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Zhao Y, Zhou C, Guo B, Yang X, Wang H. Pyrococcus furiosus Argonaute-mediated porcine epidemic diarrhea virus detection. Appl Microbiol Biotechnol 2024; 108:137. [PMID: 38229331 DOI: 10.1007/s00253-023-12919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, induces severe vomiting and acute watery diarrhea in unweaned piglets. The pig industry has suffered tremendous financial losses due to the high mortality rate of piglets caused by PEDV. Consequently, a simple and rapid on-site diagnostic technology is crucial for preventing and controlling PEDV. This study established a detection method for PEDV using recombinase-aided amplification (RAA) and Pyrococcus furiosus Argonaute (PfAgo), which can detect 100 copies of PEDV without cross-reactivity with other pathogens. The entire reaction of RAA and PfAgo to detect PEDV does not require sophisticated instruments, and the reaction results can be observed with the naked eye. Overall, this integrated RAA-PfAgo cleavage assay is a practical tool for accurately and quickly detecting PEDV. KEY POINTS: • PfAgo has the potential to serve as a viable molecular diagnostic tool for the detection and diagnosis of viral genomes • The RAA-PfAgo detection technique has a remarkable level of sensitivity and specificity • The RAA-PfAgo detection system can identify PEDV without needing advanced equipment.
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Affiliation(s)
- Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Wu Q, Liu X, Wang J, Xu S, Zeng F, Chen L, Zhang G, Wang H. An isothermal nucleic acid amplification-based enzymatic recombinase amplification method for dual detection of porcine epidemic diarrhea virus and porcine rotavirus A. Virology 2024; 594:110062. [PMID: 38522136 DOI: 10.1016/j.virol.2024.110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
Viral diarrhea is the predominant digestive tract sickness in piglings, resulting in substantial profit losses in the porcine industry. Porcine rotavirus A (PoRVA) and porcine epidemic diarrhea virus (PEDV) are the main causes of grave gastroenteritis and massive dysentery, especially in piglets. PoRVA and PEDV have high transmissibility, exhibit similar clinical symptoms, and frequently co-occur. Therefore, to avoid financial losses, a quick, highly efficient, objective diagnostic test for the prevention and detection of these diseases is required. Enzymatic recombinase amplification (ERA) is a novel technology based on isothermal nucleic acid amplification. It demonstrates high sensitivity and excellent specificity, with a short processing time and easy operability, compared with other in vitro nucleic acid amplification technologies. In this study, a dual ERA method to detect and distinguish between PEDV and PoRVA nucleic acids was established. The method shows high sensitivity, as the detection limits were 101 copies/μL for both viruses. To test the usefulness of this method in clinical settings, we tested 64 swine clinical samples. Our results were 100% matched with those acquired using a commercially available kit. Therefore, we have successfully developed a dual diagnostic ERA nucleic acids method for detecting and distinguishing between PEDV and PoRVA.
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Affiliation(s)
- Qianwen Wu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Jingyu Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Sijia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Fanliang Zeng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Ling Chen
- Ganzhou Quannan County Agriculture and Rural Bureau, Ganzhou, 341800, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
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Saidi LK, Md Rani ZZ, Sulaiman SA, Jamal R, Ismail A, Alim AA, Ayob SNSA, Dee CF, Hamzah AA, Abdul Murad NA. Development of DNA-Based Lateral Flow Assay for Detection of LDLR Gene Mutation for Familial Hypercholesterolemia. Malays J Med Sci 2024; 31:92-106. [PMID: 38984253 PMCID: PMC11229576 DOI: 10.21315/mjms2024.31.3.6] [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: 05/16/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2024] Open
Abstract
Background The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Methods Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Results Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. Conclusion The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection.
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Affiliation(s)
- Lina Khalida Saidi
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Zam Zureena Md Rani
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Siti Aishah Sulaiman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kelantan, Malaysia
| | - Anis Amirah Alim
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Sharipah Nadzirah Syed Ahmad Ayob
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
- Institute of Nano Electronic Engineering (INEE), Universiti Malaysia Perlis, Perlis, Malaysia
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Flores-Contreras EA, Carrasco-González JA, Linhares DCL, Corzo CA, Campos-Villalobos JI, Henao-Díaz A, Melchor-Martínez EM, Iqbal HMN, González-González RB, Parra-Saldívar R, González-González E. Emergent Molecular Techniques Applied to the Detection of Porcine Viruses. Vet Sci 2023; 10:609. [PMID: 37888561 PMCID: PMC10610968 DOI: 10.3390/vetsci10100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | | | - Daniel C. L. Linhares
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Cesar A. Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA;
| | | | | | - Elda M. Melchor-Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Reyna Berenice González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Everardo González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
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