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Arunrut N, Jitrakorn S, Tondee B, Saksmerprome V, Kiatpathomchai W. Real-time triplex loop-mediated isothermal amplification (LAMP) using a turbidimeter for detection of shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV). JOURNAL OF AQUATIC ANIMAL HEALTH 2024; 36:205-219. [PMID: 38923038 DOI: 10.1002/aah.10218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/24/2023] [Accepted: 02/19/2024] [Indexed: 06/28/2024]
Abstract
OBJECTIVE The World Organization for Animal Health still regulates the infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp. The existing disease identification approach is time consuming, necessitates expensive equipment, and requires specialized expertise, thereby limiting the accessibility of shrimp disease screening on farms. Loop-mediated isothermal amplification (LAMP) is recognized for its ability to detect inhibitory substances with high sensitivity and specificity. METHODS We developed a real-time triplex LAMP assay that combines the simplicity of point-of-care testing with the accuracy of a turbidimeter. Using a set of three LAMP primers, our technology enables rapid DNA amplification in a single reaction within 45 min and with a low detection limit (10 copies/reaction). RESULT We tested 192 shrimp samples from different sources and demonstrated the clinical utility of our method, achieving 100% specificity (95% confidence interval = 93.40-100.00%), 100% sensitivity (97.36-100.00%), and 100% accuracy (98.10-100.00%) in detecting IHHNV DNA, with a high Cohen's kappa value (1) compared to the standard quantitative polymerase chain reaction assay. CONCLUSION The high technology readiness level of our method makes it a versatile platform for any real-time LAMP assay, and its low cost and simplicity make it well suited for fast deployment and use in shrimp farming.
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Affiliation(s)
- Narong Arunrut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sarocha Jitrakorn
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Benyatip Tondee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Vanvimon Saksmerprome
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wansika Kiatpathomchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
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Kibenge F, Kibenge M, Montes de Oca M, Godoy M. Parvoviruses of Aquatic Animals. Pathogens 2024; 13:625. [PMID: 39204226 PMCID: PMC11357303 DOI: 10.3390/pathogens13080625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Family Parvoviridae consists of small, non-enveloped viruses with linear, single-stranded DNA genomes of approximately 4-6 kilobases, subdivided into three subfamilies, Parvovirinae, Densovirinae, and Hamaparvovirinae, and unassigned genus Metalloincertoparvovirus. Parvoviruses of aquatic animals infect crustaceans, mollusks, and finfish. This review describes these parvoviruses, which are highly host-specific and associated with mass morbidity and mortality in both farmed and wild aquatic animals. They include Cherax quadricarinatus densovirus (CqDV) in freshwater crayfish in Queensland, Australia; sea star-associated densovirus (SSaDV) in sunflower sea star on the Northeastern Pacific Coast; Clinch densovirus 1 in freshwater mussels in the Clinch River, Virginia, and Tennessee, USA, in subfamily Densovirinae; hepatopancreatic parvovirus (HPV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in farmed shrimp worldwide; Syngnathid ichthamaparvovirus 1 in gulf pipefish in the Gulf of Mexico and parts of South America; tilapia parvovirus (TiPV) in farmed tilapia in China, Thailand, and India, in the subfamily Hamaparvovirinae; and Penaeus monodon metallodensovirus (PmMDV) in Vietnamese P. monodon, in unassigned genus Metalloincertoparvovirus. Also included in the family Parvoviridae are novel parvoviruses detected in both diseased and healthy animals using metagenomic sequencing, such as zander parvovirus from zander in Hungary and salmon parvovirus from sockeye salmon smolts in British Columbia, Canada.
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Affiliation(s)
- Frederick Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Molly Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5480000, Chile; (M.M.d.O.); or (M.G.)
| | - Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5480000, Chile; (M.M.d.O.); or (M.G.)
- Laboratorio de Biotecnología Aplicada, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Sede de la Patagonia, Universidad San Sebastián, Puerto Montt 5480000, Chile
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Li X, Zhu S, Zhang X, Ren Y, He J, Zhou J, Yin L, Wang G, Zhong T, Wang L, Xiao Y, Zhu C, Yin C, Yu X. Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes. Front Bioeng Biotechnol 2023; 11:1215466. [PMID: 37720320 PMCID: PMC10502170 DOI: 10.3389/fbioe.2023.1215466] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The rapid diagnosis of pathogenic infections plays a vital role in disease prevention, control, and public health safety. Recombinase-aided amplification (RAA) is an innovative isothermal nucleic acid amplification technology capable of fast DNA or RNA amplification at low temperatures. RAA offers advantages such as simplicity, speed, precision, energy efficiency, and convenient operation. This technology relies on four essential components: recombinase, single-stranded DNA-binding protein (SSB), DNA polymerase, and deoxyribonucleoside triphosphates, which collectively replace the laborious thermal cycling process of traditional polymerase chain reaction (PCR). In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) system, a groundbreaking genome engineering tool, has garnered widespread attention across biotechnology, agriculture, and medicine. Increasingly, researchers have integrated the recombinase polymerase amplification system (or RAA system) with CRISPR technology, enabling more convenient and intuitive determination of detection results. This integration has significantly expanded the application of RAA in pathogen detection. The step-by-step operation of these two systems has been successfully employed for molecular diagnosis of pathogenic microbes, while the single-tube one-step method holds promise for efficient pathogen detection. This paper provides a comprehensive review of RAA combined with CRISPR-Cas and its applications in pathogen detection, aiming to serve as a valuable reference for further research in related fields.
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Affiliation(s)
- Xiaoping Li
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Shuying Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Xinling Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Yanli Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Jing He
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Jiawei Zhou
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Liliang Yin
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Gang Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ling Wang
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
| | - Chunying Zhu
- Clinical Psychology Department, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang Province, 310005, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
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Shao H, Jian J, Peng D, Yao K, Abdulsalam S, Huang W, Kong L, Li C, Peng H. Recombinase Polymerase Amplification Coupled with CRISPR-Cas12a Technology for Rapid and Highly Sensitive Detection of Heterodera avenae and Heterodera filipjevi. PLANT DISEASE 2023:PDIS02220386RE. [PMID: 36167511 DOI: 10.1094/pdis-02-22-0386-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The cereal cyst nematodes Heterodera avenae and Heterodera filipjevi are recognized as cyst nematodes that infect cereal crops and cause severe economic losses worldwide. Rapid, visual detection of cyst nematodes is essential for more effective control of this pest. In this study, recombinase polymerase amplification (RPA) combined with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a (formerly known as cpf1) was developed for the rapid detection of H. avenae and H. filipjevi from infested field samples. The RPA reaction was performed at a wide range of temperatures from 35 to 42°C within 15 min. There was no cross-reactivity between H. avenae, H. filipjevi, and the common closely related plant-parasitic nematodes, indicating the high specificity of this assay. The detection limit of RPA-Cas12a was as low as 10-4 single second-stage juvenile (J2), 10-5 single cyst, and 0.001 ng of genomic DNA, which is 10 times greater than that of RPA-lateral flow dipstick (LFD) detection. The RPA-Cas12a assay was able to detect 10-1 single J2 of H. avenae and H. filipjevi in 10 g of soil. In addition, the RPA-LFD assay and RPA-Cas12a assays could both quickly detect H. avenae and H. filipjevi from naturally infested soil, and the entire detection process could be completed within 1 h. These results indicated that the RPA-Cas12a assay developed herein is a simple, rapid, specific, sensitive, and visual method that can be easily adapted for the quick detection of H. avenae and H. filipjevi in infested fields.
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Affiliation(s)
- Hudie Shao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Jinzhuo Jian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Ke Yao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Sulaiman Abdulsalam
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
- Division of Agricultural Colleges/Department of Crop Protection, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Chuanren Li
- College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, P.R. China
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
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Rapid sample preparation and low-resource molecular detection of hepatopancreatic parvoviruses (HPV) by recombinase polymerase amplification lateral flow detection assay in shrimps (Fenneropenaeus merguiensis). PLoS One 2022; 17:e0276164. [PMID: 36350876 PMCID: PMC9645652 DOI: 10.1371/journal.pone.0276164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Viral diseases are a major problem in shrimp aquaculture facilities as these diseases reduce growth rates, which inevitably lead to production and profit losses. Hepatopancreatic parvoviruses (HPV) are common diseases in shrimp that appear to be associated with high or low levels of replication in specific genetic lineages. Selective breeding may result in resistance to HPV and improved body traits such as body weight, meat yield and shrimp colour, facilitating shrimp farming. HPV virus titre is commonly determined by quantitative PCR (qPCR), which is a time-consuming method requiring laboratory equipment unsuitable for field implementation. The aim of this study was to develop a simple, robust, rapid and reliable method to detect HPV in low-resource environments. Methods We developed a rapid shrimp HPV test that uses (1) a simple three-step sample preparation protocol, followed by (2) isothermal recombinase polymerase amplification (RPA) and lateral flow strip detection (LFD). Analytical sensitivity testing was performed in a background banana shrimp sample matrix, and retrospective testing of Fenneropenaeus merguiensis hepatopancreas tissues (n = 33) with known qPCR viral titres was used to determine diagnostic sensitivity and specificity. Results The rapid shrimp HPV test could detect as little as 35 genome-equivalent copies per reaction in homogenized F. merguiensis banana shrimp. Retrospective testing of stored tissues (n = 33) indicated 100% diagnostic sensitivity (95% confidence interval, CI: 86–100%) and 100% specificity (95% CI: 66–100%) for detection of HPV. Conclusion The rapid shrimp HPV test could be completed in only 40 minutes, and required only homogenization pestles, some pipettors, and a small heating block for single temperature incubation at 39°C. Critically, our procedure eliminated the time-consuming purification of nucleic acids from samples and when combined with RPA-LFD offers a user-friendly HPV detection format that can potentially be performed on-site. Our approach represents a major step forward in the development of a simple and sensitive end-point method for quick determination of unfavourable HPV virus numbers in shrimp, and has great potential to advance on-site management of shrimps in aquaculture.
