1
|
Zhu Y, Zhang M, Jie Z, Guo S, Zhu Z, Tao SC. Strategic nucleic acid detection approaches for diagnosing African swine fever (ASF): navigating disease dynamics. Vet Res 2024; 55:131. [PMID: 39375775 PMCID: PMC11460097 DOI: 10.1186/s13567-024-01386-8] [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: 06/12/2024] [Accepted: 09/04/2024] [Indexed: 10/09/2024] Open
Abstract
African swine fever (ASF) is a devastating disease caused by African swine fever virus (ASFV) and leads to significant economic losses in the pig farming industry. Given the absence of an effective vaccine or treatment, the mortality rate of ASF is alarmingly close to 100%. Consequently, the ability to rapidly and accurately detect ASFV on site and promptly identify infected pigs is critical for controlling the spread of this pandemic. The dynamics of the ASF virus load and antibody response necessitate the adoption of various detection strategies at different stages of infection, a topic that has received limited attention to date. This review offers detailed guidance for choosing appropriate ASF diagnostic techniques tailored to the clinical manifestations observed from the acute to chronic phases, including asymptomatic cases. We comprehensively summarize and evaluate the latest advancements in ASFV detection methods, such as CRISPR-based diagnostics, biosensors, and microfluidics. Additionally, we address the challenges of false negatives or positives due to ASF variants or the use of injected live attenuated vaccines. This review provides an exhaustive list of diagnostic tests suitable for detecting each stage of symptoms and potential target genes for developing new detection methods. In conclusion, we highlight the current challenges and future directions in ASFV detection, underscoring the need for continued research and innovation in this field.
Collapse
Affiliation(s)
- Yuanshou Zhu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
- Center of Community-Based Health Research, Fudan University, Shanghai, 200240, China
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhigang Zhu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
2
|
Xu J, Wang Y, Zhang Y, Wang S, Su N, Chang X, Ren W, Zou Y, Liu S, Li L, Li J, Bao J, Wang Z. Establishment of a RAA-CRISPR Cas12a based diagnostic method for peste des petits ruminants virus N gene and M gene. J Virol Methods 2024; 329:114971. [PMID: 38876255 DOI: 10.1016/j.jviromet.2024.114971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
Peste des petis ruminants (PPR) is an acute, highly contagious fatal disease affecting both domestic and wild small ruminants, caused by Morbillivirus caprinae (also known as peste des petis ruminants virus (PPRV)). Herein, a rapid method based on recombinase aided amplification-clustered regularly interspaced short palindromic repeats-Cas12a (RAA-CRISPR Cas12a) to detect PPRV was developed. CRISPR RNAs and RAA primers for PPRV-N (nucleocapsid) and PPRV-M (matrix) fragments were designed. The reaction system was constructed following screening and optimization. Detection could be completed within in 50 minutes at 37°C. Detection of gradient dilutions of plasmids carrying of PPRV N and M gene fragments indicated a minimum limit of detection of 10 copies/μL. There were no cross-reactions with related viruses and all tested lineages of PPRV were detected successfully. The method also showed good repeatability. The detection of clinical samples (previously detected using reverse transcription polymerase chain reaction (RT-PCR)) indicated good consistency between the RAA-CRISPR Cas12a method and RT-PCR. Thus, the RAA-CRISPR Cas12a method for rapid PPRV diagnosis has strong specificity, high sensitivity, and stable repeatability. Moreover, the results can be observed visually under blue or UV light or using lateral flow strips without complex instruments.
