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Zhang Z, Zhang Z, Wang C, Zhai X, Wang W, Chen X, Zhang T. Detection method for reverse transcription recombinase-aided amplification of avian influenza virus subtypes H5, H7, and H9. BMC Vet Res 2024; 20:203. [PMID: 38755641 PMCID: PMC11097555 DOI: 10.1186/s12917-024-04040-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Avian influenza virus (AIV) not only causes huge economic losses to the poultry industry, but also threatens human health. Reverse transcription recombinase-aided amplification (RT-RAA) is a novel isothermal nucleic acid amplification technology. This study aimed to improve the detection efficiency of H5, H7, and H9 subtypes of AIV and detect the disease in time. This study established RT-RAA-LFD and real-time fluorescence RT-RAA (RF-RT-RAA) detection methods, which combined RT-RAA with lateral flow dipstick (LFD) and exo probe respectively, while primers and probes were designed based on the reaction principle of RT-RAA. RESULTS The results showed that RT-RAA-LFD could specifically amplify H5, H7, and H9 subtypes of AIV at 37 °C, 18 min, 39 °C, 20 min, and 38 °C, 18 min, respectively. The sensitivity of all three subtypes for RT-RAA-LFD was 102 copies/µL, which was 10 ∼100 times higher than that of reverse transcription polymerase chain reaction (RT-PCR) agarose electrophoresis method. RF-RT-RAA could specifically amplify H5, H7, and H9 subtypes of AIV at 40 °C, 20 min, 38 °C, 16 min, and 39 °C, 17 min, respectively. The sensitivity of all three subtypes for RF-RT-RAA was 101 copies/µL, which was consistent with the results of real-time fluorescence quantification RT-PCR, and 100 ∼1000 times higher than that of RT-PCR-agarose electrophoresis method. The total coincidence rate of the two methods and RT-PCR-agarose electrophoresis in the detection of clinical samples was higher than 95%. CONCLUSIONS RT-RAA-LFD and RF-RT-RAA were successfully established in this experiment, with quick response, simple operation, strong specificity, high sensitivity, good repeatability, and stability. They are suitable for the early and rapid diagnosis of Avian influenza and they have positive significance for the prevention, control of the disease, and public health safety.
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Affiliation(s)
- Zongshu Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Zichuang Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chunguang Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xianghe Zhai
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Wenjing Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xi Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Tie Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China.
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2
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Mao X, Xu M, Luo S, Yang Y, Zhong J, Zhou J, Fan H, Li X, Chen Z. Advancements in the synergy of isothermal amplification and CRISPR-cas technologies for pathogen detection. Front Bioeng Biotechnol 2023; 11:1273988. [PMID: 37885449 PMCID: PMC10598474 DOI: 10.3389/fbioe.2023.1273988] [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: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
In the realm of pathogen detection, isothermal amplification technology has emerged as a swift, precise, and sensitive alternative to conventional PCR. This paper explores the fundamental principles of recombinase polymerase amplification (RPA) and recombinase-aid amplification (RAA) and reviews the current status of integrating the CRISPR-Cas system with RPA/RAA techniques. Furthermore, this paper explores the confluence of isothermal amplification and CRISPR-Cas technology, providing a comprehensive review and enhancements of existing combined methodologies such as SHERLOCK and DETECTR. We investigate the practical applications of RPA/RAA in conjunction with CRISPR-Cas for pathogen detection, highlighting how this integrated approach significantly advances both research and clinical implementation in the field. This paper aims to provide readers with a concise understanding of the fusion of RPA/RAA and CRISPR-Cas technology, offering insights into their clinical utility, ongoing enhancements, and the promising prospects of this integrated approach in pathogen detection.
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Affiliation(s)
- Xiaolei Mao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Minghui Xu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shuyin Luo
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yi Yang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiaye Zhong
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiawei Zhou
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Huayan Fan
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Zhi Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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3
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Cui H, Zhang C, Tu F, Zhao K, Kong Y, Pu J, Zhang L, Chen Z, Sun Y, Wei Y, Liang C, Liu J, Liu J, Guo Z. Rapid detection of influenza A viruses using a real-time reverse transcription recombinase-aided amplification assay. Front Cell Infect Microbiol 2023; 12:1071288. [PMID: 36683681 PMCID: PMC9849684 DOI: 10.3389/fcimb.2022.1071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Influenza A viruses (IAVs) are important pathogens of respiratory infections, causing not only seasonal influenza but also influenza pandemics and posing a global threat to public health. IAVs infection spreads rapidly, widely, and across species, causing huge losses, especially zoonotic IAVs infections that are more harmful. Fast and sensitive detection of IAVs is critical for controlling the spread of this disease. Methods Here, a real-time reverse transcription recombinase-aided amplification (real-time RT-RAA) assay targeting conserved positions in the matrix protein gene (M gene) of IAVs, is successfully established to detect IAVs. The assay can be completed within 20 min at 42°C. Results The sensitivity of the real-time RT-RAA assay was 142 copies per reaction at 95% probability, which was comparable to the sensitivity of the RT-qPCR assay. The specificity assay showed that the real-time RT-RAA assay was specific to IAVs, and there was no cross-reactivity with other important viruses. In addition, 100%concordance between the real-time RT-RAA and RT-qPCR assays was achieved after testing 120 clinical specimens. Discussion The results suggested that the real-time RT-RAA assay we developed was a specific, sensitive and reliable diagnostic tool for the rapid detection of IAVs.