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Tomar PS, Patel S, Dash PK, Kumar JS. Simple and Field Amenable Loop-Mediated Isothermal Amplification-Lateral Flow Dipstick Assay for Detection of West Nile Virus in Human Clinical Samples. J Appl Microbiol 2022; 133:3512-3522. [PMID: 36007965 DOI: 10.1111/jam.15783] [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: 03/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022]
Abstract
AIM West Nile encephalitis caused by infection with the West Nile virus (WNV) is endemic in many regions of the world and is a global public health threat. The aim of this report was to develop a method using colorimetry based reverse-transcription loop-mediated isothermal amplification (cRT-LAMP) and RT-LAMP combined with lateral-flow dipstick (LFD) for rapidly detecting WNV in low-infrastructure settings. METHODS AND RESULTS The primers for the cRT-LAMP and RT-LAMP-LFD assay were designed based on env gene of the WNV. Primers concentration, temperature, and time were optimized for cRT-LAMP and RT-LAMP-LFD. The diagnostic performance of the cRT-LAMP and RT-LAMP-LFD assay was evaluated using human serum samples from 110 patients who were clinically suspected to be infected with WNV. The RT-LAMP was performed in a heating block at 63°C for 40 minutes. The LAMP amplicons were visible in the lateral-flow dipstick within 5 minutes. The detection limit of the developed cRT-LAMP and RT-LAMP-LFD assay was 10 copies and this assay showed high degree of specificity for WNV. Compared with quantitative real-time RT-PCR assay, the kappa value of cRT-LAMP and RT-LAMP-LFD were 0.970. CONCLUSIONS These results showed that the newly developed WNV specific cRT-LAMP and RT-LAMP-LFD assays can be employed as an alternative method for screening of WN suspected human samples. The results revealed that the assay could potentially identify the virus without interference from human serum samples. Collectively, the all results revealed that cRT-LAMP and RT-LAMP-LFD assay offers suitable field based diagnosis of WNV. SIGNIFICANCE AND IMPACT OF STUDY The cRT-LAMP and LAMP-LFD platform for the detection of WNV is rapid, accurate, and simple-to-perform. Our present method has not only a short turnaround time but also avoided cross-contamination problem. Moreover, the use of simple lateral flow dipsticks broadens its application potential to the point-of-care use in resource-limited settings during outbreak situations. To the best of our knowledge this is the first report for the development of cRT-LAMP and LAMP-LFD assay for rapid, simple, specific, and sensitive detection of WNV using human clinical samples and EvaGreen dye.
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Affiliation(s)
- Priyanka Singh Tomar
- Division of Virology, Defence Research and Development Establishment, Jhansi Road, Gwalior- 474002, Madhya Pradesh, India
| | - Sapan Patel
- School of Studies in Botany, Jiwaji University, Gwalior
| | | | - Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment, Jhansi Road, Gwalior- 474002, Madhya Pradesh, India
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Shrimp genome sequence contains independent clusters of ancient and current Endogenous Viral Elements (EVE) of the parvovirus IHHNV. BMC Genomics 2022; 23:565. [PMID: 35933380 PMCID: PMC9357335 DOI: 10.1186/s12864-022-08802-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Background Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. Endogenous viral elements (EVE) play a role in this process probably via production of negative-sense Piwi-interacting RNA (piRNA)-like fragments. These bind with Piwi proteins to dampen viral replication via the RNA interference (RNAi) pathway. We searched a genome sequence (GenBank record JABERT000000000) of the giant tiger shrimp (Penaeus monodon for the presence of EVE related to a shrimp parvovirus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Results The shrimp genome sequence contained three piRNA-like gene clusters containing scrambled IHHNV EVE. Two clusters were located distant from one another in pseudochromosome 35 (PC35). Both PC35 clusters contained multiple sequences with high homology (99%) to GenBank records DQ228358 and EU675312 that were both called “non-infectious IHHNV Type A” (IHHNV-A) when originally discovered. However, our results and those from a recent Australian P. monodon genome assembly indicate that the relevant GenBank records for IHHNV-A are sequence-assembly artifacts derived from scrambled and fragmental IHHNV-EVE. Although the EVE in the two PC35 clusters showed high homology only to IHHNV-A, the clusters were separate and distinct with respect to the arrangement (i.e., order and reading direction) and proportional content of the IHHNV-A GenBank records. We conjecture that these 2 clusters may constitute independent allele-like clusters on a pair of homologous chromosomes. The third EVE cluster was found in pseudochromosome 7 (PC7). It contained EVE with high homology (99%) only to GenBank record AF218266 with the potential to protect shrimp against current types of infectious IHHNV. One disadvantage was that some EVE in PC7 can give false positive PCR test results for infectious IHHNV. Conclusions Our results suggested the possibility of viral-type specificity in EVE clusters. Specificity is important because whole EVE clusters for one viral type would be transmitted to offspring as collective hereditary units. This would be advantageous if one or more of the EVE within the cluster were protective against the disease caused by the cognate virus. It would also facilitate gene editing for removal of non-protective EVE clusters or for transfer of protective EVE clusters to genetically improve existing shrimp breeding stocks that might lack them. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08802-3.
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Liu F, Zhang C, Wang Y, Chen G. A review of the current and emerging detection methods of marine harmful microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152913. [PMID: 34999066 DOI: 10.1016/j.scitotenv.2022.152913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
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Preena PG, Kumar TVA, Johny TK, Dharmaratnam A, Swaminathan TR. Quick hassle-free detection of cyprinid herpesvirus 2 (CyHV-2) in goldfish using recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2022; 30:1211-1220. [PMID: 35194344 PMCID: PMC8854473 DOI: 10.1007/s10499-021-00806-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is the etiological agent of herpesviral hematopoietic necrosis disease (HVHND), which causes severe mortality in ornamental goldfish (Carassius auratus), crucian carp (Carassius auratus), and gibel/prussian carp (Carassius gibelio). Quick and hassle-free point-of-care detection of CyHV-2 is vital for the maintenance of ornamental fish health. In this manuscript, we describe the development of a rapid and sensitive RPA (recombinase polymerase amplification) assay, coupled with lateral flow dipsticks (LFD), that can achieve sensitive diagnosis of CyHV-2 in goldfish within 20 min at 36 °C with the satisfactory detection limit of 102 gene copies per reaction. This is the first report wherein major capsid protein (MCP) of CyHV-2 was targeted for RPA-LFD assay development. The assay did not show any cross-reactivity with other viral pathogens like cyprinid herpesvirus 3 (CyHV-3), spring viremia of carp virus (SVCV), infectious spleen and kidney necrosis virus (ISKNV), and viral nervous necrosis virus (VNNV). Furthermore, screening of CyHV-2 infection in CyHV-2-infected goldfish did not yield any false positive/negative results. In short, the RPA-LFD assay developed in this study presents a simple, rapid, and sensitive method for point-of-care diagnosis of CyHV-2, especially under resource-limited conditions.
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Affiliation(s)
- Prasannan Geetha Preena
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, CMFRI Campus, P.O. Number 1603, Kochi, Kerala India 682 018
| | - Thaliyil Veetil Arun Kumar
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, CMFRI Campus, P.O. Number 1603, Kochi, Kerala India 682 018
- Krishi Vigyan Kendra, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana India 132001
| | - Tina Kollannoor Johny
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, CMFRI Campus, P.O. Number 1603, Kochi, Kerala India 682 018
| | - Arathi Dharmaratnam
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, CMFRI Campus, P.O. Number 1603, Kochi, Kerala India 682 018
| | - Thangaraj Raja Swaminathan
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, CMFRI Campus, P.O. Number 1603, Kochi, Kerala India 682 018
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Li C, Ju Y, Shen P, Wu X, Cao L, Zhou B, Yan X, Pan Y. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Detection Assay for Rapid and Visual Detection of Ralstonia solanacearum in Tobacco. PLANT DISEASE 2021; 105:3985-3989. [PMID: 34236213 DOI: 10.1094/pdis-04-21-0688-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a serious soilborne disease that results in severe losses to tobacco (Nicotiana tabacum) production in China. In this study, a novel RPA-LFD assay for the rapid visual detection of R. solanacearum was established using recombinase polymerase amplification (RPA) and lateral-flow dipstick (LFD). The RPA-LFD assay was performed at 37°C in 30 min without complex equipment. Targeting the sequence of the RipTALI-9 gene, we designed RPA primers (Rs-rpa-F/R) and an LF probe (Rs-LF-probe) that showed high specificity to R. solanacearum. The sensitivity of RPA-LFD assay to R. solanacearum was the same as that in conventional PCR at 1 pg genomic DNA, 103 CFU/g artificially inoculated tobacco stems, and 104 CFU/g artificially inoculated soil. The RPA-LFD assay could also detect R. solanacearum from plant and soil samples collected from naturally infested tobacco fields. These results suggest that the RPA-LFD assay developed in this study is a rapid, accurate molecular diagnostic tool with high sensitivity for the detection of R. solanacearum.
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Affiliation(s)
- Changfeng Li
- Cotton Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yuliang Ju
- Key Laboratory of Biology and Sustainable Management of Plant Disease and Pests of Anhui Higher Education Institutes, Anhui Agricultural University, Hefei 230036, China
| | - Pengfei Shen
- Key Laboratory of Biology and Sustainable Management of Plant Disease and Pests of Anhui Higher Education Institutes, Anhui Agricultural University, Hefei 230036, China
| | - Xun Wu
- Key Laboratory of Biology and Sustainable Management of Plant Disease and Pests of Anhui Higher Education Institutes, Anhui Agricultural University, Hefei 230036, China
| | - Le Cao
- Key Laboratory of Biology and Sustainable Management of Plant Disease and Pests of Anhui Higher Education Institutes, Anhui Agricultural University, Hefei 230036, China
| | - Benguo Zhou
- Institute of Tobacco, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Xiaoming Yan
- Cotton Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yuemin Pan
- Key Laboratory of Biology and Sustainable Management of Plant Disease and Pests of Anhui Higher Education Institutes, Anhui Agricultural University, Hefei 230036, China
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Wang P, Ma C, Liao L, Yu J, Yi L, Qiao Y, Liu X, Gao S, Shen H, Lu Q. Simultaneous visual diagnosis of acute hepatopancreatic necrosis disease and Enterocytozoon hepatopenaei infection in shrimp with duplex recombinase polymerase amplification. JOURNAL OF FISH DISEASES 2021; 44:1753-1763. [PMID: 34237791 DOI: 10.1111/jfd.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Shrimp is a globally popular seafood. Shrimp farming has been challenged by various infectious diseases that lead to significant economic losses. The prevention of two important shrimp infectious diseases, the acute hepatopancreatic necrosis disease (AHPND) and the Enterocytozoon hepatopenaei (EHP) infection, is highly dependent on early and accurate diagnostic. On-site monitoring of the two diseases in shrimp farming facilities demands point-of-care-testing (POCT) type of diagnostic assays. This study established a duplex recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) combined assay that could simultaneously diagnose the two diseases. The optimized RPA-LFD assay could finish the diagnostic in 35 min with good specificity, and the sensitivity reached 101 and 102 gene copies per reaction for EHP and AHPND, respectively, which were at the same level as the currently available molecular diagnostic assays. Test results of clinical samples showed 100% agreement of this assay with the industrial standard nested polymerase chain reaction (PCR) assays, and samples with both diseases were simultaneously identified. Because of the isothermal 37℃ amplification and the visual reading of the signal on dipsticks, the dependence on equipment is minimal. This duplex RPA-LFD assay is well suited for simultaneous POCT diagnostic of the two important shrimp infectious diseases. Moreover, the principle can be applied to multiplex POCT diagnostic of other infectious diseases in aquaculture.
