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Hu H, Liu L, Wei XY, Duan JJ, Deng JY, Pei DS. Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172414. [PMID: 38631624 DOI: 10.1016/j.scitotenv.2024.172414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/15/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Li Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jin-Jing Duan
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing 400025, China; School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jiao-Yun Deng
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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Lin L, Zheng Y, Huang H, Zhuang F, Chen H, Zha G, Yang P, Wang Z, Kong M, Wei H, Zou X, Lin M. A visual method to detect meat adulteration by recombinase polymerase amplification combined with lateral flow dipstick. Food Chem 2021; 354:129526. [PMID: 33735694 DOI: 10.1016/j.foodchem.2021.129526] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Determining the animal source in meat and meat products is crucial to prevent meat adulteration and fraud. Conventional methods require considerable operator skills, expensive instruments and are unable to provide fast mobile on-site detection systems to detect contamination of meat products. We developed a visual method based on recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) to identify beef (Bos taurus), sheep (Ovis aries), pork (Sus scrofa), duck (Anas platyrhynchos) and chicken (Gallus gallus). The reaction was completed within 20 min. The results were determined by the naked eye. The detection limits of the RPA-LFD assays for duck, beef, sheep, chicken and pork were 101/µL, 102/µL, 102/µL, 101/µL and 101/µL, respectively. Furthermore, the RPA-LFD assays could differentiate species in boiled, microwaved, pressure-cooked or fried samples. These RPA-LFD assays represent a rapid, mobile detection system for determining meat product contamination.
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Affiliation(s)
- Liyun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Yuzhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Huiying Huang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Fenluan Zhuang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Huixia Chen
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Guangcai Zha
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Peikui Yang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Zhonghe Wang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Meilan Kong
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Huagui Wei
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Xianghui Zou
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, China.
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Chen Y, Gong QL, Wang Q, Wang W, Wei XY, Jiang J, Ni HB. Prevalence of hepatitis E virus among swine in China from 2010 to 2019: A systematic review and meta-analysis. Microb Pathog 2020; 150:104687. [PMID: 33301857 DOI: 10.1016/j.micpath.2020.104687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023]
Abstract
Hepatitis E virus (HEV) is a zoonotic pathogen that has spread worldwide. The HEV reservoir associated with livestock hepatitis E poses a huge threat to public health. Awareness of the prevalence and spatial distribution of livestock hepatitis E is valuable to prevent and control diseases caused by HEV, especially human hepatitis E infection. Currently, swine, including pigs (Sus scrofa), are recognized as the major reservoir of HEV. Therefore, we conducted a systematic review and meta-analysis to evaluate the pooled prevalence of HEV among swine in China. A total of 71 published papers on HEV infection in swine in China (including data from 49,523 animals) from January 1, 2010 to December 31, 2019 met the standard after searching five databases including the Technology Periodical Database, the Wan Fang Database, the China National Knowledge Infrastructure, PubMed, and ScienceDirect. A random effects model was used to calculate the pooled prevalence of HEV in swine. The results showed that the seroprevalence was 48.0% (95% confidence interval (CI) 39.6-56.9) and the prevalence of HEV RNA was 14.4% (95% CI 10.7-18.5). The estimated overall prevalence was 34.1% (95% CI 27.2-41.4). Central China (68.0%, 95% CI 42.2-89.1) had a significantly higher prevalence than other regions. In the publication year subgroup, the prevalence in 2016 or later (27.2%, 95% CI 19.3-36.0) was significantly lower than that in 2011 or earlier (49.0%, 95% CI 36.2-61.8). The prevalence of IgG (42.9%, 95% CI 31.7-54.6) was significantly higher than that of IgM (4.9%, 95% CI 1.6-9.7). Suckling piglets (15.6%, 95% CI 6.6-27.1) had a lower prevalence compared with that in other age groups. In all sample types, body fluids showed the highest prevalence (50.5%, 95% CI 41.7-59.3). Moreover, the pooled prevalence of HEV in boars was higher than that in sows (35.4% > 17.3%). The analysis suggested that HEV infection is common among swine in China. Further strengthening HEV testing in boars, controlling environmental pollution, and reducing the mixed feeding of different stages could contribute to reducing HEV infection in pigs in China and the risk of porcine HEV infection in humans.
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Affiliation(s)
- Yu Chen
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, PR China
| | - Qing-Long Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, 130118, PR China
| | - Qi Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, 130118, PR China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, PR China
| | - Xin-Yu Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, PR China
| | - Jing Jiang
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, PR China.
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, PR China.
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Ngamdee T, Yin LS, Vongpunsawad S, Poovorawan Y, Surareungchai W, Lertanantawong B. Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection. Anal Chim Acta 2020; 1134:10-17. [PMID: 33059855 DOI: 10.1016/j.aca.2020.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.
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Affiliation(s)
- Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Lee Su Yin
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, 08100, Malaysia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Werasak Surareungchai
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand; Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand
| | - Benchaporn Lertanantawong
- Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand; Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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