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Affiliation(s)
- Huan Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
- College of Animal Medicine, Jilin University, Changchun, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Fei Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Kui Zhao
- College of Animal Medicine, Jilin University, Changchun, China
| | - Yunyi Kong
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Jie Pu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Lei Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Zhaoliang Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuanyuan Sun
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yujie Wei
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Chuncai Liang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
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4
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Cui H, Tu F, Zhang C, Zhang C, Zhao K, Liu J, Dong S, Chen L, Liu J, Guo Z. Real-Time Reverse Transcription Recombinase-Aided Amplification Assay for Rapid Amplification of the N Gene of SARS-CoV-2. Int J Mol Sci 2022; 23:ijms232315269. [PMID: 36499594 PMCID: PMC9736922 DOI: 10.3390/ijms232315269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/08/2022] Open
Abstract
COVID-19 was officially declared a global pandemic disease on 11 March 2020, with severe implications for healthcare systems, economic activity, and human life worldwide. Fast and sensitive amplification of the severe acute respiratory syndrome virus 2 (SARS-CoV-2) nucleic acids is critical for controlling the spread of this disease. Here, a real-time reverse transcription recombinase-aided amplification (RT-RAA) assay, targeting conserved positions in the nucleocapsid protein gene (N gene) of SARS-CoV-2, was successfully established for SARS-CoV-2. The assay was specific to SARS-CoV-2, and there was no cross-reaction with other important viruses. The sensitivity of the real-time RT-RAA assay was 142 copies per reaction at 95% probability. Furthermore, 100% concordance between the real-time RT-RAA and RT-qPCR assays was achieved after testing 72 clinical specimens. Further linear regression analysis indicated a significant correlation between the real-time RT-RAA and RT-qPCR assays with an R2 value of 0.8149 (p < 0.0001). In addition, the amplicons of the real-time RT-RAA assay could be directly visualized by a portable blue light instrument, making it suitable for the rapid amplification of SARS-CoV-2 in resource-limited settings. Therefore, the real-time RT-RAA method allows the specific, sensitive, simple, rapid, and reliable detection of SARS-CoV-2.
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Affiliation(s)
- Huan Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- College of Animal Medicine, Jilin University, Changchun 130062, China
| | - Fei Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Cheng Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Chunmao Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Kui Zhao
- College of Animal Medicine, Jilin University, Changchun 130062, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Shishan Dong
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Ligong Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- Correspondence: (J.L.); (Z.G.); Tel.: +86-431-86985932 (J.L.); +86-431-86985975 (Z.G.)
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- Correspondence: (J.L.); (Z.G.); Tel.: +86-431-86985932 (J.L.); +86-431-86985975 (Z.G.)
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5
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Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus. Microorganisms 2022; 10:microorganisms10122351. [PMID: 36557604 PMCID: PMC9784193 DOI: 10.3390/microorganisms10122351] [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: 09/04/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p < 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p < 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.
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6
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Wang Y, Nie M, Deng H, Lai S, Zhou Y, Sun X, Zhu L, Xu Z. Establishment of a reverse transcription recombinase-aided amplification detection method for porcine group a rotavirus. Front Vet Sci 2022; 9:954657. [PMID: 36187816 PMCID: PMC9519424 DOI: 10.3389/fvets.2022.954657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine rotavirus type A (PoRVA) is the main cause of dehydration and diarrhea in piglets, which has a great impact on the development of the pig industry worldwide. A rapid, accurate and sensitive detection method is conducive to the monitoring, control, and removal of PoRVA. In this study, a PoRVA real-time fluorescent reverse transcription recombinase-aided amplification (RT-RAA) assay was developed. Based on the PoRVA VP6 gene, specific primers and probes were designed and synthesized. The sensitivity of RT-RAA and TaqMan probe-based RT-qPCR was 7 copies per reaction and 5 copies per reaction, respectively. The sensitivity of the RT-RAA method was close to TaqMan probe-based RT-qPCR. The detection results of RT-RAA and TaqMan probe-based quantitative real-time RT-PCR methods were completely consistent in 241 clinical samples. Therefore, we successfully established a rapid and specific RT-RAA diagnostic method for PoRVA.