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Affiliation(s)
- Pei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Lei Liao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Junwei Yu
- Ustar Biotechnologies (Hangzhou) Ltd, Zhejiang, China
| | - Longyu Yi
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Xin Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
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Yang X, Dong Y, Ma C, Qiao Y, Jiang G, Chen S, Dong J, Shen H, Gao S. Establishment of a visualized isothermal nucleic acid amplification method for on-site diagnosis of acute hepatopancreatic necrosis disease in shrimp farm. JOURNAL OF FISH DISEASES 2021; 44:1293-1303. [PMID: 34041767 DOI: 10.1111/jfd.13388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a significant deadly infectious disease in the shrimp farming industry, causing serious economic losses globally every year. Because of the rapid progress speed, lack of effective treatment and high mortality rate of AHPND, monitoring with frequent diagnostic tests is vital for a successful prevention. The conventional histopathological diagnosis fell far short of the requirement for efficient monitoring, and the polymerase chain reaction (PCR)-based molecular diagnostic methods that rely on sophisticated thermocycler and trained personnel are hardly applicable in the field. Combining the recombinase polymerase amplification (RPA) and the lateral flow strips (LFSs), a diagnostic method suitable for on-site everyday monitoring of AHPND has been established in this study. This RPA-LFS method targeted the binary toxic photorhabdus insect-related genes PirA and PirB on a virulence plasmid of the AHPND-causative Vibrio parahaemolyticus strains. The diagnostic test was completed within 30 min at 37°C and showed good specificity and good sensitivity of 20 fg DNA of the AHPND shrimp or one colony-forming unit of the causative bacterium per reaction, which was better than the administration-approved standard AP4 assay. Crude templates from sample boiling could be directly used. Tests of clinical samples showed 100% consistency of this method with the standard AP4 assay. This RPA-LFS method can be a good choice for on-site diagnosis of AHPND with quick response time, easy procedure and low demand for resources, and should have significant value for the control of spreading of this dangerous disease in farmed shrimp.
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Affiliation(s)
- Xiaohan Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
- College of Life Science and Technology, Hua Zhong University of Science and Technology, Wuhan, China
| | - Yu Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Chao Ma
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Shiqi Chen
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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Li ZR, Yang ZX, Li ZH, Gao X, Hu ZY, Yang H, Liao DF. Development and evaluation of recombinase polymerase amplification combined with lateral flow dipstick assays for co-detection of epizootic haemorrhagic disease virus and the Palyam serogroup virus. BMC Vet Res 2021; 17:286. [PMID: 34433470 PMCID: PMC8390197 DOI: 10.1186/s12917-021-02977-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/22/2021] [Indexed: 11/29/2022] Open
Abstract
Background Epizootic haemorrhagic disease virus (EHDV) and the Palyam serogroup viruses (PALV) have led to significant economic losses associated with livestock production globally. A rapid, sensitive and specific method for the detection of EHDV and PALV is critical for virus detection, monitoring, and successful control and elimination of related diseases. Results In the present study, a recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) assay for the co-detection of genome segment 1 (Seg-1) of EHDV and PALV was developed and evaluated. The analytical sensitivities of the established RPA-LFD assay in the detection of EHDV and PALV were 7.1 copies/µL and 6.8 copies/µL, respectively. No cross-reaction with other members of the genus Orbivirus, including African horse sickness virus, bluetongue virus, Guangxi orbivirus, Tibet orbivirus and Yunnan orbivirus was observed. The established RPA-LFD assay accurately detected 39 EHDV strains belonging to 5 serotypes and 29 PALV strains belonging to 3 serotypes. The trace back results of quantitative real-time polymerase chain reaction (qRT-PCR) and the established RPA-LFD assay on sentinel cattle were consistent. The coincidence rates of qRT-PCR and the established RPA-LFD assay in 56 blood samples from which EHDV or PALV had been isolated and 96 blood samples collected from cattle farms were more than 94.8 %. The results demonstrated that the established RPR-LFD assay is specific, sensitive and reliable, and could be applied in early clinical diagnosis of EHDV and PALV. Conclusions This study highlights the development and application of the RPA-LFD assay in the co-detection of EHDV and PALV for the first time. The assay could be used as a potential optional rapid, reliable, sensitive and low-cost method for field diagnosis of EHDV and PALV. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-02977-9.
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Affiliation(s)
- Zhuo-Ran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Yunnan, 650224, Kunming, China
| | - Zhen-Xing Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Yunnan, 650224, Kunming, China
| | - Zhan-Hong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Yunnan, 650224, Kunming, China
| | - Xiang Gao
- Animal Disease Control and Prevention Center of Jinghong, Yunnan, 666100, Jinghong, China
| | - Zhong-Yan Hu
- Animal Disease Control and Prevention Center of Jinghong, Yunnan, 666100, Jinghong, China
| | - Heng Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Yunnan, 650224, Kunming, China.
| | - De-Fang Liao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Yunnan, 650224, Kunming, China.
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Recombinase polymerase amplification lateral flow dipstick (RPA-LF) detection of Babesia orientalis in water buffalo (Bubalus babalis, Linnaeus, 1758). Vet Parasitol 2021; 296:109479. [PMID: 34120031 DOI: 10.1016/j.vetpar.2021.109479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/11/2021] [Accepted: 05/28/2021] [Indexed: 12/30/2022]
Abstract
Babesiosis caused by Babesia orientalis, an intraerythrocytic apicomplexan protozoan, is one of the most important diseases for water buffalo in central and southern China, leading to huge economic losses, and its main diagnostic method is microscopic examination. In this study, a recombinase polymerase amplification - lateral flow dipstick (RPA-LF) assay, targeting the mitochondrial COXI gene of B. orientalis, was developed to detect B. orientalis in water buffalo. The RPA-LF assay was carried out as an isothermal reaction at 37 °C within 15 min. The specificity assay showed no cross-reactivity with other protozoa, and the sensitivity assay revealed the minimum detection limit was 0.25 parasite/μL, which was 40-fold more sensitive than that of conventional PCR (0.25 versus10 parasites/μL blood). Moreover, the RPA-LF method was successfully applied to test clinical samples, with no significant difference being observed between RPA-LF and conventional PCR results. Compared with conventional PCR, the novel RPA-LF method had the advantages of simple operation, short time, high sensitivity, and high specificity for B. orientalis detection, indicating the potential use of RPA-LF for rapid field detection of B. orientalis.
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Jaroenram W, Hayakijkosol O, Owens L, Elliman J. Establishing a gold standard method for the detection of Cherax reovirus using reverse transcriptase, quantitative, polymerase chain reaction. J Virol Methods 2021; 293:114169. [PMID: 33887279 DOI: 10.1016/j.jviromet.2021.114169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
Cherax reovirus infects redclaw crayfish (Cherax quadricarinatus) and it may be involved in mortalities between 5-20 % and stunting of up to 40 % of survivors. The sequence of the RNA-dependent RNA polymerase was used to develop a reverse transcription, quantitative, PCR (RT-qPCR) which was specific against seven other crustacean viruses (Athtab bunyavirus, Chequa iflavirus, Macrobrachium rosenbergii nodavirus, Gill-associated virus, Taura syndrome virus, White spot syndrome virus, and Penaeus stylirostris Penstylhamaparvovirus) although GAV produced a reaction that was easily separated by melt curve analysis. A strong linear correlation (r2 = 0.9965) was obtained between viral quantities ranging from 107 to 10 viral copies/reaction with an amplification efficiency of 0.92. This RT-qPCR is 2-times faster and 100 times more sensitive than a standard RT-PCR using agarose gel electrophoresis with the potential to detect the virus down to 7.64 copies/reaction in clinical samples. In clinical crayfish samples, it was able to detect Cherax reovirus in crayfish when the traditional RT-PCR was negative. Its' measurement of uncertainty was less than 2% (0.02-1.9), similar to PCRs for other crustacean viruses. This RT-qPCR is proposed as the gold standard and should be used for the screening of populations of C. quadricarinatus for broodstock before being used in hatcheries or on farms.
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Affiliation(s)
- Wansadaj Jaroenram
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Orachun Hayakijkosol
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Leigh Owens
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
| | - Jennifer Elliman
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 Solander Road, Townsville, QLD, 4811, Australia.