Collapse
Affiliation(s)
- Jiao Xu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | | | - Shujuan Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Na Su
- Qingdao Agricultural University, Qingdao, China
| | - Xing Chang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Weijie Ren
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yanli Zou
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shan Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jingyue Bao
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China.
| |
Collapse
|
3
|
Jiang G, Yang X, Li Z, Mao J, Zeng P, Wang D, Wu Z, Liu C, Qiu Y, Cui Y, Zhou J, Liu J, Hou L. Recombinant Polymerase Amplification Coupled with CRISPR/Cas12a Detection System for Rapid Visual Detection of Porcine Circovirus 3. Animals (Basel) 2024; 14:2527. [PMID: 39272312 PMCID: PMC11393983 DOI: 10.3390/ani14172527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/18/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
The porcine circovirus type 3 (PCV3) infection is an emerging disease associated with clinical signs of porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs. Currently, there is a lack of effective vaccines and therapeutics against this disease. Therefore, rapid, effective, sensitive, and specific detection methods are crucial for the timely identification, prevention, and control of PCV3. In this study, we developed one- and two-pot visual detection methods for PCV3 using a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas12a detection system combined with recombinase polymerase amplification (RPA). These two methods demonstrated no cross-reactivity with eight other swine viruses and exhibited minimum detection limits of five and two copies of viral DNA, respectively, revealing their high specificity and sensitivity. During a clinical sample detection within 30 min, the coincidence rates between the one- and two-pot detection methods and real-time quantitative polymerase chain reaction (qPCR) were 100%. In conclusion, both one- and two-pot RPA-CRISPR/Cas12a detection methods have significant potential for the rapid, sensitive, and specific visual detection of PCV3.
Collapse
Affiliation(s)
- Genghong Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhaoyang Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingyu Mao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Penghui Zeng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dedong Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhi Wu
- Loudi Livestock, Aquaculture and Agricultural Machinery Affairs Center, Loudi 417000, China
| | - Changzhe Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yonghui Qiu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yongqiu Cui
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianwei Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jue Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lei Hou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
4
|
He W, Liao K, Li R, Peng W, Qian B, Zeng D, Tang F, Xue F, Jung YS, Dai J. Development of a CRISPR/Cas12a-based fluorescent detection method of Senecavirus A. BMC Vet Res 2024; 20:258. [PMID: 38877537 PMCID: PMC11179212 DOI: 10.1186/s12917-024-04116-6] [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: 10/12/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Senecavirus A (SVA), identified in 2002, is known to cause porcine idiopathic vesicular disease (PIVD), which presents with symptoms resembling other vesicular diseases. This similarity complicates field diagnosis. Conventional molecular diagnostic techniques are limited by their cost, sensitivity, and requirement for complicated instrumentation. Therefore, developing an effective and accurate diagnostic method is crucial for timely identification and isolation of affected pigs, thereby preventing further disease spread. METHODS In this study, we developed a highly-specific and ultra-sensitive SVA detection method powered by CRISPR/Cas12a. To enhance the availability in laboratories with varied equipment conditions, microplate reader and ultraviolet light transilluminator were introduced. Moreover, PCR amplification has also been incorporated into this method to improve sensitivity. The specificity and sensitivity of this method were determined following the preparation of the recombinant Cas12a protein and optimization of the CRISPR/Cas12a-based trans-cleavage system. RESULTS The method demonstrated no cross-reactivity with ten kinds of viruses of swine. The minimum template concentration required to activate substantial trans-cleavage activity was determined to be 106 copies/µL of SVA templates. However, when PCR amplification was incorporated, the method achieved a detection limit of one copy of SVA templates per reaction. It also exhibited 100% accuracy in simulated sample testing. The complete testing process does not exceed three hours. CONCLUSIONS Importantly, this method utilizes standard laboratory equipment, making it accessible for use in resource-limited settings and facilitating widespread and ultra-sensitive screening during epidemics. Overall, the development of this method not only broadens the array of tools available for detecting SVA but also holds significant promise for controlling the spread of PIVD.
