroenteritis or septicemia when people contact to seawater or seafood containing V. vulnificus. Timely diagnosis is regard as essential to disease surveillance. In this paper, we aimed at developing a quick and sensitive method for the detection of Vibrio vulnificus using real time recombinase polymerase amplification (real time RPA). Specific primers and an exo probe were designed on the basis of the vvhA gene sequence available in GenBank. Target DNA could be amplified and labeled with specific fluorophore within 20 min at 38 °C. The method exhibited a high specificity, only detecting Vibrio vulnificus and not showing cross-reaction with other bacteria. The sensitivity of this method was 2 pg per reaction (20 μL) for DNA, or 200 copies per reaction (20 μL) for standard plasmid. The detection limit (LOD) stated as the target level that would be detected 95% of the time and estimated was 1.58 × 102 copies by fit of the probit to the results of 8 replicates in different concentration. For quantitative analysis of the real time RPA, the second order polynomial regression was adopted in our study. The results showed the correlation coefficients were raised above 0.98, which suggested this model might be a better choice for the quantitative analysis of real time RPA compared to the routine linear regression model. For artificially contaminated plasma samples, Vibrio vulnificus could be detected within 16 min by real time RPA at concentration as low as 1.2 × 102 CFU/mL or 2.4 CFU per reaction (20 μL). Thus, the real time RPA method established in this study shows great potential for detecting Vibrio vulnificus in the research laboratory and disease diagnosis.
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15
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Wang X, Xu LL, Zuo XY, Lin JW, Jin Z, Shen R, Du D, Tang YZ. Rapid detection of the New Delhi metallo-β-lactamase (NDM) gene by recombinase polymerase amplification. INFECTION GENETICS AND EVOLUTION 2020; 87:104678. [PMID: 33321225 DOI: 10.1016/j.meegid.2020.104678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) is a series of enzyme conferring resistance to β-lactam antibiotics including the carbapenems. The blaNDM gene has been reported in a variety of Gram-negative bacilli, especially in the Enterobacteriaceae and Acinetobacter spp., which is deeply disconcerting for public health worldwide. In this study, recombinase polymerase amplification assays using a basic detection (Basic-RPA) and a real-time fluorescent detection (Exo-RPA) were established for detecting blaNDM gene. The RPA reactions were performed at 39 °C and finished within 20 min. Using different copy numbers of pMD18T-NDM plasmid DNA as templates, we identified the detection limit of Basic-RPA assay (1.85 × 103 copies/μL), conventional PCR assay (1.85 × 104 copies/μL), Exo-RPA assay (1.85 × 102 copies/μL) and real-time PCR assay (1.85 × 102 copies/μL). Both Basic-RPA and Exo-RPA assays were highly specific for detecting blaNDM, as there were no cross-reactions with the strains without blaNDM gene. Examination of 62 clinical samples by RPA assays and PCR assays showed the same results, suggesting that RPA assays are reliable in clinical diagnosis. The amplification time of RPA is much shorter than that of other molecular techniques, it is easy to implement and has the potential for clinical application.
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Affiliation(s)
- Xiao Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ling-Ling Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiang-Yi Zuo
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jia-Wen Lin
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Rong Shen
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China
| | - Dan Du
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of medicine, Xiamen University, Xiamen, Fujian, China.
| | - You-Zhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Mukama O, Nie C, Habimana JDD, Meng X, Ting Y, Songwe F, Al Farga A, Mugisha S, Rwibasira P, Zhang Y, Zeng L. Synergetic performance of isothermal amplification techniques and lateral flow approach for nucleic acid diagnostics. Anal Biochem 2020; 600:113762. [PMID: 32387190 DOI: 10.1016/j.ab.2020.113762] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/23/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
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17
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Wang Y, Cui Y, Yu Z, Li Y, Bai C, Sun P, Zhu W, Li Y. Development of a recombinase-aided amplification assay for detection of orf virus. J Virol Methods 2020; 280:113861. [PMID: 32343981 DOI: 10.1016/j.jviromet.2020.113861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/23/2022]
Abstract
Orf, caused by orf virus (ORFV), is an important zoonotic disease that infects goat and sheep, leading to huge economic losses. ORFV can also cause cutaneous lesions in people who come in close contact with the diseased animals. Although accurate diagnostic methods for ORFV infection exist, there is a need for a rapid, specific, and sensitive method for easy clinical application. Here, we successfully established a recombinase-aided amplification (RAA) assay for rapid detection of ORFV. The analytical sensitivity of the assay for ORFV detection is 1 × 101 copies per reaction. Moreover, no cross-reaction was observed with other common DNA viruses. A total of 45 archived suspected ORFV infected nasal scab skin samples were examined by RAA and SYBR Green-based real-time polymerase chain reaction (PCR). Compared with the real-time PCR assay, the kappa values of the RAA assay for ORFV detection was 0.845 (p <0.001), indicating that both assay results were fully in agreement. In conclusion, this detection assay provides a rapid, sensitive, and specific method for ORFV detection and is suitable for ORFV clinical testing.