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Mai HN, Aranguren Caro LF, Cruz-Flores R, Dhar AK. Development of a Recombinase Polymerase Amplification (RPA) assay for acute hepatopancreatic necrosis disease (AHPND) detection in Pacific white shrimp (Penaeus vannamei). Mol Cell Probes 2021; 57:101710. [PMID: 33722662 DOI: 10.1016/j.mcp.2021.101710] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is currently the most important bacterial disease of shrimp that has caused enormous losses to the shrimp industry worldwide. The causative agent of AHPND are Vibrio spp. Carrying plasmids containing the pirA and pirB genes which encode binary toxins, PirAB. Currently, AHPND is mostly diagnosed by PCR-based platforms which require the use of sophisticated laboratory instrumentation and are not suitable for a point-of-care diagnostics. Therefore, the availability of an alternative method based on isothermal amplification would be suitable for AHPND detection outside a laboratory setting and extremely useful at a pond side location. Isothermal amplification is based on the nucleic acid amplification at a single temperature and does not require the use of a thermal cycler. In this study, we developed an isothermal Recombinase Polymerase Amplification (RPA) assay for AHPND detection targeting both pirA and pirB genes, simultaneously and evaluated the specificity and sensitivity of the assay. The assay could detect AHPND without any cross-reaction with other microbial pathogens and Specific Pathogen Free (SPF) shrimp. The limit of detection of the assay was 5 copies of pirAB genes. To evaluate the reliability of the assay in detecting AHPND, DNA from Penaeus vannamei shrimp displaying acute and chronic infection were analyzed by the RPA assay and the results were compared with SYBR Green real-time PCR assay. While there was a 100% conformity between the two assay while detecting acute phase infection, RPA appeared to be more sensitive in detecting chronic phase infection. The data suggest that RPA assay described here would be a reliable method in detecting AHPND outside a standard laboratory setting.
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Affiliation(s)
- Hung Nam Mai
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Luis F Aranguren Caro
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Roberto Cruz-Flores
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA.
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Kumar Y. Isothermal amplification-based methods for assessment of microbiological safety and authenticity of meat and meat products. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Fang W, Cai Y, Zhu L, Wang H, Lu Y. Rapid and Highly Sensitive Detection of Toxigenic Vibrio cholerae Based on Recombinase-Aided Amplification Combining with Lateral Flow Assay. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01909-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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21
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Jaroenram W, Kampeera J, Arunrut N, Sirithammajak S, Jaitrong S, Boonnak K, Khumwan P, Prammananan T, Chaiprasert A, Kiatpathomchai W. Ultrasensitive detection of Mycobacterium tuberculosis by a rapid and specific probe-triggered one-step, simultaneous DNA hybridization and isothermal amplification combined with a lateral flow dipstick. Sci Rep 2020; 10:16976. [PMID: 33046776 PMCID: PMC7550604 DOI: 10.1038/s41598-020-73981-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/07/2020] [Indexed: 02/01/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an insidious scourge that has afflicted millions of people worldwide. Although there are many rapid methods to detect it based on loop-mediated isothermal amplification (LAMP) and a lateral flow dipstick (LFD), this study made further improvements using a new set of primers to enhance LAMP performance and a novel DNA probe system to simplify detection and increase specificity. The new probe system eliminates the post-LAMP hybridization step typically required for LFD assays by allowing co-hybridization and amplification of target DNA in one reaction while preventing self-polymerization that could lead to false-positive results. The improved assay was named Probe-Triggered, One-Step, Simultaneous DNA Hybridization and LAMP Integrated with LFD (SH-LAMP-LFD). SH-LAMP-LFD was simpler to perform and more sensitive than previously reported LAMP-LFD and PCR methods by 100 and 1000 times, respectively. It could detect a single cell of Mtb. The absence of cross-reactivity with 23 non-TB bacteria, and accurate test results with all 104 blind clinical samples have highlighted its accuracy. Its robustness and portability make SH-LAMP-LFD suitable for users in both low and high resource settings.
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Affiliation(s)
- Wansadaj Jaroenram
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Jantana Kampeera
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Narong Arunrut
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sarawut Sirithammajak
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sarinya Jaitrong
- Tuberculosis Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Pakapreud Khumwan
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Therdsak Prammananan
- Tuberculosis Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Angkana Chaiprasert
- Drug Resistant Tuberculosis Fund, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand.
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Tsai SK, Chen CC, Lin HJ, Lin HY, Chen TT, Wang LC. Combination of multiplex reverse transcription recombinase polymerase amplification assay and capillary electrophoresis provides high sensitive and high-throughput simultaneous detection of avian influenza virus subtypes. J Vet Sci 2020; 21:e24. [PMID: 32233132 PMCID: PMC7113572 DOI: 10.4142/jvs.2020.21.e24] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 12/30/2019] [Indexed: 11/20/2022] Open
Abstract
The pandemic of avian influenza viruses (AIVs) in Asia has caused enormous economic loss in poultry industry and human health threat, especially clade 2.3.4.4 H5 and H7 subtypes in recent years. The endemic chicken H6 virus in Taiwan has also brought about human and dog infections. Since wild waterfowls is the major AIV reservoir, it is important to monitor the diversified subtypes in wildfowl flocks in early stage to prevent viral reassortment and transmission. To develop a more efficient and sensitive approach is a key issue in epidemic control. In this study, we integrate multiplex reverse transcription recombinase polymerase amplification (RT-RPA) and capillary electrophoresis (CE) for high-throughput detection and differentiation of AIVs in wild waterfowls in Taiwan. Four viral genes were detected simultaneously, including nucleoprotein (NP) gene of all AIVs, hemagglutinin (HA) gene of clade 2.3.4.4 H5, H6 and H7 subtypes. The detection limit of the developed detection system could achieve as low as one copy number for each of the four viral gene targets. Sixty wild waterfowl field samples were tested and all of the four gene signals were unambiguously identified within 6 h, including the initial sample processing and the final CE data analysis. The results indicated that multiplex RT-RPA combined with CE was an excellent alternative for instant simultaneous AIV detection and subtype differentiation. The high efficiency and sensitivity of the proposed method could greatly assist in wild bird monitoring and epidemic control of poultry.
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Affiliation(s)
- Shou Kuan Tsai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chen Chih Chen
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.,Animal Biologics Pilot Production Center, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Han Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Han You Lin
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Ting Tzu Chen
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Lih Chiann Wang
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan.
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Hu J, Wang Y, Ding H, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Recombinase polymerase amplification with polymer flocculation sedimentation for rapid detection of Staphylococcus aureus in food samples. Int J Food Microbiol 2020; 331:108691. [PMID: 32534163 DOI: 10.1016/j.ijfoodmicro.2020.108691] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 01/02/2023]
Abstract
Currently, rapid, sensitive, and convenient visual detection methods for Staphylococcus aureus (S. aureus) are scarce. In this study, a novel detection method based on recombinase polymerase amplification (RPA) and polymer flocculation sedimentation (PFS) was developed. Twelve effective primer combinations derived from four forward primers F1, F2, F3, F4, and three reverse primers R1, R2, R3 targeting the nuc gene of S. aureus were designed and screened by a polymerase chain reaction and RPA methods. RPA reaction conditions, including temperature, time, and volume as well as PEG8000 and NaCl concentrations range, were optimized. Moreover, the specificity and sensitivity of the RPA-PFS assay were further analyzed. Finally, the potential use of the RPA-PFS assay was evaluated using artificially S. aureus contaminated food samples, including pork, beef, shrimp, fish, cheese, cabbage, leftover rice, egg, milk, and orange juice. Results showed that the SA5 (F2/R2) combination was the optimal primer candidate. The optimal temperature range, the shortest time and the minimal volume of RPA reaction were 40-42 °C, 10 min and 10 μL, respectively and the optimal PEG8000/NaCl concentrations were 0.2 g/mL and 2.5 M, respectively, for the adsorption between magnetic beads and RPA products. The RPA-PFS method could detect as little as 13 fg genomic DNA of S. aureus and was also specific for five target S. aureus as well as twenty-seven non-target foodborne bacteria. The limit of detection of RPA-PFS for S. aureus in artificially contaminated food samples was 38 CFU/mL (g). Besides, RPA-PFS has directly been judged by the naked eye and has totally taken less than 20 min. In short, the assay RPA-PFS developed in this study is a rapid, sensitive, and specific visual detection method for S. aureus.
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Affiliation(s)
- Jinqiang Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou 450000, Henan Province, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou 450000, Henan Province, China.
| | - Yi Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Huimin Ding
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Chunpeng Jiang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yao Geng
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Xincheng Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Jianzhou Jing
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Hui Gao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Zhangcun Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Caiwen Dong
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
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Xiong Y, Luo Y, Li H, Wu W, Ruan X, Mu X. Rapid visual detection of dengue virus by combining reverse transcription recombinase-aided amplification with lateral-flow dipstick assay. Int J Infect Dis 2020; 95:406-412. [PMID: 32272263 DOI: 10.1016/j.ijid.2020.03.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Dengue caused by infection with the dengue virus (DENV) is endemic in the tropical and subtropical regions of the world and of greatest public health concern. With more large outbreaks in rural areas, the purpose of this study was to develop a point-of-care test using recombinase-aided amplification and lateral-flow dipsticks for rapidly detecting DENV in low-resource settings. METHODS The primers for the recombinase-aided amplification (RAA) assay were designed based on 3' UTR of the DENV genome and screened. The RAA temperature, time and the concentration of primers were then optimized, as well as the lateral-flow dipstick assay (LFD) time. Finally, the diagnostic performance of the reverse transcription (RT)-RAA-LFD assay was evaluated using blood samples from 247 patients who were clinically suspected to be infected with DENV. RESULTS The RAA primer pair F1/R2 was the optimal combination for detecting DENV. The RT-RAA was performed in an incubator block at 37°C for 20minutes, and the amplicons were visible in the flow dipsticks from a naked eye within 3minutes. The detection limit of the developed RT-RAA-LFD assay was 10 copies/μL with high specificity for DENV. Compared with commercial reverse transcription quantitative PCR assay, the kappa value of RT-RAA-LFD in the 247 clinical samples was 0.957. CONCLUSIONS In this study, a rapid and visual point-of-care test based on RT-RAA and LFD assay was developed. It was found to be suitable for reliable detection of DENV in low-resource settings with limited laboratory capabilities and optimal storage conditions.