Collapse
Affiliation(s)
- Wei He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruixue Li
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dexin Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
- Sanya Institute of Nanjing Agricultural University, Sanya, 572024, China.
| | - Yong Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianjun Dai
- China Pharmaceutical University, Nanjing, 211198, China
| |
Collapse
|
5
|
Tesfagaber W, Wang W, Wang L, Zhao R, Zhu Y, Li F, Sun E, Liu R, Bu Z, Meng G, Zhao D. A highly efficient blocking ELISA based on p72 monoclonal antibody for the detection of African swine fever virus antibodies and identification of its linear B cell epitope. Int J Biol Macromol 2024; 268:131695. [PMID: 38642684 DOI: 10.1016/j.ijbiomac.2024.131695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Due to the absence of effective vaccine and treatment, African swine fever virus (ASFV) control is entirely dependent on accurate and early diagnosis, along with culling of infected pigs. The B646L/p72 is the major capsid protein of ASFV and is an important target for developing a diagnostic assays and vaccines. Herein, we generated a monoclonal antibody (mAb) (designated as 2F11) against the trimeric p72 protein, and a blocking ELISA (bELISA) was established for the detection of both genotype I and II ASFV antibodies. To evaluate the performance of the diagnostic test, a total of 506 porcine serum samples were tested. The average value of percent of inhibition (PI) of 133 negative pig serum was 8.4 % with standard deviation (SD) 6.5 %. Accordingly, the cut-off value of the newly established method was set at 28 % (mean + 3SD). Similarly, a receiver operating characteristic (ROC) was applied to determine the cut off value and the p72-bELISA exhibited a sensitivity of 100 % and a specificity of 99.33 % when the detection threshold was set at 28 %. The bELISA was also able to specifically recognize anti-ASFV sera without cross-reacting with other positive serums for other major swine pathogens. Moreover, by designing a series of overlapped p72 truncated proteins, the linear B cell epitope recognized by 2F11 mAb was defined to be 283NSHNIQ288. Amino acid sequence comparison revealed that the amino acid sequence 283NSHNIQ288 is highly conserved between different ASFV isolates. Our findings indicate that the newly established mAb based blocking ELISA may have a great potential in improving the detection of ASFV antibodies and provides solid foundation for further studies.
Collapse
Affiliation(s)
- Weldu Tesfagaber
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Wan Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Lulu Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Rui Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China; College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, People's Republic of China
| | - Yuanmao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Fang Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Encheng Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Renqiang Liu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Zhigao Bu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China.
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing 100083, People's Republic of China.
| | - Dongming Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China; College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, People's Republic of China.
| |
Collapse
|
6
|
Chen Y, Zhang X, Yang X, Su L, Chen W, Zhao J, Hu Y, Wang Y, Wu Y, Dong Y. PfAgo-Based Zika Virus Detection. Viruses 2024; 16:539. [PMID: 38675882 PMCID: PMC11054744 DOI: 10.3390/v16040539] [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: 02/27/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
As a mosquito-borne flavivirus, Zika virus (ZIKV) has been identified as a global health threat. The virus has been linked to severe congenital disabilities, including microcephaly and other congenital malformations, resulting in fatal intrauterine death. Therefore, developing sensitive and specific methods for the early detection and accurate diagnosis of the ZIKV is essential for controlling its spread and mitigating its impact on public health. Herein, we set up a novel nucleic acid detection system based on Pyrococcus furiosus Argonaute (PfAgo)-mediated nucleic acid detection, targeting the non-structural protein 5 (NS5) region of the ZIKV genome (abbreviated ZIKV-PAND). Without preamplification with the polymerase chain reaction (PCR), the minimum detection concentration (MDC) of ZIKV-PAND was about 10 nM. When introducing an amplification step, the MDC can be dramatically decreased to the aM level (8.3 aM), which is comparable to qRT-PCR assay (1.6 aM). In addition, the diagnostic findings from the analysis of simulated clinical samples or Zika virus samples using ZIKV-PAND show a complete agreement of 100% with qRT-PCR assays. This correlation can aid in the implementation of molecular testing for clinical diagnoses and the investigation of ZIKV infection on an epidemiological scale.