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Affiliation(s)
- Yushun Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mincai Nie
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huidan Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yuancheng Zhou
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xiangan Sun
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine Sichuan Key Laboratory of Animal Epidemic Disease and Human Health, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- College of Veterinary Medicine Sichuan Key Laboratory of Animal Epidemic Disease and Human Health, Sichuan Agricultural University, Chengdu, China
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7
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Zhao J, Li Y, Xue Q, Zhu Z, Zou M, Fang F. A novel rapid visual detection assay for Toxoplasma gondii combining recombinase-aided amplification and lateral flow dipstick coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD). Parasite 2022; 29:21. [PMID: 35420541 PMCID: PMC9009239 DOI: 10.1051/parasite/2022021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Toxoplasmosis, a parasitic disease resulting from Toxoplasma gondii infection, remains prevalent worldwide, and causes great harm to immunodepressed patients, pregnant women and newborns. Although various molecular approaches to detect T. gondii infection are available, they are either costly or technically complex. This study aimed at developing a rapid visual detection assay using recombinase-aided amplification (RAA) and lateral flow dipstick (LFD) coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD) to detect T. gondii. The RAA-Cas13a-LFD assay was performed in an incubator block at 37 °C within 2 h, and the amplification results were visualized and determined through LFD by the naked eye. The detection limit was 1 × 10-6 ng/μL by our developed RAA-Cas13a-LFD protocol, 100-fold higher than that by qPCR assay (1 × 10-8 ng/μL). No cross-reaction occurred either with the DNA of human blood or Ascaris lumbricoides, Digramma interrupta, Entamoeba coli, Fasciola gigantica, Plasmodium vivax, Schistosoma japonicum, Taenia solium, and Trichinella spiralis, and the positive rate by RAA-Cas13a-LFD assay was identical to that by qPCR assay (1.50% vs. 1.50%) in detecting T. gondii infection in the unknown blood samples obtained from clinical settings. Our findings demonstrate that this RAA-Cas13a-LFD assay is not only rapid, sensitive, and specific and allows direct visualization by the naked eye, but also eliminates sophisticated and costly equipment. More importantly, this technique can be applied to on-site surveillance of T. gondii.
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Affiliation(s)
- Jinhong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China - Provincial Key Laboratory of Active Biological Macro-Molecules, Wuhu 241002, Anhui, China
| | - Yuanyuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Qiqi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhiwei Zhu
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Minghui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Fang Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
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8
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Five years of porcine circovirus 3: what have we learned about the clinical disease, immune pathogenesis, and diagnosis. Virus Res 2022; 314:198764. [DOI: 10.1016/j.virusres.2022.198764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/24/2022]
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9
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Bian Z, Cai R, Jiang Z, Song S, Li Y, Chu P, Zhang K, Yang D, Gou H, Li C. Single Multiple Cross Displacement Amplification for Rapid and Real-Time Detection of Porcine Circovirus 3. Front Vet Sci 2021; 8:726723. [PMID: 34540937 PMCID: PMC8448386 DOI: 10.3389/fvets.2021.726723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2016, a novel porcine circovirus, PCV3, has been infecting pigs, causing significant economic losses to the pig industry. In recent years, the infection rate of PCV3 has been increasing, and thus rapid and accurate detection methods for PCV3 are essential. In this study, we established a novel probe-based single multiple cross displacement amplification (P-S-MCDA) method for PCV3. The method was termed as P-S-MCDA. The P-S-MCDA uses seven primers to amplify the capsid gene, and the assay can be performed at 60°C for 30 min, greatly shortening the reaction time. The results of P-S-MCDA can not only be monitored in real time through fluorescence signals but also be determined by observing the fluorescence of the reaction tubes using a smartphone-based cassette. This method demonstrated good specificity and the same sensitivity as qPCR, with a minimum detection limit of 10 copies. In 139 clinical samples, the coincidence rate with qPCR was 100%. The P-S-MCDA can be widely applied in PCV3 detection in laboratories or in rural areas.