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Affiliation(s)
- Yufeng Xiong
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yasha Luo
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Huan Li
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Weixiang Wu
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xiaolin Ruan
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xiaoping Mu
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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Cherkasov VR, Mochalova EN, Babenyshev AV, Vasilyeva AV, Nikitin PI, Nikitin MP. Nanoparticle Beacons: Supersensitive Smart Materials with On/Off-Switchable Affinity to Biomedical Targets. ACS NANO 2020; 14:1792-1803. [PMID: 31944662 DOI: 10.1021/acsnano.9b07569] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Smart materials that can switch between different states under the influence of chemical triggers are highly demanded in biomedicine, where specific responsiveness to biomarkers is imperative for precise diagnostics and therapy. Superior selectivity of drug delivery to malignant cells may be achieved with the nanoagents that stay "inert" until "activation" by the characteristic profile of microenvironment cues (e.g., tumor metabolites, angiogenesis factors, microRNA/DNA, etc.). However, despite a wide variety and functional complexity of smart material designs, their real-life applications are hindered by very limited sensitivity to inputs. Here, we present ultrasensitive smart nanoagents with input-dependent On/Off switchable affinity to a biomedical target based on a combination of gold nanoparticles with low-energy polymer structures. In the proposed method, a nanoparticle-based agent is surface coated with a custom designed flexible polymer chain, which has an input-switchable structure that regulates accessibility of the terminal receptor for target binding. Implementation of the concept with a DNA-model of such polymer has yielded nanoagents that have input-dependent cell-targeting capabilities and responsiveness to as little as 30 fM of DNA input in 15 min lateral flow assay. Thus, we show that surface phenomena can augment nanoagents with capability for switchable affinity without compromising the sensitivity to inputs. The proposed approach is promising for development of next-generation theranostic agents and ultrasensitive nanosensors for point-of-care diagnostics.
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Affiliation(s)
- Vladimir R Cherkasov
- Moscow Institute of Physics and Technology , 9 Institutskii per. , 141700 Dolgoprudny, Moscow Region , Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences , 38 Vavilov St , 119991 Moscow , Russia
| | - Elizaveta N Mochalova
- Moscow Institute of Physics and Technology , 9 Institutskii per. , 141700 Dolgoprudny, Moscow Region , Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences , 38 Vavilov St , 119991 Moscow , Russia
| | - Andrey V Babenyshev
- Moscow Institute of Physics and Technology , 9 Institutskii per. , 141700 Dolgoprudny, Moscow Region , Russia
- Prokhorov General Physics Institute of the Russian Academy of Sciences , 38 Vavilov St , 119991 Moscow , Russia
| | - Alexandra V Vasilyeva
- Moscow Institute of Physics and Technology , 9 Institutskii per. , 141700 Dolgoprudny, Moscow Region , Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences , 38 Vavilov St , 119991 Moscow , Russia
| | - Maxim P Nikitin
- Moscow Institute of Physics and Technology , 9 Institutskii per. , 141700 Dolgoprudny, Moscow Region , Russia
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Li Z, Pinto Torres JE, Goossens J, Stijlemans B, Sterckx YGJ, Magez S. Development of a recombinase polymerase amplification lateral flow assay for the detection of active Trypanosoma evansi infections. PLoS Negl Trop Dis 2020; 14:e0008044. [PMID: 32069278 PMCID: PMC7048301 DOI: 10.1371/journal.pntd.0008044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/28/2020] [Accepted: 01/09/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Animal trypanosomosis caused by Trypanosoma evansi is known as "surra" and is a widespread neglected tropical disease affecting wild and domestic animals mainly in South America, the Middle East, North Africa and Asia. An essential necessity for T. evansi infection control is the availability of reliable and sensitive diagnostic tools. While DNA-based PCR detection techniques meet these criteria, most of them require well-trained and experienced users as well as a laboratory environment allowing correct protocol execution. As an alternative, we developed a recombinase polymerase amplification (RPA) test for Type A T. evansi. The technology uses an isothermal nucleic acid amplification approach that is simple, fast, cost-effective and is suitable for use in minimally equipped laboratories and even field settings. METHODOLOGY/PRINCIPLE FINDINGS An RPA assay targeting the T. evansi RoTat1.2 VSG gene was designed for the DNA-based detection of T. evansi. Comparing post-amplification visualization by agarose gel electrophoresis and a lateral flow (LF) format reveals that the latter displays a higher sensitivity. The RPA-LF assay is specific for RoTat1.2-expressing strains of T. evansi as it does not detect the genomic DNA of other trypanosomatids. Finally, experimental mouse infection trials demonstrate that the T. evansi specific RPA-LF can be employed as a test-of-cure tool. CONCLUSIONS/SIGNIFICANCE Compared to other DNA-based parasite detection methods (such as PCR and LAMP), the T. evansi RPA-LF (TevRPA-LF) described in this paper is an interesting alternative because of its simple read-out (user-friendly), short execution time (15 minutes), experimental sensitivity of 100 fg purified genomic T. evansi DNA, and ability to be carried out at a moderate, constant temperature (39°C). Therefore, the TevRPA-LF is an interesting tool for the detection of active T. evansi infections.
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Affiliation(s)
- Zeng Li
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Medical Biochemistry and the Infla-Med Centre of Excellence, University of Antwerp (UA), Campus Drie Eiken, Wilrijk, Belgium
| | - Joar Esteban Pinto Torres
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Julie Goossens
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Benoit Stijlemans
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Myeloid Cell Immunology, VIB Center for Inflammation Research, Brussels, Belgium
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry and the Infla-Med Centre of Excellence, University of Antwerp (UA), Campus Drie Eiken, Wilrijk, Belgium
| | - Stefan Magez
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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27
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Zhang Y, Hu J, Li Q, Guo J, Zhang G. Detection of microorganisms using recombinase polymerase amplification with lateral flow dipsticks. METHODS IN MICROBIOLOGY 2020. [DOI: 10.1016/bs.mim.2019.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Li XN, Shen XX, Li MH, Qi JJ, Wang RH, Duan QX, Zhang RQ, Fan T, Bai XD, Fan GH, Xie Y, Ma XJ. Applicability of duplex real time and lateral flow strip reverse-transcription recombinase aided amplification assays for the detection of Enterovirus 71 and Coxsackievirus A16. Virol J 2019; 16:166. [PMID: 31888694 PMCID: PMC6937715 DOI: 10.1186/s12985-019-1264-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the two main etiological agents of Hand, Foot and Mouth Disease (HFMD). Simple and rapid detection of EV71 and CA16 is critical in resource-limited settings. METHODS Duplex real time reverse-transcription recombinase aided amplification (RT-RAA) assays incorporating competitive internal amplification controls (IAC) and visible RT-RAA assays combined with lateral flow strip (LFS) for detection of EV71 and CA16 were developed respectively. Duplex real time RT-RAA assays were performed at 42 °C within 30 min using a portable real-time fluorescence detector, while LFS RT-RAA assays were performed at 42 °C within 30 min in an incubator. Recombinant plasmids containing conserved VP1 genes were used to analyze the sensitivities of these two methods. A total of 445 clinical specimens from patients who were suspected of being infected with HFMD were used to evaluate the performance of the assays. RESULTS The limit of detection (LoD) of the duplex real time RT-RAA for EV71 and CA16 was 47 copies and 38 copies per reaction, respectively. The LoD of the LFS RT-RAA for EV71 and CA16 were both 91 copies per reaction. There was no cross reactivity with other enteroviruses. Compared to reverse transcription-quantitative PCR (RT-qPCR), the clinical diagnostic sensitivities of the duplex real time RT-RAA assay were 92.3% for EV71 and 99.0% for CA16, and the clinical diagnostic specificities were 99.7 and 100%, respectively. The clinical diagnostic sensitivities of the LFS RT-RAA assay were 90.1% for EV71 and 94.9% for CA16, and the clinical diagnostic specificities were 99.7 and 100%, respectively. CONCLUSIONS The developed duplex real time RT-RAA and LFS RT-RAA assays for detection of EV71 and CA16 are potentially suitable in primary clinical settings.
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Affiliation(s)
- Xin-Na Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Ming-Hui Li
- Department of hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Jing Shun Dong Jie 8#, Beijing, 100015, China
| | - Ju-Ju Qi
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Rui-Huan Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Qing-Xia Duan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Tao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Xue-Ding Bai
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China
| | - Yao Xie
- Department of hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Jing Shun Dong Jie 8#, Beijing, 100015, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China.
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Wang H, Zhou S, Wen J, Sun M, Jiang Y, Lu L, Xie J. A real-time reverse-transcription isothermal recombinase polymerase amplification assay for the rapid detection of genotype III grass carp (Ctenopharyngodon idella) reovirus. J Virol Methods 2019; 277:113802. [PMID: 31843672 DOI: 10.1016/j.jviromet.2019.113802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 11/06/2019] [Accepted: 12/12/2019] [Indexed: 02/04/2023]
Abstract
Grass carp (Ctenopharyngodon idella) hemorrhagic disease, which is characterized by external and internal hemorrhage, is a serious infectious disease affecting grass carp production. Strains of the causative agent, grass carp reovirus (GCRV), are divided into genotypes I, II and III, which are represented by the isolates GCRV-873, GCRV-HZ08 and GCRV-104, respectively. In this study, a real-time reverse-transcription recombinase polymerase amplification (real-time RT-RPA) assay was developed to detect the genotype III grass carp reovirus GCRV-104. The assay was based on the detection of the vp55 gene which encodes the outer fiber protein of the virus. A portable ESE-Quant Tube scanner, with a dimension of 17.4 × 18.8 cm, weighing about 1 kg, and equipped with temperature settings to amplify the DNA isothermally and spectral devices to detect the amplified products using fluorescence, was used to complete the assay. Under the optimal conditions, the assay took approximately 10 min to complete at 37 °C and showed no cross-reactions with other aquatic viruses. Consequently, this rapid real-time RT-RPA assay is a useful method for the simple, rapid and reliable detection of genotype III GCRV strains in resource-limited diagnostic laboratories.
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Affiliation(s)
- Hao Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China.
| | - Shuting Zhou
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China; Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jinxuan Wen
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China
| | - Meng Sun
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China
| | - Yousheng Jiang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China.
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture Shanghai Ocean University, Shanghai, PR China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, PR China.
| | - Jing Xie
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai Ocean University, Shanghai, PR China.