Collapse
Affiliation(s)
- Yuhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xianyi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lifang Su
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Weiran Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jixiang Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yunhong Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yuan Wang
- School of Basic Medicine, Hubei University of Arts and Sciences, Xiangyang 441053, China
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan 430072, China
| | - Yanming Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Industrial Biotechnology and Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| |
Collapse
|
7
|
Tan M, Liao C, Liang L, Yi X, Zhou Z, Wei G. Recent advances in recombinase polymerase amplification: Principle, advantages, disadvantages and applications. Front Cell Infect Microbiol 2022; 12:1019071. [PMID: 36519130 PMCID: PMC9742450 DOI: 10.3389/fcimb.2022.1019071] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
After the outbreak of SARS-CoV-2, nucleic acid testing quickly entered people's lives. In addition to the polymerase chain reaction (PCR) which was commonly used in nucleic acid testing, isothermal amplification methods were also important nucleic acid testing methods. Among several common isothermal amplification methods like displaced amplification, rolling circle amplification, and so on, recombinase polymerase amplification (RPA) was recently paid more attention to. It had the advantages like a simple operation, fast amplification speed, and reaction at 37-42°C, et al. So it was very suitable for field detection. However, there were still some disadvantages to RPA. Herein, our review mainly summarized the principle, advantages, and disadvantages of RPA. The specific applications of RPA in bacterial detection, fungi detection, virus detection, parasite detection, drug resistance gene detection, genetically modified food detection, and SARS-CoV-2 detection were also described. It was hoped that the latest research progress on RPA could be better delivered to the readers who were interested in RPA.
Collapse
|
8
|
Li J, Tang L, Li T, Li K, Zhang Y, Ni W, Xiao MM, Zhao Y, Zhang ZY, Zhang GJ. Tandem Cas13a/crRNA-Mediated CRISPR-FET Biosensor: A One-for-All Check Station for Virus without Amplification. ACS Sens 2022; 7:2680-2690. [PMID: 36073895 DOI: 10.1021/acssensors.2c01200] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The path toward field-effect transistor (FET) application from laboratory to clinic has delivered a compelling push in the biomedical domain, yet ultrasensitive and timely pathogen identification without PCR remains a long-lasting challenge. Herein, we create a generic check station termed "CRISPR-FET", first incorporating the CRISPR/Cas13a system within the FET modality, for accelerated and unamplified detection of viral RNA. Unlike conventional FETs bearing target-specific receptors, this sensor holds three unique advancements: (i) an ingenious sensing mechanism is used, which converts the signal of a large-sized analyte into an on-chip cleavage response of an immobilized CRISPR reporter, enabling signal generation events to occur all within the Debye length; (ii) the multipurpose inspection of the CoV ORF1ab, CoV N gene, and HCV RNA unveils the potential for "one-for-all" scalable FET-based molecular diagnostics; and (iii) it is shown that Cas13a-crRNAs targeting different sites of the viral genome can be deployed in tandem to amplify the FET response, empowering the detection limit down to 1.56 aM, which is a world-record level of sensitivity in the FET for direct viral gene sensing. Notably, a brilliant clinical applicability was made in distinguishing HCV-infected patients from normal controls. Overall, this study sheds new insights into FET-based nucleic acid sensing technology and invokes a vision for its possible future roles in diagnosis of various viral diseases.