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Affiliation(s)
- 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
| | - Yongqiu Cui
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Zhaorong Yu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yeqiu Li
- 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
| | - Pei Sun
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Wen Zhu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, PR China.
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Li Z, Pinto Torres JE, Goossens J, Stijlemans B, Sterckx YGJ, Magez S. Development of a recombinase polymerase amplification lateral flow assay for the detection of active Trypanosoma evansi infections. PLoS Negl Trop Dis 2020; 14:e0008044. [PMID: 32069278 PMCID: PMC7048301 DOI: 10.1371/journal.pntd.0008044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/28/2020] [Accepted: 01/09/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Animal trypanosomosis caused by Trypanosoma evansi is known as "surra" and is a widespread neglected tropical disease affecting wild and domestic animals mainly in South America, the Middle East, North Africa and Asia. An essential necessity for T. evansi infection control is the availability of reliable and sensitive diagnostic tools. While DNA-based PCR detection techniques meet these criteria, most of them require well-trained and experienced users as well as a laboratory environment allowing correct protocol execution. As an alternative, we developed a recombinase polymerase amplification (RPA) test for Type A T. evansi. The technology uses an isothermal nucleic acid amplification approach that is simple, fast, cost-effective and is suitable for use in minimally equipped laboratories and even field settings. METHODOLOGY/PRINCIPLE FINDINGS An RPA assay targeting the T. evansi RoTat1.2 VSG gene was designed for the DNA-based detection of T. evansi. Comparing post-amplification visualization by agarose gel electrophoresis and a lateral flow (LF) format reveals that the latter displays a higher sensitivity. The RPA-LF assay is specific for RoTat1.2-expressing strains of T. evansi as it does not detect the genomic DNA of other trypanosomatids. Finally, experimental mouse infection trials demonstrate that the T. evansi specific RPA-LF can be employed as a test-of-cure tool. CONCLUSIONS/SIGNIFICANCE Compared to other DNA-based parasite detection methods (such as PCR and LAMP), the T. evansi RPA-LF (TevRPA-LF) described in this paper is an interesting alternative because of its simple read-out (user-friendly), short execution time (15 minutes), experimental sensitivity of 100 fg purified genomic T. evansi DNA, and ability to be carried out at a moderate, constant temperature (39°C). Therefore, the TevRPA-LF is an interesting tool for the detection of active T. evansi infections.
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Affiliation(s)
- Zeng Li
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Medical Biochemistry and the Infla-Med Centre of Excellence, University of Antwerp (UA), Campus Drie Eiken, Wilrijk, Belgium
| | - Joar Esteban Pinto Torres
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Julie Goossens
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Benoit Stijlemans
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry and the Infla-Med Centre of Excellence, University of Antwerp (UA), Campus Drie Eiken, Wilrijk, Belgium
| | - Stefan Magez
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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19
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Chen Z, Huang J, Zhang F, Zhou Y, Huang H. Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay. Mol Cell Probes 2019; 49:101475. [PMID: 31655105 DOI: 10.1016/j.mcp.2019.101475] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.
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Affiliation(s)
- Zhengwei Chen
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China; Center of Engineering Training, Zhejiang University of Science and Technology, Hangzhou, P.R. China.
| | - Jun Huang
- College of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Fang Zhang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China.
| | - Yang Zhou
- College of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Huijie Huang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China.