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30
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Zeng F, Wu M, Ma L, Han Z, Shi Y, Zhang Y, Liu C, Zhang S, Cong F, Liu S. Rapid and sensitive real-time recombinase polymerase amplification for detection of Marek's disease virus. Mol Cell Probes 2019; 48:101468. [PMID: 31580913 DOI: 10.1016/j.mcp.2019.101468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
Marek's disease (MD) is one of the most devastating diseases of poultry. It's caused by the highly infectious alphaherpesvirus MD virus serotype 1 (MDV-1). In this study, a rapid and easy-to-use assay based on recombinase polymerase amplification (RPA) was developed for MDV detection. Primer-probe sets targeting the highly conserved region of Meq gene were designed and applied to the RPA assay. The assay was carried out on a real-time thermostatic fluorescence detector at 39 °C for 20 min. As revealed by the results, no cross-reactions were found with the Newcastle disease virus (NDV), chicken infectious anemia virus (CAV), infectious bursal disease virus (IBDV), avian infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), avain influenza virus (AIV), avian leucosis virus (ALV), avian reovirus (ARV), Marek's disease virus serotype 2 (MDV-2) and turkey herpes virus (HVT), indicating appropriate specificity of the assay. Plasmid DNA standards were used to determine the sensitivity of the assay and the detection limit was 102copies/μL. To further evaluate the clinical performance, 94 clinical samples were subjected to the RPA assay and 28 samples were tested MDV positive, suggesting that the real-time RPA assay was sufficient enough for clinical sample detection. Thus, a highly specific and sensitive real-time RPA assay was established and validated as a candidate for MDV diagnosis. Additionally, the portability of real-time RPA assay makes it suitable to be potentially applied in clinical diagnosis in the field, especially in resource-limited settings.
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Affiliation(s)
- Fanwen Zeng
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China; College of Animal Science of South China Agricultural University, Guangzhou, 510640, China
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Lei Ma
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Zongxi Han
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, 150026, China
| | - Yue Shi
- Beijing Senkang Biotech Development Co., Ltd., Beijing, 101400, China
| | - Yanping Zhang
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, 150026, China
| | - Changjun Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, 150026, China
| | - Shouquan Zhang
- College of Animal Science of South China Agricultural University, Guangzhou, 510640, China.
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Shengwang Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, 150026, China.
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31
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Guo Z, Chen Z, Liu X, Chen J, Chen G, Liu Z, Yang G, Lan Q. Detection of Listeria monocytogenesand Staphylococcus aureus viaduplex recombinase polymerase amplification. J Food Saf 2019. [DOI: 10.1111/jfs.12628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhengyang Guo
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
- School of Food Science and TechnologyHenan University of Technology Zhengzhou China
| | - Zhaobin Chen
- West China School of Public HealthSichuan University Chengdu China
- Microbiological Clinical LaboratoryShenzhen Nanshan Center for Disease Control and Prevention Shenzhen China
| | - Xiaoqing Liu
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
| | - Jing Chen
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
| | - Guopei Chen
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
| | - Zhongdong Liu
- School of Food Science and TechnologyHenan University of Technology Zhengzhou China
| | - Guowu Yang
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
| | - Quanxue Lan
- Food Inspection InstituteShenzhen Academy of Metrology & Quality Inspection Shenzhen China
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Wu L, Ye L, Wang Z, Cui Y, Wang J. Utilization of recombinase polymerase amplification combined with a lateral flow strip for detection of Perkinsus beihaiensis in the oyster Crassostrea hongkongensis. Parasit Vectors 2019; 12:360. [PMID: 31340841 PMCID: PMC6657052 DOI: 10.1186/s13071-019-3624-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/19/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Perkinsosis, a disease caused by the protist Perkinsus, is responsible for mass mortalities of many molluscan species worldwide. The rapid, early and accurate detection of Perkinsus infection is necessary to react to outbreaks, and manage disease transmission. Current methods for diagnosis of Perkinsus spp. are time-consuming or require professional equipment and experienced personnel, rendering them unsuitable for field application. Recombinase polymerase amplification (RPA) assay is a highly sensitive and selective isothermal amplification technique that operates at temperatures of 37-42 °C, requires minimal sample preparation, and is capable of amplifying as low as 1-10 target DNA copies in less than 20 minutes. METHODS We report a novel RPA assay that amplifies the internal transcriber spacer (ITS) region of P. beihaiensis, which, followed by rapid detection of amplicons using a lateral flow (LF) strip, enables easy visualization of results by the naked eye. RESULTS The LF-RPA assay successfully amplified P. beihaiensis DNA using a set of primers of 20-25 bp in length. After incubation at 37 °C for 25 min, results were read within 5 min by the naked eye on a lateral flow strip. Our LF-RPA assay was comparably sensitive to qPCR assay, and capable of detecting as few as 26 copies of P. beihaiensis DNA. Cross-amplification occurred with other two Perkinsus species, P. olseni and P. chesapeaki, but not with other potential pathogen taxa in culture environments. We compared the performance of LF-RPA, conventional PCR and qPCR assays on 60 oyster samples. While LF-RPA assay results were 86.2% as sensitive, 77.4% as specific, and generally in agreement with those of conventional PCR results, they were more (93.3%) sensitive, (86.7%) specific, and agreed better with qPCR assay results. Future research should focus on developing simple DNA extraction methods that do not require professional laboratories and complicated extraction procedures, to facilitate application of this LF-RPA assay in the field. CONCLUSIONS Our LF-RPA assay provides a rapid and efficient method for detecting species of Perkinsus. This novel assay has potential to be used in field applications.
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Affiliation(s)
- Lin Wu
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
- Shanghai Ocean University, Shanghai, 201306 China
| | - Lingtong Ye
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
| | - Zhaorui Wang
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300384 China
| | - Yingyi Cui
- Zhongshan Center for Animal Disease Prevention and Control, Zhongshan, 528455 Guangdong China
| | - Jiangyong Wang
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
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Liu L, Yang D, Liu G. Signal amplification strategies for paper-based analytical devices. Biosens Bioelectron 2019; 136:60-75. [DOI: 10.1016/j.bios.2019.04.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
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Liu X, Yan Q, Huang J, Chen J, Guo Z, Liu Z, Cai L, Li R, Wang Y, Yang G, Lan Q. Influence of design probe and sequence mismatches on the efficiency of fluorescent RPA. World J Microbiol Biotechnol 2019; 35:95. [PMID: 31187258 DOI: 10.1007/s11274-019-2620-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 02/24/2019] [Indexed: 11/27/2022]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal amplification technique. Because of its short detection cycle and high specificity, it has been applied in various fields. However, the design of probe on the efficiency of RPA is not well understood and the effect of sequence mismatches of oligonucleotides on the performance of RPA is rarely discussed. In this study, we found that different primers with the same probe have a slight effect on the efficiency of fluorescent RPA, and different probes with the same amplified region have a great influence on the efficiency of fluorescent RPA. We summarized the design rules of probes suitable for fluorescent RPA by analyzing the experimental data. The rule is that the best distance between fluorescent groups in the probe is 1-2 bases, and the G content should be reduced as far as possible. In addition, we verified this rule by designing a series of probes. Furthermore, we found the base mismatches of the probe had a significant effect on RPA, which can lead to false positives and can change the amplification efficiency. However, 1-3 mismatches covering the center of the primer sequence only affect the amplification efficiency of RPA, not its specificity. And with an increase in the number of primer mismatches, the efficiency of RPA will decrease accordingly. This study suggests that the efficiency of fluorescent RPA is closely related to the probe. We recommend that when designing a fluorescent probe, one must consider the presence of closely related non-targets and specific bases.
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Affiliation(s)
- Xiaoqing Liu
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Qiongying Yan
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Jianfei Huang
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Jing Chen
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Zhengyang Guo
- Henan University of Technology, Zhengzhou, 450001, China
| | - Zhongdong Liu
- Henan University of Technology, Zhengzhou, 450001, China
| | - Lin Cai
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Risheng Li
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Yan Wang
- China HYK Gene Technology Company Limited, Shenzhen, 518131, China
| | - Guowu Yang
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China
| | - Quanxue Lan
- Shenzhen Academy of Metrology & Quality Inspection, Shenzhen, 518131, China.
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Jiao Y, Jiang J, Wu Y, Xia Z. Rapid detection of Cucumber green mottle mosaic virus in watermelon through a recombinase polymerase amplification assay. J Virol Methods 2019; 270:146-149. [PMID: 31136756 DOI: 10.1016/j.jviromet.2019.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 01/28/2023]
Abstract
Cucumber green mottle mosaic virus (CGMMV), a member of the genus Tobamovirus, is an important quarantine plant virus worldwide, and often causes seriously damages to productions of watermelon, melon, cucumber and other cucurbit crops. In this study, we developed a novel isothermal recombinase polymerase amplification (RPA) technique for detection of CGMMV in watermelon samples. A pair of CGMMV specific RPA primers was prepared based on the conserved CGMMV coat protein gene sequences. The result showed that this RPA detection method can be performed at 38 °C and completed in about 30 min, and there was no cross-reactivity with other common cucurbit viruses. Sensitivity assay showed that this RPA method was more sensitive compared with the regular RT-PCR. Using field-collected watermelon tissue samples, we have demonstrated that this newly developed method is rapid, easy to use and reliable for CGMMV detection, especially in resource-limited laboratories or on-site facilities.
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Affiliation(s)
- Yubing Jiao
- College of plant protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Junyun Jiang
- College of plant protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhua Wu
- College of plant protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Zihao Xia
- College of plant protection, Shenyang Agricultural University, Shenyang 110866, China.
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Wu Y, Tian K, Zhang Y, Guo H, Li N, Wang Z, Zhao J. Rapid and visual detection of Lawsonia intracellularis with an improved recombinase polymerase amplification assay combined with a lateral flow dipstick. BMC Vet Res 2019; 15:97. [PMID: 30898117 PMCID: PMC6429820 DOI: 10.1186/s12917-019-1841-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/10/2019] [Indexed: 12/05/2022] Open
Abstract
Background Lawsonia intracellularis (L. intracellularis) is the etiologic agent of porcine proliferative enteropathy (PPE), which is reported in many swine breeding countries all over the world, and has caused enormous economic losses in intensive pig production systems. Therefore, the aim of this study was to develop a simple and rapid method for on-site detection of Lawsonia intracellularis (L. intracellularis). As the isothermal recombinase polymerase amplification (RPA) can be performed at a constant temperature and its product is directly observed on a lateral-flow dipstick (LFD) with naked eyes without electrophoresis, the RPA-LFD assay should be useful for field diagnosis of L. intracellularis as well as its detection from clinical samples. Results The established RPA-LFD assay could be finished in 30 min at a wide temperature range of 25 to 40 °C, and the amplicons could be visualized by naked eyes. The developed RPA-LFD assay was specific to dnaA gene of L. intracellularis, and did not detect nucleic acids extracted from other common gastrointestinal pathogens. The minimum detection of this RPA-LFD method was 400 L. intracellularis per reaction, which was as sensitive as conventional PCR. Further, the RPA-LFD assay was performed with 150 clinical fecal samples and the detection results were compared with conventional PCR. Results showed that the coincidence rate of RPA-LFD and conventional PCR was 100%. Conclusions The combined RPA with LFD assay provides a simple, rapid, specific and sensitive alternative for field diagnosis of L. intracellularis infection.