Collapse
Affiliation(s)
- Jiahao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Lina Tang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Tingxian Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Kun Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Yulin Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Wei Ni
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Meng-Meng Xiao
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Youyun Zhao
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Zhi-Yong Zhang
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| |
Collapse
|
9
|
Cao G, Xiong Y, Nie F, Chen X, Peng L, Li Y, Yang M, Huo D, Hou C. Non-nucleic acid extraction and ultra-sensitive detection of African swine fever virus via CRISPR/Cas12a. Appl Microbiol Biotechnol 2022; 106:4695-4704. [PMID: 35715648 DOI: 10.1007/s00253-022-11999-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 12/26/2022]
Abstract
Early diagnosis of the African swine fever virus (ASFV) is the main preventive measure for ASFV. Here, we developed a fluorescent biosensor and lateral flow assay (LFA) strip based on direct PCR combined with CRISPR/Cas12a system for ASF. Direct PCR can simultaneously split samples and efficiently amplify without sacrificing sensitivity, which eliminated the steps of nucleic acid extraction. Furthermore, by the CRISPR/Cas12a, the biosensor addressed false positives caused by non-specific amplification and had high sensitivity with the actual limit of detection (LOD) of 7.6×10-4 ng·μL-1 (4 copies·μL-1). In addition, the strategy was built on the lateral flow assay (LFA) strip to achieve visual and portable detection for point-of-care testing. Moreover, the biosensor by a fluorometer and LFA strip showed a high accuracy to rival qPCR in actual sample detection. Therefore, the biosensor is an ultra-sensitive and specific tool that can replace traditional methods. KEY POINTS: • No nucleic acid extraction, direct PCR-simplified steps, and reduced time and cost • CRISPR/Cas12a solved the false positives caused by nonspecific amplification • The combination of the LFA strip and biosensor is more convenient for POC detection.
Collapse
Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing, 400044, People's Republic of China
| | - Xiaolong Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lan Peng
- Chongqing Medical and Pharmaceutical College Basic Department, Chongqing, 401331, People's Republic of China
| | - Yingguo Li
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing, 400044, People's Republic of China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China. .,Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China.
| |
Collapse
|
10
|
Jiang C, Tao D, Geng Y, Yang H, Xu B, Chen Y, Hu C, Chen H, Xie S, Guo A. Sensitive and Specific Detection of Lumpy Skin Disease Virus in Cattle by CRISPR-Cas12a Fluorescent Assay Coupled with Recombinase Polymerase Amplification. Genes (Basel) 2022; 13:genes13050734. [PMID: 35627121 PMCID: PMC9141258 DOI: 10.3390/genes13050734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Lumpy skin disease (LSD) is a severe and highly infectious pox disease of cattle caused by the lumpy skin disease virus (LSDV). To facilitate early control of LSD, this study aimed to develop a new rapid on-site LSDV detection method using an orf068 gene-based recombinase polymerase amplification assay (RPA) coupled with a CRISPR-Cas12a-based fluorescence assay (RPA-Cas12a-fluorescence assay). The results showed that the sensitivity of our RPA-Cas12a-fluorescence assay for detecting LSDV orf068 gene reached 5 copies/μL with plasmid as a template, and 102 TCID50/mL with viral genomic DNA as a template. No cross-reaction with other common bovine viruses was observed. Further, an on-site RPA-Cas12a-fluorescence assay of 40 clinical samples from cattle with or without LSD showed a diagnostic sensitivity of 96.3% (95% CI: 81.0-99.9%) and specificity of 92.31% (95% CI: 62.1-99.6%), which was close to those of the quantitative PCR assay. Therefore, our RPA-Cas12a-fluorescence assay has promising prospects in on-site rapid LSDV detection.
Collapse
Affiliation(s)
- Chuanwen Jiang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Dagang Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Yuanchen Geng
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Hao Yang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - 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, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Shengsong Xie
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- 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, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (S.X.); (A.G.); Tel.: +86-2787-2871-15 (A.G.)
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of China Agriculture and Rural Affairs, Wuhan 430070, China
- Correspondence: (S.X.); (A.G.); Tel.: +86-2787-2871-15 (A.G.)