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20
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A simple and efficient method for potential point-of-care diagnosis of human papillomavirus genotypes: combination of isothermal recombinase polymerase amplification with lateral flow dipstick and reverse dot blot. Anal Bioanal Chem 2019; 411:7451-7460. [PMID: 31588523 DOI: 10.1007/s00216-019-02113-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022]
Abstract
Cervical cancer is the second most common cancer in the world's woman population with a high incidence in developing countries where diagnostic conditions for the cancer are poor. The main culprit causing the cancer is the human papillomavirus (HPV). HPV is divided into three major groups, i.e., high-risk (HR) group, probable high-risk (pHR) group, and low-risk (LR) group according to their potential of causing cervical cancer. Therefore, developing a sensitive, reliable, and cost-effective point-of-care diagnostic method for the virus genotypes in developing countries even worldwide is of high importance for the cancer prevention and control strategies. Here we present a combined method of isothermal recombinase polymerase amplification (RPA), lateral flow dipstick (LFD), and reverse dot blot (RDB), in quick point-of-care identification of HPV genotypes. The combined method is highly specific to HPV when the conserved L1 genes are used as targeted genes for amplification. The method can be used in identification of HPV genotypes at point-of-care within 1 h with a sensitivity of low to 100 fg of the virus genomic DNA. We have demonstrated that it is an excellent diagnostic point-of-care assay in monitoring the disease without time-consuming and expensive procedures and devices.
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21
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Development of a Rapid Test Method for Salmonella enterica Detection Based on Fluorescence Probe-Based Recombinase Polymerase Amplification. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01526-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Xi Y, Xu CZ, Xie ZZ, Zhu DL, Dong JM, Xiao G. Development of a reverse transcription recombinase polymerase amplification assay for rapid detection of human respiratory syncytial virus. Mol Cell Probes 2019; 45:8-13. [PMID: 30922817 DOI: 10.1016/j.mcp.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023]
Abstract
Respiratory syncytial virus (RSV) is one of the most important causative agents that causing respiratory tract infection in children and associated with high morbidity and mortality. A diagnostic method would be a robust tool for identification of RSV infection, especially in the resource-limited settings. Recombinase polymerase amplification (RPA) is a novel isothermal amplification technique which has been widely employed to detect human/animal pathogens. In present study, a probe-based reverse transcription RPA (RT-RPA) assay was established for the detection of RSV. The primers and probe were designed based on the sequences of the conserved nucleocapsid (N) gene. The minimal detection limit of the RT-RPA assay for the detection of RSV B was 19 copies of RNA molecules at 95% probability, whereas the detection limit for RSV A was 104 copies molecule. The assay was RSV-specific since it had no non-specific reactions with other common human pathogens. The clinical performance of the RT-RPA assay was validated using 188 nasopharyngeal aspirates (NPAs). The nucleic acid extraction of the samples was performed by use of the magnetic bead-based kit which didn't require the heavy and expensive centrifuge. The coincidence rates between RT-RPA and qRT-PCR for the clinical samples was 96%, indicating the RT-RPA assay had good diagnostic performance on clinical samples. The real-time RT-RPA assay combined with the manual genome extraction method make it potential to detect clinical samples in field, providing a possible solution for RSV diagnosis in remote rural areas in developing countries.
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Affiliation(s)
- Yun Xi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Chang-Zhi Xu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhi-Zhi Xie
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dong-Lin Zhu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie-Ming Dong
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Gang Xiao
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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LIN YUSHENG, JIANG JINXIU. TaqMan-based real-time quantitative fluorescence PCR for detection of Orf virus. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i3.88032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Contagious ecthyma, also known as scabby mouth or Orf, is a zoonosis, which is caused by the Orf virus (ORFV). Human contact with infected animals can cause cutaneous lesions. To prevent and control ORFV effectively, rapid detection method is very important and highly needed. Real-time quantitative fluorescence PCR (qPCR) assay is considered as a rapid techonology to detect ORFV, and has been used for clinical diagnosis and epidemiological investigation. In present study, we developed a TaqMan-based qPCR assay for detection of ORFV. Beacon Designer 7.9 was used to design specific primers and probes were based on the ORFV020 gene sequence of the virus (GenBank Accession No. KF666563.1). The method had no cross-reactions with other common bacteria and viruses, was highly specific; the sensitivity test result showed that it could detect 10 copies of ORFV genomic DNA, and was more sensitive than conventional PCR. Both intra- and inter-variabilities were less than 2%, indicating the high stability and repeatability of the method. Additionally, 99 clinical samples from sheep and goats with suspected contagious ecthyma were tested using the developed assay and conventional PCR. The results showed that the developed assay was more sensitive and faster than conventional PCR. It can be concluded that the assay was suitable for routine detection of the ORFV and the epidemiological investigation.