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Affiliation(s)
- Yanyang Wu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kaiyue Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuhan Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Huifang Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ning Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zeng Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.
| | - Jun Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.
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Hu J, Huang R, Sun Y, Wei X, Wang Y, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Sensitive and rapid visual detection of Salmonella Typhimurium in milk based on recombinase polymerase amplification with lateral flow dipsticks. J Microbiol Methods 2019; 158:25-32. [DOI: 10.1016/j.mimet.2019.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
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Wang Z, Yang PP, Zhang YH, Tian KY, Bian CZ, Zhao J. Development of a reverse transcription recombinase polymerase amplification combined with lateral-flow dipstick assay for avian influenza H9N2 HA gene detection. Transbound Emerg Dis 2018; 66:546-551. [PMID: 30403438 DOI: 10.1111/tbed.13063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/11/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022]
Abstract
H9N2 avian influenza viruses (AIVs) have been detected from wild birds and domestic poultry worldwide. Serious diseases combined with secondary infection have caused high mortality and great economic losses to poultry industry. Therefore, simple, rapid, sensitive and accurate methods suitable for field detection of H9N2 AIVs are crucial to efficiently control virus infection and spread in time. In this study, an isothermal reverse transcription recombinase polymerase amplification with lateral-flow dipstick (RT-RPA-LFD) assay for detection of hemagglutinin (HA) gene of H9 subtype influenza viruses was developed. The optimal forward and reverse primers targeting HA gene of H9 subtype influenza viruses were labeled with fluorescein isothiocyanate (FITC) and biotin at the 5'-end, respectively. The amplification reaction could be finished in 20 min at a wide temperature range of 30-42°C, and then the products could be visualized with naked eyes. The developed H9 RT-RPA-LFD was able to detect 0.15 pg of H9N2 AIV RNA, which was 10 times more sensitive than that of conventional RT-PCR. The H9 RT-RPA-LFD assay did not detect nucleic acids extracted from H9 negative samples or from other poultry respiratory pathogens. The clinical performance of H9 RT-RPA-LFD was determined by testing 120 cloacal samples collected from chickens with respiratory syndromes. The coincidence rate of the detection results between RT-RPA-LFD and conventional RT-PCR was 95.8%. Therefore, the developed RT-RPA-LFD assay provides a rapid, reliable and sensitive method for field diagnosis of H9 subtype AIVs.
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Affiliation(s)
- Zeng Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pan-Pan Yang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Yu-Han Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Kai-Yue Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Chuan-Zhou Bian
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Jun Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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A novel method to detect meat adulteration by recombinase polymerase amplification and SYBR green I. Food Chem 2018; 266:73-78. [DOI: 10.1016/j.foodchem.2018.05.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022]
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40
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Xu J, Wang X, Yang L, Kan B, Lu X. Rapid detection of mcr-1 by recombinase polymerase amplification. J Med Microbiol 2018; 67:1682-1688. [PMID: 30355422 DOI: 10.1099/jmm.0.000865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The plasmid-mediated mcr-1 gene conferring colistin resistance has a strong ability to spread. The objective of this study was to establish a rapid and sensitive recombinase polymerase amplification (RPA) method for plasmid-mediated polymyxin-resistant gene mcr-1 detection. METHODS Using the reported sequence of the mcr-1 gene, we designed specific primers and probes for RPA. Twenty mcr-1-positive strains carrying IncI2/IncHI2/IncX4/IncP plasmids were screened by RPA in this study. The performance of this new assay was compared to that of PCR, TaqMan probe real-time PCR and SYBR Green-based real-time PCR. RESULTS Twenty mcr-1-positive samples and three negative samples were tested by RPA and the positive detection rate for the mcr-1-positive samples was 100 %. The detection limit of RPA was approximately 100 fg. Compared with real-time PCR, the RPA assay was more effective due to shorter reaction times, simpler instruments and higher sensitivity, while it had the same high specificity as real-time PCR. CONCLUSION RPA detection based on the mcr-1 gene was successfully applied in our study. The plasmid-mediated mcr-1 gene conferring colistin drug resistance has a strong ability to spread, suggesting the need to further strengthen the detection of this resistance gene in surveillance. Therefore, we require more sensitive detection methods than have previously been available and the RPA assay established in this study meets these detection needs.
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Affiliation(s)
- Jialiang Xu
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), PR China.,2School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, PR China
| | - Xiaoxun Wang
- 3State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China.,4Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China.,1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), PR China.,2School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, PR China
| | - Liya Yang
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), PR China.,2School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, PR China.,3State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China.,4Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China
| | - Biao Kan
- 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), PR China.,3State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China.,4Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China
| | - Xin Lu
- 3State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China.,4Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, PR China.,1Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), PR China
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Cui J, Zhao Y, Sun Y, Yu L, Liu Q, Zhan X, Li M, He L, Zhao J. Detection of Babesia gibsoni in dogs by combining recombinase polymerase amplification (RPA) with lateral flow (LF) dipstick. Parasitol Res 2018; 117:3945-3951. [PMID: 30293152 DOI: 10.1007/s00436-018-6104-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/30/2018] [Indexed: 01/16/2023]
Abstract
Babesia gibsoni is a protozoan parasite responsible for the majority of reported cases of canine babesiosis in China. Currently, microscopic examination of the Giemsa-stained thin blood smears is the main diagnosis method in clinic. Here, we report the recombinase polymerase amplification-lateral flow (LF-RPA) dipstick detection method for targeting B. gibsoni cytochrome c oxidase subunit I (cox I) gene. The reaction takes only 20-30 min under isothermal temperatures between 30 and 45 °C. Specificity was evaluated using DNA from related apicomplexan parasites and their host, while the sensitivity was calculated based on the DNA from the experimental B. gibsoni-infected dogs. Results indicated that the LF-RPA method is 20 times more sensitive than the conventional PCR based on 18S rRNA and has no cross reaction with any other test DNAs. The applicability of the LF-RPA method was further evaluated using 15 samples collected from clinic. Thirteen of the 15 samples (86.67%) were detected as positive by LF-RPA, while 10 of them (66.67%) were found positive by conventional PCR. Overall, the novel LF-RPA assay is effective for the detection of B. gobsini and has considerable advantages over the conventional PCR in sensitivity, specificity, simplicity in operation, less time consumption, and visual detection. The LF-RPA method may facilitate the surveillance and early detection of B. gibsoni infection in dogs.
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Affiliation(s)
- Jie Cui
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yangnan Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yali Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Long Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Qin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xueyan Zhan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muxiao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Laboratory for Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
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Cowley JA, Rao M, Coman GJ. Real-time PCR tests to specifically detect IHHNV lineages and an IHHNV EVE integrated in the genome of Penaeus monodon. DISEASES OF AQUATIC ORGANISMS 2018; 129:145-158. [PMID: 29972375 DOI: 10.3354/dao03243] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infectious hypodermal and hematopoietic necrosis virus (IHHNV) can cause mass mortalities in western blue shrimp Penaeus stylirostris, runt deformity syndrome in Pacific white shrimp P. vannamei and scalloped abdominal shell deformities in black tiger shrimp P. monodon. In P. monodon, however, PCR-based diagnosis of IHHNV can be complicated by the presence of a chromosome-integrated, non-replicating endogenous viral element (EVE). To facilitate high-throughput screening of P. monodon for IHHNV infection and/or EVE sequences, here we report real-time PCR tests designed to specifically detect IHHNV Lineage I, II and III but not EVE Type A sequences and vice versa. Using 108 dsDNA copies of plasmid (p)DNA controls containing either IHHNV or EVE-Type A sequences, both tests displayed absolute specificity. The IHHNV-q309 PCR reliably detected down to ≤10 copies of pDNA, at which levels a 309F/R PCR amplicon was just detectable, and the presence of an IHHNV-EVE sequence did not significantly impact its sensitivity. The IHHNV-qEVE PCR was similarly sensitive. Testing of batches of P. monodon clinical samples from Vietnam/Malaysia and Australia identified good diagnostic concordance between the IHHNV-q309 and 309F/R PCR tests. As expected for a sequence integrated into host chromosomal DNA, IHHNV-qEVE PCR Ct values were highly uniform among samples from shrimp in which an EVE was present. The highly specific and sensitive IHHNV-q309 and IHHNV-qEVE real-time PCR tests described here should prove useful for selecting broodstock free of IHHNV infection and in maintaining breeding populations of P. monodon specific pathogen free for IHHNV, and if desired, also free of IHHNV-EVE sequences.
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Affiliation(s)
- Jeff A Cowley
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
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Wang H, Sun M, Xu D, Podok P, Xie J, Jiang Y, Lu L. Rapid visual detection of cyprinid herpesvirus 2 by recombinase polymerase amplification combined with a lateral flow dipstick. JOURNAL OF FISH DISEASES 2018; 41:1201-1206. [PMID: 29806130 DOI: 10.1111/jfd.12808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
Herpesviral haematopoietic necrosis (HVHN), caused by cyprinid herpesvirus 2 (CyHV-2), causes significant losses in crucian carp (Carassius carassius) aquaculture. Rapid and convenient DNA assay detection of CyHV-2 is useful for field diagnosis. Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that can amplify DNA within 30 min at ~37°C by simulating in vivo DNA recombination. Herein, a rapid and convenient detection assay based on RPA with a lateral flow dipstick (LFD) was developed for detecting CyHV-2. The highly conserved ORF72 of CyHV-2 was targeted by specific and sensitive primers and probes. The optimized assay takes only 15 min at 38°C using a water bath, with analysis of products by 2% agarose gel electrophoresis within 30 min. A simple lateral flow strip based on the unique probe in reaction buffer was developed for visualization. The entire RPA-LFD assay takes 50 min less than the routine PCR method, is 100 times more sensitive and displays no cross-reaction with other aquatic viruses. The combined isothermal RPA and lateral flow assay (RPA-LFD) provides a simple, rapid, reliable method that could improve field diagnosis of CyHV-2 when resources are limited.