| |
Collapse
|
11
|
Onyilagha C, Nguyen K, Luka PD, Hussaini U, Adedeji A, Odoom T, Ambagala A. Evaluation of a Lateral Flow Assay for Rapid Detection of African Swine Fever Virus in Multiple Sample Types. Pathogens 2022; 11:pathogens11020138. [PMID: 35215082 PMCID: PMC8877915 DOI: 10.3390/pathogens11020138] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022] Open
Abstract
Antibody-based lateral flow assay (LFA) is a quick and inexpensive tool used to detect pathogens in field samples, especially in hard-to-reach remote areas that may have limited access to central laboratories during an outbreak or surveillance. In this study, we investigated the ability of a commercially available LFA, PenCheck®, to detect African swine fever virus (ASFV) in clinical samples derived from pigs infected with highly virulent ASFV strains. The assay was specific and positively identified the majority of pigs showing high fever during the early stages (between 3 and 5 days) of infection. PenCheck® LFA also detected ASFV in serum and tissue samples collected from pigs that succumbed to experimental ASFV infection and whole blood, plasma, and tissue samples from the field. The limit of detection of the assay was ASFV titer 107.80 TCID50/mL, corresponding to ASFV real-time PCR values below 23 Ct. Although the sensitivity of the assay is less than that of the laboratory-based real-time PCR assays, the results obtained with the PenCheck® LFA in this study suggest that it can be used as a herd-level, field-deployable, and easy-to-use diagnostic tool to identify ASF-affected farms when access to portable molecular assays or central laboratories is not possible.
Collapse
Affiliation(s)
- Chukwunonso Onyilagha
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (C.O.); (K.N.)
| | - Kelvin Nguyen
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (C.O.); (K.N.)
| | - Pam D. Luka
- Virology Division, National Veterinary Research Institute, P.M.B 01, Vom 930001, Plateau, Nigeria; (P.D.L.); (U.H.); (A.A.)
| | - Ularamu Hussaini
- Virology Division, National Veterinary Research Institute, P.M.B 01, Vom 930001, Plateau, Nigeria; (P.D.L.); (U.H.); (A.A.)
| | - Adeyinka Adedeji
- Virology Division, National Veterinary Research Institute, P.M.B 01, Vom 930001, Plateau, Nigeria; (P.D.L.); (U.H.); (A.A.)
| | - Theophilus Odoom
- Accra Laboratory, Veterinary Services Directorate, Accra P.O. Box M161, Ghana;
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada; (C.O.); (K.N.)
- Department of Comparative Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Correspondence: ; Tel.: +1-204-789-2013
| |
Collapse
|
12
|
Wei N, Zheng B, Niu J, Chen T, Ye J, Si Y, Cao S. Rapid Detection of Genotype II African Swine Fever Virus Using CRISPR Cas13a-Based Lateral Flow Strip. Viruses 2022; 14:v14020179. [PMID: 35215773 PMCID: PMC8879322 DOI: 10.3390/v14020179] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/01/2023] Open
Abstract
The African swine fever virus (ASFV) is a dsDNA virus that can cause serious, highly infectious, and fatal diseases in wild boars and domestic pigs. The ASFV has brought enormous economic loss to many countries, and no effective vaccine or treatment for the ASFV is currently available. Therefore, the on-site rapid and accurate detection of the ASFV is key to the timely implementation of control. The RNA-guided, RNA-targeting CRISPR effector CRISPR-associated 13 (Cas13a; previously known as C2c2) exhibits a “collateral effect” of promiscuous RNase activity upon the target recognition. The collateral cleavage activity of LwCas13a is activated to degrade the non-targeted RNA, when the crRNA of LwCas13a binds to the target RNA. In this study, we developed a rapid and sensitive ASFV detection method based on the collateral cleavage activity of LwCas13a, which combines recombinase-aided amplification (RAA) and a lateral flow strip (named CRISPR/Cas13a-LFD). The method was an isothermal detection at 37 °C, and the detection can be used for visual readout. The detection limit of the CRISPR/Cas13a-LFD was 101 copies/µL of p72 gene per reaction, and the detection process can be completed within an hour. The assay showed no cross-reactivity to eight other swine viruses, including classical swine fever virus (CSFV), and has a 100% coincidence rate with real-time PCR detection of the ASFV in 83 clinical samples. Overall, this method is sensitive, specific, and practicable onsite for the ASFV detection, showing a great application potential for monitoring the ASFV in the field.