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Zeng R, Luo J, Gao S, Xu L, Song Z, Dai F. Rapid detection of Cucumber green mottle mosaic virus by reverse transcription recombinase polymerase amplification. Mol Cell Probes 2019; 43:84-85. [DOI: 10.1016/j.mcp.2018.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
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Pang J, Wang Q, Fei Y, Zhu P, Qiao L, Huang H, Dang C, Gao W. A real-time recombinase polymerase amplification assay for the rapid detection of Vibrio harveyi. Mol Cell Probes 2019; 44:8-13. [PMID: 30610902 DOI: 10.1016/j.mcp.2019.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022]
Abstract
Vibrio harveyi is a pathogen that infects fish and shellfish worldwide, causing severe economic losses for the aquaculture industry. As the early diagnosis of V. harveyi infection is crucial to disease surveillance and prevention in cultured marine animals, a fast and accurate method to detect V. harveyi is required. Here, we performed recombinase polymerase amplification (RPA) using novel primers specifically designed to recognize the V. harveyi toxR gene, which encodes a transmembrane protein, and then hybridized this gene with a carboxy fluorescein (FAM)-labeled probe. The optimal conditions for the real-time RPA assay were a probe concentration of 90 nM and a 20 min incubation at 37 °C. The sensitivity of our real-time RPA assay was 50 copies of the standard plasmid, while that of real-time PCR was 500 copies. In V. harveyi-spiked Pseudosciaena crocea samples, the sensitivity of our real-time RPA was 60 CFUs per reaction, while that of PCR was 600 CFUs per reaction. SPSS probit regression analysis indicated that the limit of detection (LOD) of our RPA assay, with 95% probability, was 18 copies. The LOD was reached within 20 min and was highly reproducible across eight independent assays. Our novel RPA method successfully differentiated V. harveyi from all other tested Vibrio species, including some that were closely related. Our real-time RPA assay, in combination with a rapid DNA extraction protocol, is a fast and accurate tool for the detection of V. harveyi and for monitoring disease outbreaks. This tool will be valuable for the aquaculture industry.
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Affiliation(s)
| | - Qiong Wang
- Marine Environmental Monitoring Center of Ningbo, State Oceanic Administration, China.
| | - Yuejun Fei
- Marine Environmental Monitoring Center of Ningbo, State Oceanic Administration, China
| | - Peng Zhu
- Ningbo University, Ningbo, 315211, China; Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | | | | | | | - Weifang Gao
- Ningbo Institute of Oceanography, Ningbo, 315832, China
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Li J, Macdonald J, von Stetten F. Review: a comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 2019; 144:31-67. [DOI: 10.1039/c8an01621f] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RPA is a versatile complement or replacement of PCR, and now is stepping into practice.
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Affiliation(s)
- Jia Li
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
| | - Joanne Macdonald
- Inflammation and Healing Research Cluster
- Genecology Research Centre
- School of Science and Engineering
- University of the Sunshine Coast
- Australia
| | - Felix von Stetten
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
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Ma L, Zeng F, Cong F, Huang B, Zhu Y, Wu M, Xu F, Yuan W, Huang R, Guo P. Development and evaluation of a broadly reactive reverse transcription recombinase polymerase amplification assay for rapid detection of murine norovirus. BMC Vet Res 2018; 14:399. [PMID: 30547776 PMCID: PMC6295035 DOI: 10.1186/s12917-018-1736-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Murine norovirus (MNV) is recognized as the most prevalent viral pathogen in captive mouse colonies. The rapid detection assay for MNV would be a useful tool for monitoring and preventing MNV infection. A recombinase polymerase amplification (RPA) assay was established in this study to provide a solution for rapid and sensitive detection of MNV. Results The detection limit of the RT-RPA assay for the detection of MNV was 1 × 102 copies of RNA molecules per reaction. The assay was specific since there was no cross-reaction with other common murine viruses. In addition, the broad reactivity of the RT-RPA assay was validated using the synthesized template carrying seven point mutations among several MNV strains. The MNV RT-RPA assay could detect as few as 1 × 102 copies of the mutant per reaction, suggesting the assay could be broadly reactive against a large diversity of MNV strains. Forty eight clinical samples including 16 gastric tissue specimens, 16 cecal tissue specimens and 16 fecal specimens were tested for the validation of the new developed RT-RPA assay. The detection results of RT-RPA and RT-qPCR for clinical samples were very similar, except that a gastric tissue sample which was positive by RT-qPCR, with a RNA titer of 27 copies, was negative by RT-RPA. Conclusions A broadly reactive RT-RPA assay was successfully established for MNV detection.