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Affiliation(s)
- Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Rujian Cai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
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10
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Zhang W, Xu L, Liu Q, Cao Y, Yang K, Song X, Shao Y, Tu J, Qi K. Enzymatic recombinase amplification coupled with CRISPR-Cas12a for ultrasensitive, rapid, and specific Porcine circovirus 3 detection. Mol Cell Probes 2021; 59:101763. [PMID: 34509634 DOI: 10.1016/j.mcp.2021.101763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/28/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022]
Abstract
Porcine circovirus type 3 (PCV3) is a disease associated with porcine dermatitis and nephrotic syndrome (PDNS) that has caused significant economic losses to swine herds since its discovery in 2016. To develop a simple, on-site, rapid, and sensitive assay to combat the spread of PCV3, we optimized the CRISPR/Cas12a (also known as Cpf1) system combined with enzymatic recombinase amplification (ERA) nucleic acid amplification to diagnose PCV3. The results showed that the ERA-CRISPR/Cas12a reaction could detect PCV3 within 1 h in genomic DNA harboring a minimum of seven copies. Additionally, we confirmed no cross-reactivity with PCV2, PCV4, or other porcine viruses, revealing the good specificity of this technique. These results demonstrated the ability of ERA-CRISPR/Cas12a to detect DNA at the single-molecule level and provide a rapid, simple, ultrasensitive, one-pot point-of-care test for PCV3 and suggest its potential for a variety of nucleic acid detection applications.
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Affiliation(s)
- Wuyin Zhang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Liang Xu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Qi Liu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yingli Cao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Kankan Yang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China.
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Shushan District West Yangtze River Road 130#, Hefei, 230036, Anhui Province, People's Republic of China.
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11
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Tu F, Zhang Y, Xu S, Yang X, Zhou L, Ge X, Han J, Guo X, Yang H. Detection of pseudorabies virus with a real-time recombinase-aided amplification assay. Transbound Emerg Dis 2021; 69:2266-2274. [PMID: 34273259 DOI: 10.1111/tbed.14241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
Pseudorabies (PR) is an acute infectious disease of pigs caused by pseudorabies virus (PRV), which has caused great economic losses to the pig industry worldwide. Reliable and timely diagnose is crucial for the surveillance, control and eradication of PR. Here, a real-time fluorescent recombinase-aided amplification (real-time RAA) assay was established to detect PRV. Primers and probes were designed based on the conserved regions of the PRV gE gene. The assay was specific for the detection of wild-type PRV, showing no cross-reactivity with other important porcine viruses (including PRV gE-deleted vaccine strains). Analytical sensitivity of the assay was three 50% tissue culture infectious doses (TCID50 ) of PRV DNA per reaction with 95% reliability, which is comparable to that of a PRV-specific real-time PCR (qPCR) assay. In diagnosis of 206 clinical tissue samples, the diagnose accordance rate between the real-time RAA assay and qPCR assay was 97.57% (201/206). Interestingly, the amplified products of real-time RAA could be visualized under a portable blue light instrument, making it possible for the rapid detection of PRV in resource-limited settings and on-site screening. Therefore, our developed real-time RAA assay is a diagnostic method for the rapid detection of PRV in the field.
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Affiliation(s)
- Fei Tu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Shengkui Xu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xintan Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
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12
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He Z, Tong Z, Tan B, He X, Zhang T, Guo Y, Jin L, He N, Li S, Chen Z. Rapid Detection of DNA Methylation with a Novel Real-Time Fluorescence Recombinase-Aided Amplification Assay. J Biomed Nanotechnol 2021; 17:1364-1370. [PMID: 34446139 DOI: 10.1166/jbn.2021.3111] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Researchers have conducted in-depth research on DNA methylation mechanism, which is related to various diseases such as deficiency of imprinted gene and occurrence of tumors. This study provides a novel rapid quantitative detection assay and real-time fluorescence recombinase-aided amplification assay (RAA) for DNA methylation. Firstly, specific sequence of methylation genes was chosen and primers and fluorogenic probe for RAA experiment were designed and synthesized. Lastly, these amplification products were proven by sequencing and analysis. Results showed that the amplification efficiency and template concentration of RAA had linear dependent (R² > 95%) when the concentration range was 4.64×108 copies/μL˜4.64×10⁴ copies/μL. The test assay can also detect positive samples when the template concentration is below 4.64×10⁴ copies/μL. Remarkably, the entire experiment process only takes 15-20 minutes, so it is beneficial for rapid bedside simple screening of some special DNA methylation sites, such as detection of resistance genes. In a word, this method has very great potential for diseases with DNA methylation in clinical settings, especially if methylation analysis needs to be done quickly and easily.