Collapse
Affiliation(s)
- Ning Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Bohan Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Junjun Niu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Jing Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Youhui Si
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: (Y.S.); (S.C.)
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (N.W.); (B.Z.); (J.N.); (T.C.); (J.Y.)
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: (Y.S.); (S.C.)
| |
Collapse
|
13
|
Wang Y, Wang B, Xu D, Zhang M, Zhang X, Wang D. Development of a ladder-shape melting temperature isothermal amplification (LMTIA) assay for detection of African swine fever virus (ASFV). J Vet Sci 2022; 23:e51. [PMID: 35698807 PMCID: PMC9346532 DOI: 10.4142/jvs.22001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Due to the unavailability of an effective vaccine or antiviral drug against the African swine fever virus (ASFV), rapid diagnosis methods are needed to prevent highly contagious African swine fever. Objectives The objective of this study was to establish the ladder-shape melting temperature isothermal amplification (LMTIA) assay for the detection of ASFV. Methods LMTIA primers were designed with the p72 gene of ASFV as the target, and plasmid pUC57 was used to clone the gene. The LMTIA reaction system was optimized with the plasmid as the positive control, and the performance of the LMTIA assay was compared with that of the commercial real-time polymerase chain reaction (PCR) kit in terms of sensitivity and detection rate using 200 serum samples. Results Our results showed that the LMTIA assay could detect the 104 dilution of DNA extracted from the positive reference serum sample, which was the same as that of the commercial real-time PCR kit. The coincidence rate between the two assays was 100%. Conclusions The LMTIA assay had high sensitivity, good detection, and simple operation. Thus, it is suitable for facilitating preliminary and cost-effective surveillance for the prevention and control of ASFV.
Collapse
Affiliation(s)
- Yongzhen Wang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| | - Borui Wang
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Dandan Xu
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Meng Zhang
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiaohua Zhang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| | - Deguo Wang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| |
Collapse
|
14
|
Yang K, Liang Y, Li Y, Liu Q, Zhang W, Yin D, Song X, Shao Y, Tu J, Qi K. Reverse transcription-enzymatic recombinase amplification coupled with CRISPR-Cas12a for rapid detection and differentiation of PEDV wild-type strains and attenuated vaccine strains. Anal Bioanal Chem 2021; 413:7521-7529. [PMID: 34686895 PMCID: PMC8536470 DOI: 10.1007/s00216-021-03716-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/20/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that causes acute watery diarrhea and vomiting in unweaned piglets, and is associated with high mortality, thus causing severe economic losses in the pig industry. Currently, although attenuated vaccines are commonly used in commercial pig farms in China, they do not completely protect against all mutated wild-type strains. Existing nucleic acid assays have high sensitivity and specificity, but the complexity of the assay process and expensive instrumentation hinder disease detection. Here, reverse transcription–enzymatic recombinase amplification (RT-ERA) was combined with the CRISPR-Cas12a system to develop a rapid diagnostic method to distinguish PEDV wild-type strains from attenuated vaccine strains. The protocol used crRNA and RT-ERA amplification primers against open reading frame 3 (ORF3), followed by Cas12a/crRNA complex detection of predefined target sequences at 37 °C for 30 min, thus producing results visible to the naked eye under LED blue light. The assay is highly sensitive and specific, detecting as few as two copies of the target gene per test and showing no cross-reactivity with other porcine pathogens. Overall, this integrated RT-ERA pre-amplification and Cas12a/crRNA cleavage assay is a practical tool for reliable and rapid detection of PEDV for diagnostic differentiation.