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Affiliation(s)
- Lei Ma
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Fanwen Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510640, China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Bihong Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yujun Zhu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Miaoli Wu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Fengjiao Xu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Wen Yuan
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Ren Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Pengju Guo
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China.
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KARABASANAVAR NAGAPPA, BAGALKOTE PRASHANTHS, RAJASHEKARA DB, MANJUNATHA SS, VEERANNA KC. Phylogenetic analysis of Orf virus associated with contagious ecthyma (orf) outbreak in Tellicherry goats (Capra hircus). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i2.79288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Orf virus (ORFV) is a member of genus Parapoxvirus that causes contagious ecthyma in goats. A pox-like disease was investigated in Tellicherry goats (31 female) maintained at a semi-organized farm. History revealed recent introduction of Tellicherry goats for breeding purpose and housing of the new entrants in to a farm already having a mild form of pox-like disease. Newly introduced and stressed Tellicherry goats developed severe form of infection with 100% morbidity. Affected goats showed lesions around lips (100%), commissure (53%) and oral cavity (65%); exanthematic dermatitis was evident in 94% of the affected goats followed by ulceration (47%) and nodular lesions (24%). Scab samples were collected from affected goats to confirm the clinical diagnosis. Genus Parapoxvirus was confirmed by the amplification of specific 594 bp and 235 bp amplicons. Further, Orf virus specific amplicon of size 1,206 bp was also amplified for the confirmation. Sequence analysis of PCR amplicons showed close resemblance of the outbreak strain with reported Indian Orf virus isolates. Based on the homology of the outer envelope protein B2L gene sequence of Orf virus, the source of infection to the Tellicherry goats was traced to the local goat. Although Orf virus is zoonotic; however, no occupational transmission was noticed in the present outbreak.
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Cheng HY, Li WJ, Li XM, Fan QL, Tang XD, Liu MJ, Ma WT, Chen DK. Pathogenicity of blood orf virus isolates in the development of dairy goat contagious pustular dermatitis. Vet Microbiol 2018; 219:178-182. [PMID: 29778194 DOI: 10.1016/j.vetmic.2018.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/09/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022]
Abstract
Contagious pustular dermatitis is an exanthematous zoonotic disease caused by the orf virus. Pandemic outbreaks of this disease cause great economic losses, while the pathogenesis of this disease still remains obscure. In this study, blood samples were collected from 628 asymptomatic goats across China for PCR-based virus detection. We detected the orf virus in the blood of asymptomatic goats. Moreover, the orf virus obtained from the blood of infected goats was infectious and induced typical symptoms of contagious pustular dermatitis after inoculation of uninfected dairy goats. In summary, our data provide evidence that asymptomatic animals may be carriers of orf virus. Our findings should contribute to elucidating the details underlying the pathogenesis of contagious pustular dermatitis.
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Affiliation(s)
- Hong-Yu Cheng
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China
| | - Wei-Juan Li
- Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Xing-Ming Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China
| | - Qin-Lei Fan
- China Animal Health and Epidemiology Center, Qingdao 266032, Shandong Province, China
| | - Xi-Dian Tang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China
| | - Ming-Jie Liu
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China
| | - Wen-Tao Ma
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China.
| | - De-Kun Chen
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling 712100, Shaanxi Province, China.