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Affiliation(s)
- Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Zengrui Tong
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Boyu Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Xuliang He
- Department of General Surgery, People's Hospital of Zhuzhou City Affiliated to Changsha Medical College, Zhuzhou 412011, P. R. China
| | - Tao Zhang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yuan Guo
- Department of Laboratory, Central Hospital of Zhuzhou City, Zhuzhou 412007, P. R. China
| | - Lian Jin
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
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13
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Qin Z, Xiang X, Xue L, Cai W, Gao J, Yang J, Liang Y, Wang L, Chen M, Pang R, Li Y, Zhang J, Hu Y, Wu Q. Development of a novel RAA-based microfluidic chip for absolute quantitative detection of human norovirus. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Qin Z, Xue L, Cai W, Gao J, Jiang Y, Yang J, Liang Y, Wang L, Zhang J, Hu Y, Wu Q. Development of a recombinase-aided amplification assay for rapid detection of human norovirus GII.4. BMC Infect Dis 2021; 21:248. [PMID: 33750333 PMCID: PMC7941963 DOI: 10.1186/s12879-021-05942-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/28/2021] [Indexed: 12/28/2022] Open
Abstract
Background Human noroviruses are one of the main causes of foodborne illnesses and represent a serious public health concern. Rapid and sensitive assays for human norovirus detection are undoubtedly necessary for clinical diagnosis, especially in regions without more sophisticated equipment. Method The rapid reverse transcription recombinase-aided amplification (RT-RAA) is a fast, robust and isothermal nucleic acid detection method based on enzyme reaction. This method can complete the sample detection at 39 °C in 30 min. In this study, we successfully established a rapid reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of human norovirus GII.4 and applied this assay to clinical samples, as well as comparison with commercial reverse transcription real-time fluorescence quantitative PCR (RT-qPCR). Results At 95% probability, the detection sensitivity of RT-RAA was 3.425 log10 genomic copies (LGC)/reaction. Moreover, no cross-reaction was observed with other norovirus genogroups and other common foodborne viruses. Stool samples were examined by RT-RAA and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). Compared of RT-qPCR, kappa values for human norovirus detection with RT-RAA were 0.894 (p < 0.001), indicating that both assays were in agreement. Conclusion This RT-RAA assay provides a rapid, specific, and sensitive assay for human norovirus detection and is suitable for clinical testing.
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Affiliation(s)
- Zhiwei Qin
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.,Faculty Agriculture and Food, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Weicheng Cai
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Jiale Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yanhui Liang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Linping Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yongdan Hu
- Faculty Agriculture and Food, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.
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15
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Tu F, Yang X, Xu S, Chen D, Zhou L, Ge X, Han J, Zhang Y, Guo X, Yang H. Development of a fluorescent probe-based real-time reverse transcription recombinase-aided amplification assay for the rapid detection of classical swine fever virus. Transbound Emerg Dis 2020; 68:2017-2027. [PMID: 32979245 DOI: 10.1111/tbed.13849] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/05/2020] [Accepted: 09/17/2020] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF), which is caused by the CSF virus (CSFV), remains one of the most economically important diseases of the global swine industry. Rapid and reliable detection of CSFV is critical for controlling CSF. In this study, a novel fluorescent probe-based real-time reverse transcription recombinase-aided amplification (rRT-RAA) assay, targeting a highly conserved position within the 5' non-translated region (5'NTR) among all CSFV genotypes, was developed for the detection of CSFV. The assay is highly specific to CSFV and does not cross react with other important viruses. Sensitivity analysis revealed that the assay could detect two 50% tissue culture infectious dose (TCID50 ) of CSFV RNA per reaction at 95% probability, which is comparable to that of a documentary reverse transcription quantitative PCR (RT-qPCR) assay for CSFV. The rRT-RAA assay exhibited good reproducibility, with intra- and inter-assay coefficient of variation values of <8.0%. Of the 135 samples (including 102 clinical tissue samples and 33 different cell culture isolates of CSFV), 50 and 52 samples were tested positive for CSFV by rRT-RAA and RT-qPCR, respectively. The coincidence rate between the two assays was 98.5% (133/135). Further linear regression analysis showed a significant correlation between the rRT-RAA and RT-qPCR assays with an R2 value of 0.8682. Interestingly, the amplification products of the rRT-RAA assay could be directly observed with naked eyes under a portable blue light imager, making it possible for an on-site testing. Our results indicate that the rRT-RAA assay is a robust diagnostic tool for the rapid detection of CSFV.
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Affiliation(s)
- Fei Tu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xintan Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Shengkui Xu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Dengjin Chen
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
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