Collapse
Affiliation(s)
- Kankan Yang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yueqiao Liang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yanan Li
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qi Liu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wuyin Zhang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Dongdong Yin
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiangjun Song
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Ying Shao
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jian Tu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Kezong Qi
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-Safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| |
Collapse
|
15
|
Ceruti A, Kobialka RM, Ssekitoleko J, Okuni JB, Blome S, Abd El Wahed A, Truyen U. Rapid Extraction and Detection of African Swine Fever Virus DNA Based on Isothermal Recombinase Polymerase Amplification Assay. Viruses 2021; 13:v13091731. [PMID: 34578312 PMCID: PMC8472937 DOI: 10.3390/v13091731] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is the causative agent of a deadly disease in pigs and is spread rapidly across borders. Samples collected from suspected cases must be sent to the reference laboratory for diagnosis using polymerase chain reaction (PCR). In this study, we aimed to develop a simple DNA isolation step and real-time recombinase polymerase amplification (RPA) assay for rapid detection of ASFV. RPA assay based on the p72 encoding B646L gene of ASFV was established. The assays limit of detection and cross-reactivity were investigated. Diagnostic performance was examined using 73 blood and serum samples. Two extraction approaches were tested: silica-column-based extraction method and simple non-purification DNA isolation (lysis buffer and heating, 70 °C for 20 min). All results were compared with well-established real-time PCR. In a field deployment during a disease outbreak event in Uganda, 20 whole blood samples were tested. The assay’s analytical sensitivity was 3.5 DNA copies of molecular standard per µL as determined by probit analysis on eight independent assay runs. The ASFV RPA assay only detected ASFV genotypes. Compared to real-time PCR, RPA diagnostic sensitivity and specificity were 100%. Using the heating/lysis buffer extraction procedure, ASFV-RPA revealed better tolerance to inhibitors than real-time PCR (97% and 38% positivity rate, respectively). In Uganda, infected animals were identified before the appearance of fever. The ASFV-RPA assay is shown to be as sensitive and specific as real-time PCR. Moreover, the combination of the simple extraction protocol allows its use at the point of need to improve control measures.
Collapse
Affiliation(s)
- Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
| | - Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
| | - Judah Ssekitoleko
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala P.O. Box 7062, Uganda; (J.S.); (J.B.O.)
- National Agricultural Research Organisation, Entebbe P.O. Box 295, Uganda
| | - Julius Boniface Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala P.O. Box 7062, Uganda; (J.S.); (J.B.O.)
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, 17493 Greifswald, Germany;
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
- Correspondence:
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
| |
Collapse
|
16
|
Yang B, Shi Z, Ma Y, Wang L, Cao L, Luo J, Wan Y, Song R, Yan Y, Yuan K, Tian H, Zheng H. LAMP assay coupled with CRISPR/Cas12a system for portable detection of African swine fever virus. Transbound Emerg Dis 2021; 69:e216-e223. [PMID: 34370390 DOI: 10.1111/tbed.14285] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/05/2021] [Accepted: 08/07/2021] [Indexed: 12/26/2022]
Abstract
African swine fever (ASF) is one of the most severe infectious diseases of pigs. In this study, a loop-mediated isothermal amplification (LAMP) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was established in one tube for the detection of the African swine fever virus (ASFV) p72 gene. The single-stranded DNA-fluorophore quencher reporter and CRISPR-derived RNA were screened and selected for the CRISPR detection system. In combination with LAMP amplification assay, the detection limit for the LAMP-CRISPR assay can reach 7 copies/μl of p72 gene per reaction. Furthermore, this method displays no cross-reactivity with other porcine DNA or RNA viruses. The performance of the LAMP-CRISPR assay was compared with real-time qPCR tests for clinical samples; a good consistency between the LAMP-CRISPR assay and real-time qPCR was observed. The method shed a light on the convenient, portable, low cost, highly sensitive and specific detection of ASFV, demonstrating a great application potential for monitoring on-site ASFV in the field.
Collapse
Affiliation(s)
- Bo Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Zhengwang Shi
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuan Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lijuan Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Liyan Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Juncong Luo
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ying Wan
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Song
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yiyong Yan
- Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Kehu Yuan
- Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Hong Tian
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|