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Rapid Detection of Vibrio parahaemolyticus in Shellfish by Real-Time Recombinase Polymerase Amplification. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1188-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Recombinase polymerase amplification combined with lateral flow dipstick for equipment-free detection of Salmonella in shellfish. Bioprocess Biosyst Eng 2018; 41:603-611. [PMID: 29349550 DOI: 10.1007/s00449-018-1895-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/11/2018] [Indexed: 12/20/2022]
Abstract
Salmonella is a major pathogen that causes acute foodborne outbreaks worldwide. Seafood, particularly shellfish, is a proven source of Salmonella spp. infection because many people prefer to eat it raw or lightly cooked. However, traditional identification methods are too time-consuming and complex to detect contamination of bacteria in the food chain in a timely manner, and few studies have aimed to identify Salmonella in shellfish early in the supply chain. We herein developed a method for rapid detection of Salmonella in shellfish based on the method of recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD), which targets the invasion gene A (invA). The RPA-LFD was able to function at 30-45 °C, and at the temperature of 40 °C, it only took 8 min of amplification to reach the test threshold of amplicons. The established method had both a good specificity and a sensitivity of 100 fg DNA per reaction (20 µL). Regarding practical performance, RPA-LFD performed better than real-time PCR. Another advantage of RPA-LFD is that it was capable of being performed without expensive equipments. Thus, RPA-LFD has potential for further development as a detection kit for Salmonella in shellfish and other foods under field conditions.
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Abstract
Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
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Affiliation(s)
- Ivan Magriñá Lobato
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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Bonney LC, Watson RJ, Afrough B, Mullojonova M, Dzhuraeva V, Tishkova F, Hewson R. A recombinase polymerase amplification assay for rapid detection of Crimean-Congo Haemorrhagic fever Virus infection. PLoS Negl Trop Dis 2017; 11:e0006013. [PMID: 29028804 PMCID: PMC5656326 DOI: 10.1371/journal.pntd.0006013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/25/2017] [Accepted: 10/04/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Crimean-Congo Haemorrhagic fever Virus (CCHFV) is a rapidly emerging vector-borne pathogen and the cause of a virulent haemorrhagic fever affecting large parts of Europe, Africa, the Middle East and Asia. METHODOLOGY/PRINCIPLE FINDINGS An isothermal recombinase polymerase amplification (RPA) assay was successfully developed for molecular detection of CCHFV. The assay showed rapid (under 10 minutes) detection of viral extracts/synthetic virus RNA of all 7 S-segment clades of CCHFV, with high target specificity. The assay was shown to tolerate the presence of inhibitors in crude preparations of mock field samples, indicating that this assay may be suitable for use in the field with minimal sample preparation. The CCHFV RPA was successfully used to screen and detect CCHFV positives from a panel of clinical samples from Tajikistan. CONCLUSIONS/SIGNIFICANCE The assay is a rapid, isothermal, simple-to-perform molecular diagnostic, which can be performed on a light, portable real-time detection device. It is ideally placed therefore for use as a field-diagnostic or in-low resource laboratories, for monitoring of CCHF outbreaks at the point-of-need, such as in remote rural regions in affected countries.
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Affiliation(s)
- Laura C. Bonney
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
- * E-mail:
| | - Robert J. Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Babak Afrough
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Manija Mullojonova
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Viktoriya Dzhuraeva
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Farida Tishkova
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
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Yang Y, Qin X, Zhang X, Zhao Z, Zhang W, Zhu X, Cong G, Li Y, Zhang Z. Development of real-time and lateral flow dipstick recombinase polymerase amplification assays for rapid detection of goatpox virus and sheeppox virus. Virol J 2017; 14:131. [PMID: 28716095 PMCID: PMC5514530 DOI: 10.1186/s12985-017-0792-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/03/2017] [Indexed: 12/31/2022] Open
Abstract
Background Goatpox virus (GTPV) and sheeppox virus (SPPV), which belong to the Capripoxvirus (CaPV), are economically important pathogens of small ruminants. Therefore, a sensitive, specific and rapid diagnostic assay for detection of GTPV and SPPV is necessary to accurately and promptly control these diseases. Methods Recombinase polymerase amplification (RPA) assays combined with a real-time fluorescent detection (real-time RPA assay) and lateral flow dipstick (RPA LFD assay) were developed targeting the CaPV G-protein-coupled chemokine receptor (GPCR) gene, respectively. Results The sensitivity of both CaPV real-time RPA assay and CaPV RPA LFD assay were 3 × 102 copies per reaction within 20 min at 38 °C. Both assays were highly specific for CaPV, with no cross-reactions with peste des petits ruminants virus, foot-and-mouth disease virus and Orf virus. The evaluation of the performance of these two assays with clinical sample (n = 107) showed that the CaPV real-time RPA assay and CaPV RPA LFD assay were able to specially detect SPPV or GTPV present in samples of ovine in liver, lung, kidney, spleen, skin and blood. Conclusions This study provided a highly time-efficient and simple alternative for rapid detection of GTPV and SPPV. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0792-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Xiaodong Qin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Xiangle Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Zhixun Zhao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Wei Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Xueliang Zhu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Guozheng Cong
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China
| | - Yanmin Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China.
| | - Zhidong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, China.