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Affiliation(s)
- H Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - M Sun
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - D Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - P Podok
- Faculty of Agricultural Technology, Phuket Rajabhat University, Phuket, Thailand
| | - J Xie
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Ys Jiang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Lq Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
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Soliman H, Kumar G, El-Matbouli M. Recombinase polymerase amplification assay combined with a lateral flow dipstick for rapid detection of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in salmonids. Parasit Vectors 2018; 11:234. [PMID: 29642952 PMCID: PMC5896054 DOI: 10.1186/s13071-018-2825-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Background The myxozoan Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD), is responsible for considerable losses in farmed and wild fish populations in Europe and North America. Recently, T. bryosalmonae was detected in many European countries, and strategy to control the disease in the wild and farmed fish population is yet to be developed. Recombinase polymerase amplification (RPA) is a novel isothermal nucleic acid amplification technology that does not require any thermal cycling, and lateral flow dipstick (LFD) is a rapid, cost-effective, and easy-to-handle assay that enables stable detection. Results In this study, we developed and optimized a rapid and sensitive RPA assay combined with an LFD for the detection of T. bryosalmonae. The PKD-RPA assay was specific to T. bryosalmonae, as no cross-reaction or false positive signals were observed with any of the other tested DNAs. The developed PKD-RPA assay was ten times more sensitive than an existing diagnostic polymerase chain reaction (PCR) assay for this parasite. The estimated time to perform PKD-RPA assay is 25 min compared to 4 h for PKD-PCR assay. Conclusions A novel PKD-RPA assay for the detection of T. bryosalmonae was developed. The assay offers considerable advantages including speed, sensitivity, specificity and visual detection. Applying the PKD-RPA assay combined with an LFD enhances the surveillance and early detection of T. bryosalmonae in salmonids.
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Affiliation(s)
- Hatem Soliman
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
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Recombinase polymerase amplification applied to plant virus detection and potential implications. Anal Biochem 2018; 546:72-77. [DOI: 10.1016/j.ab.2018.01.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 11/15/2022]
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Shahin K, Gustavo Ramirez-Paredes J, Harold G, Lopez-Jimena B, Adams A, Weidmann M. Development of a recombinase polymerase amplification assay for rapid detection of Francisella noatunensis subsp. orientalis. PLoS One 2018; 13:e0192979. [PMID: 29444148 PMCID: PMC5812721 DOI: 10.1371/journal.pone.0192979] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/01/2018] [Indexed: 11/18/2022] Open
Abstract
Francisella noatunensis subsp. orientalis (Fno) is the causative agent of piscine francisellosis in warm water fish including tilapia. The disease induces chronic granulomatous inflammation with high morbidity and can result in high mortality. Early and accurate detection of Fno is crucial to set appropriate outbreak control measures in tilapia farms. Laboratory detection of Fno mainly depends on bacterial culture and molecular techniques. Recombinase polymerase amplification (RPA) is a novel isothermal technology that has been widely used for the molecular diagnosis of various infectious diseases. In this study, a recombinase polymerase amplification (RPA) assay for rapid detection of Fno was developed and validated. The RPA reaction was performed at a constant temperature of 42°C for 20 min. The RPA assay was performed using a quantitative plasmid standard containing a unique Fno gene sequence. Validation of the assay was performed not only by using DNA from Fno, closely related Francisella species and other common bacterial pathogens in tilapia farms, but also by screening 78 Nile tilapia and 5 water samples. All results were compared with those obtained by previously established real-time qPCR. The developed RPA showed high specificity in detection of Fno with no cross-detection of either the closely related Francisella spp. or the other tested bacteria. The Fno-RPA performance was highly comparable to the published qPCR with detection limits at 15 and 11 DNA molecules detected, respectively. The RPA gave quicker results in approximately 6 min in contrast to the qPCR that needed about 90 min to reach the same detection limit, taking only 2.7–3 min to determine Fno in clinical samples. Moreover, RPA was more tolerant to reaction inhibitors than qPCR when tested with field samples. The fast reaction, simplicity, cost-effectiveness, sensitivity and specificity make the RPA an attractive diagnostic tool that will contribute to controlling the infection through prompt on-site detection of Fno.
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Affiliation(s)
- Khalid Shahin
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
- Aquatic Animal Diseases Lab, Division of Aquaculture, National Institute of Oceanography and Fisheries, Suez, Egypt
- * E-mail:
| | - Jose Gustavo Ramirez-Paredes
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Graham Harold
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Benjamin Lopez-Jimena
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Manfred Weidmann
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
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Real-time quantitative isothermal detection of Ostreid herpesvirus-1 DNA in Scapharca subcrenata using recombinase polymerase amplification. J Virol Methods 2018; 255:71-75. [PMID: 29428398 DOI: 10.1016/j.jviromet.2018.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 12/21/2022]
Abstract
Ostreid herpesvirus-1 (OsHV-1) is a well-known pathogen associated with high mortality rates in hatchery-reared larvae and juveniles of different bivalve species worldwide. Early, rapid and accurate diagnosis plays a fundamental role in disease prevention and control in aquaculture. Recombinase polymerase amplification (RPA) is a novel isothermal amplification method, which can amplify detectable amount of DNA at 37 °C-39 °C within 20 min. In the present study, two sets of specific primers and probes were designed for the real-time quantitative RPA (qRPA) detection of OsHV-1 DNA. The sensitivity and specificity of detection were evaluated by comparison with quantitative polymerase chain reaction (qPCR). The detection limit for qRPA assays was shown to be 5 copies DNA/reaction for the primer set ORF95, which was lower than the 100 copies required for the qPCR test. The optimal reaction temperature and time were 37 °C for 20 min, making this approach faster than qPCR. This is the first study to apply qPCR and qRPA methods to detect OsHV-1 in Scapharca subcrenata. The percentage of viral load sample detected by the two methods was 22% and the correlation of the two virus quantitative results was 0.8. Therefore, qRPA assays is sensitive, fast, and high-temperature independent relative to qPCR and is suitable for critical clinical diagnostics use and rapid field analysis in resource-limited settings.
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Poulton K, Webster B. Development of a lateral flow recombinase polymerase assay for the diagnosis of Schistosoma mansoni infections. Anal Biochem 2018; 546:65-71. [PMID: 29425749 DOI: 10.1016/j.ab.2018.01.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 12/14/2022]
Abstract
Infection with Schistosoma mansoni causes intestinal schistosomiasis, a major health problem across Africa. The accurate diagnosis of intestinal schistosomiasis is vital to inform surveillance/control programs. Diagnosis mainly relies on microscopic detection of eggs in faecal samples but many factors affect sensitivity. Molecular diagnostics are sensitive and specific but application is limited as necessary infrastructure, financial resources and skilled personnel are often lacking in endemic settings. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification/detection technology that is practical in nearly any setting. Here we developed a RPA lateral flow (LF) assay targeting the 28S rDNA region of S. mansoni. The 28S LF-RPA assay's lower limit of detection was 10pg DNA with the lower test parameters permitting sufficient amplification being 6 min and 25°C. Optimal assay parameters were 40-45°C and 10 min with an analytical sensitivity of 102 copies of DNA. Additionally the PCRD3 lateral flow detection cassettes proved more robust and sensitive compared to the Milenia HybriDetect strips. This 28S LF-RPA assay produces quick reproducible results that are easy to interpret, require little infrastructure and is a promising PON test for the field molecular diagnosis of intestinal schistosomiasis.
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Affiliation(s)
- Kate Poulton
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK; The Natural History Museum, Cromwell Road, London, UK
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Yang HL, Wei S, Gooneratne R, Mutukumira AN, Ma XJ, Tang SZ, Wu XY. Development of a recombinase polymerase amplification assay for Vibrio parahaemolyticus detection with an internal amplification control. Can J Microbiol 2018; 64:223-230. [PMID: 29351385 DOI: 10.1139/cjm-2017-0504] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A novel RPA-IAC assay using recombinase polymerase and an internal amplification control (IAC) for Vibrio parahaemolyticus detection was developed. Specific primers were designed based on the coding sequence for the toxR gene in V. parahaemolyticus. The recombinase polymerase amplification (RPA) reaction was conducted at a constant low temperature of 37 °C for 20 min. Assay specificity was validated by using 63 Vibrio strains and 10 non-Vibrio bacterial species. In addition, a competitive IAC was employed to avoid false-negative results, which co-amplified simultaneously with the target sequence. The sensitivity of the assay was determined as 3 × 103 CFU/mL, which is decidedly more sensitive than the established PCR method. This method was then used to test seafood samples that were collected from local markets. Seven out of 53 different raw seafoods were detected as V. parahaemolyticus-positive, which were consistent with those obtained using traditional culturing method and biochemical assay. This novel RPA-IAC assay provides a rapid, specific, sensitive, and more convenient detection method for V. parahaemolyticus.
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Affiliation(s)
- Huan-Lan Yang
- a Department of Food Science and Engineering, Jinan University, Guangzhou 510632, China
| | - Shuang Wei
- b Guangdong Entry-Exit Inspection and Quarantine Bureau, Guangzhou 510632, China
| | - Ravi Gooneratne
- c Centre for Food Research and Innovation, Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture & Life Sciences, Lincoln University, Christchurch 7647, New Zealand
| | - Anthony N Mutukumira
- d Massey Institute of Food Science and Technology, Institute of Food and Nutrition, Massey University, Albany Campus, New Zealand
| | - Xue-Jun Ma
- e Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shu-Ze Tang
- a Department of Food Science and Engineering, Jinan University, Guangzhou 510632, China
| | - Xi-Yang Wu
- a Department of Food Science and Engineering, Jinan University, Guangzhou 510632, China
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Ma Q, Liu H, Ye F, Xiang G, Shan W, Xing W. Rapid and visual detection of Mycobacterium tuberculosis complex using recombinase polymerase amplification combined with lateral flow strips. Mol Cell Probes 2017; 36:43-49. [DOI: 10.1016/j.mcp.2017.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 01/30/2023]
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