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Lei Z, Lian L, Zhang L, Liu C, Zhai S, Yuan X, Wei J, Liu H, Liu Y, Du Z, Gul I, Zhang H, Qin Z, Zeng S, Jia P, Du K, Deng L, Yu D, He Q, Qin P. Detection of Frog Virus 3 by Integrating RPA-CRISPR/Cas12a-SPM with Deep Learning. ACS OMEGA 2023; 8:32555-32564. [PMID: 37720737 PMCID: PMC10500685 DOI: 10.1021/acsomega.3c02929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for frog virus 3 (FV3) is proposed. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, a limit of detection (LoD) of 100 aM (60.2 copies/μL) is achieved by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, smartphone microscopy is implemented, and an LoD of 10 aM is achieved in 40 min. The proposed system detects four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32. In addition, deep learning models are deployed for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100 and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, the proposed RPA-CRISPR/Cas12a combined with smartphone readouts and artificial-intelligence-assisted classification showcases the great potential for FV3 detection, specifically POC detection of DNA virus.
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Affiliation(s)
- Zhengyang Lei
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Lijin Lian
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Likun Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Changyue Liu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Jiazhang Wei
- Department
of Otolaryngology & Head and Neck, The
People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi
Academy of Medical Sciences, 6 Taoyuan Road, Nanning, 530021, China
| | - Hong Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Ying Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Zhicheng Du
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Ijaz Gul
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Haihui Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Zhifeng Qin
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Shaoling Zeng
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Peng Jia
- Quality and
Standards Academy, Shenzhen Technology University, Shenzhen 518118, China
| | - Ke Du
- Department
of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Lin Deng
- Shenzhen
Bay Laboratory, Shenzhen 518132, China
| | - Dongmei Yu
- School
of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong 264209, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
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Volpe E, Errani F, Mandrioli L, Ciulli S. Advances in Viral Aquatic Animal Disease Knowledge: The Molecular Methods' Contribution. BIOLOGY 2023; 12:biology12030466. [PMID: 36979158 PMCID: PMC10045235 DOI: 10.3390/biology12030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Aquaculture is the fastest-growing food-producing sector, with a global production of 122.6 million tonnes in 2020. Nonetheless, aquatic animal production can be hampered by the occurrence of viral diseases. Furthermore, intensive farming conditions and an increasing number of reared fish species have boosted the number of aquatic animals' pathogens that researchers have to deal with, requiring the quick development of new detection and study methods for novel unknown pathogens. In this respect, the molecular tools have significantly contributed to investigating thoroughly the structural constituents of fish viruses and providing efficient detection methods. For instance, next-generation sequencing has been crucial in reassignment to the correct taxonomic family, the sturgeon nucleo-cytoplasmic large DNA viruses, a group of viruses historically known, but mistakenly considered as iridoviruses. Further methods such as in situ hybridisation allowed objectifying the role played by the pathogen in the determinism of disease, as the cyprinid herpesvirus 2, ostreid herpesvirus 1 and betanodaviruses. Often, a combination of molecular techniques is crucial to understanding the viral role, especially when the virus is detected in a new aquatic animal species. With this paper, the authors would critically revise the scientific literature, dealing with the molecular techniques employed hitherto to study the most relevant finfish and shellfish viral pathogens.
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Affiliation(s)
- Enrico Volpe
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Francesca Errani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Sara Ciulli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
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Naranitus P, Aiamsa-At P, Sukonta T, Hannanta-Anan P, Chaijarasphong T. Smartphone-compatible, CRISPR-based platforms for sensitive detection of acute hepatopancreatic necrosis disease in shrimp. JOURNAL OF FISH DISEASES 2022; 45:1805-1816. [PMID: 35946585 DOI: 10.1111/jfd.13702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Acute Hepatopancreatic Necrosis Disease (AHPND), caused by bacterial isolates expressing PirAB binary toxins, represents the severest and most economically destructive disease affecting penaeid shrimp. Its rapid disease progression and associated massive mortalities call for vigilant monitoring and early diagnosis, but molecular detection methods that simultaneously satisfy the requirements of sensitivity, specificity, and portability are still scarce. In this work, the CRISPR-Cas12a technology was harnessed for the development of two fluorescent assays compatible with naked-eye visualization. The first assay, AP4-Cas12a, was based on the OIE-recommended AP4 two-tubed nested PCR method and was designed to bypass the time-consuming and potentially hazardous agarose gel electrophoresis step. Using AP4-Cas12a, the detection limit of 10 copies per reaction could be achieved within less than 30 minutes post-PCR. The second assay, RPA-Cas12a, utilized recombinase polymerase amplification (RPA) to rapidly and isothermally amplify the target DNA, followed by amplicon detection by Cas12a, resulting in a protocol that can be completed in less than an hour at a constant temperature of 37°C. The detection limit of RPA-Cas12a is 100 copies of plasmid DNA or 100 fg of bacterial genomic DNA per reaction. Importantly, we validated that both assays are compatible with a previously reported smartphone-based device for facile visualization of fluorescence, thereby providing an affordable option that requires less consumables than lateral flow detection. Using this portable device for readouts, the AP4-Cas12a and RPA-Cas12a methods showed excellent concordance with the AP4-agarose gel electrophoresis approach in the evaluation of clinical samples. Therefore, the developed Cas12a assays have the potential to streamline both in-laboratory and onsite diagnosis of AHPND.
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Affiliation(s)
- Punyaporn Naranitus
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Praphutson Aiamsa-At
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanwarat Sukonta
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimkhuan Hannanta-Anan
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Thawatchai Chaijarasphong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
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