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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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Yang Y, Qin X, Song Y, Zhang W, Hu G, Dou Y, Li Y, Zhang Z. Development of real-time and lateral flow strip reverse transcription recombinase polymerase Amplification assays for rapid detection of peste des petits ruminants virus. Virol J 2017; 14:24. [PMID: 28173845 PMCID: PMC5297045 DOI: 10.1186/s12985-017-0688-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 01/18/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Peste des petits ruminants (PPR) is an economically important, Office International des Epizooties (OIE) notifiable, transboundary viral disease of small ruminants such as sheep and goat. PPR virus (PPRV), a negative-sense single-stranded RNA virus, is the causal agent of PPR. Therefore, sensitive, specific and rapid diagnostic assay for the detection of PPRV are necessary to accurately and promptly diagnose suspected case of PPR. METHODS In this study, reverse transcription recombinase polymerase amplification assays using real-time fluorescent detection (real-time RT-RPA assay) and lateral flow strip detection (LFS RT-RPA assay) were developed targeting the N gene of PPRV. RESULTS The sensitivity of the developed real-time RT-RPA assay was as low as 100 copies per reaction within 7 min at 40 °C with 95% reliability; while the sensitivity of the developed LFS RT-RPA assay was as low as 150 copies per reaction at 39 °C in less than 25 min. In both assays, there were no cross-reactions with sheep and goat pox viruses, foot-and-mouth disease virus and Orf virus. CONCLUSIONS These features make RPA assay promising candidates either in field use or as a point of care diagnostic technique.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Xiaodong Qin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Yiming Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Wei Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Gaowei Hu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Yanmin Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Zhidong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Xujiaping 1, Lanzhou, 730046, Gansu, China.
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37
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Yang Y, Qin X, Zhang W, Li Y, Zhang Z. Rapid and specific detection of porcine parvovirus by isothermal recombinase polymerase amplification assays. Mol Cell Probes 2016; 30:300-305. [DOI: 10.1016/j.mcp.2016.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/12/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
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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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Yang Y, Qin X, Wang G, Jin J, Shang Y, Zhang Z. Development of an isothermoal amplification-based assay for rapid visual detection of an Orf virus. Virol J 2016; 13:46. [PMID: 26993468 PMCID: PMC4799565 DOI: 10.1186/s12985-016-0502-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/11/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Orf virus (ORFV) is the causative agent of a severe infectious skin disease (also known as contagious ecthyma) in goats, sheep and other small ruminants. Importantly, ORFV also infect humans which causes a public health concern in the context of changing environment and increase in human populations. The rapid detection is critical in effective control of the disease and urgently needed. RESULTS A novel "point of care" molecular amplification assay for rapid visual detection of ORFV was developed based on isothermoal recombinase polymerase amplification (RPA) technology in combination with a simpler lateral flow immunoassay strip (ORFV RPA- LFD assay). The developed ORFV RPA- LFD assay was able to detect ORFV in less than 25 min. This assay was highly sensitive, with detection limit of as low as 80 copies/reaction, and highly specific, with no cross-reactions with capripox virus, foot-and-mouth disease virus and peste des petits ruminants virus. Furthermore, the ORFV RPA- LFD assay has good correlation with qPCR assay for detection of ORFV present in clinical samples. CONCLUSIONS The developed ORFV RPA-LFD assay was a sensitive and specific method for rapid detection of ORFV, and has great potential as an onsite molecular diagnostic tool in control of Orf.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China
| | - Xiaodong Qin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China
| | - Guangxiang Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China
| | - Jiaxin Jin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China.,School of Life Science, Lanzhou University, Lanzhou, Gansu, China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China
| | - Zhidong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, Gansu, China.
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