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Kappari L, Dasireddy JR, Applegate TJ, Selvaraj RK, Shanmugasundaram R. MicroRNAs: exploring their role in farm animal disease and mycotoxin challenges. Front Vet Sci 2024; 11:1372961. [PMID: 38803799 PMCID: PMC11129562 DOI: 10.3389/fvets.2024.1372961] [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: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 05/29/2024] Open
Abstract
MicroRNAs (miRNAs) serve as key regulators in gene expression and play a crucial role in immune responses, holding a significant promise for diagnosing and managing diseases in farm animals. This review article summarizes current research on the role of miRNAs in various farm animal diseases and mycotoxicosis, highlighting their potential as biomarkers and using them for mitigation strategies. Through an extensive literature review, we focused on the impact of miRNAs in the pathogenesis of several farm animal diseases, including viral and bacterial infections and mycotoxicosis. They regulate gene expression by inducing mRNA deadenylation, decay, or translational inhibition, significantly impacting cellular processes and protein synthesis. The research revealed specific miRNAs associated with the diseases; for instance, gga-miR-M4 is crucial in Marek's disease, and gga-miR-375 tumor-suppressing function in Avian Leukosis. In swine disease such as Porcine Respiratory and Reproductive Syndrome (PRRS) and swine influenza, miRNAs like miR-155 and miR-21-3p emerged as key regulatory factors. Additionally, our review highlighted the interaction between miRNAs and mycotoxins, suggesting miRNAs can be used as a biomarker for mycotoxin exposure. For example, alterations in miRNA expression, such as the dysregulation observed in response to Aflatoxin B1 (AFB1) in chickens, may indicate potential mechanisms for toxin-induced changes in lipid metabolism leading to liver damage. Our findings highlight miRNAs potential for early disease detection and intervention in farm animal disease management, potentially reducing significant economic losses in agriculture. With only a fraction of miRNAs functionally characterized in farm animals, this review underlines more focused research on specific miRNAs altered in distinct diseases, using advanced technologies like CRISPR-Cas9 screening, single-cell sequencing, and integrated multi-omics approaches. Identifying specific miRNA targets offers a novel pathway for early disease detection and the development of mitigation strategies against mycotoxin exposure in farm animals.
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Affiliation(s)
- Laharika Kappari
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | | | - Todd J. Applegate
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Ramesh K. Selvaraj
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Revathi Shanmugasundaram
- Toxicology and Mycotoxin Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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2
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Liu H, Zou J, Liu R, Chen J, Li X, Zheng H, Li L, Zhou B. Development of a TaqMan-Probe-Based Multiplex Real-Time PCR for the Simultaneous Detection of African Swine Fever Virus, Porcine Circovirus 2, and Pseudorabies Virus in East China from 2020 to 2022. Vet Sci 2023; 10:vetsci10020106. [PMID: 36851410 PMCID: PMC9964870 DOI: 10.3390/vetsci10020106] [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: 01/02/2023] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
African swine fever virus (ASFV), porcine circovirus 2 (PCV2), and pseudorabies virus (PRV) are important DNA viruses that cause reproductive disorders in sows, which result in huge losses in pig husbandry, especially in China. The multiplex qPCR assay could be utilized as a simultaneous diagnostic tool for field-based surveillance and the control of ASFV, PCV2, and PRV. Based on the conserved regions on the p72 gene of ASFV, the Cap gene of PCV2, the gE gene of PRV, and the porcine endogenous β-Actin gene, the appropriate primers and probes for a multiplex TaqMan real-time PCR test effective at concurrently detecting three DNA viruses were developed. The approach demonstrated high specificity and no cross-reactivity with major pathogens related to swine reproductive diseases. In addition, its sensitivity was great, with a detection limit of 101 copies/L of each pathogen, and its repeatability was excellent, with intra- and inter-group variability coefficients of <2%. Applying this assay to detect 383 field specimens collected from 2020 to 2022, the survey data displayed that the ASFV, PCV2, and PRV single infection rates were 22.45%, 28.46%, and 2.87%, respectively. The mixed infection rates of ASFV + PCV2, ASFV + PRV, PCV2 + PRV, and ASFV + PCV2 + PRV were 5.22%, 0.26%, 1.83%, and 0.26%, respectively. Overall, the assay established in this study provides an effective tool for quickly distinguishing the viruses causing sow reproductive disorders, suggesting its huge clinical application value in the diagnosis of swine diseases.
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Affiliation(s)
- Huaicheng Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianwen Zou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongchao Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohan Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Haixue Zheng
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Long Li
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
- Correspondence: (L.L.); (B.Z.)
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (L.L.); (B.Z.)
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3
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Wang Y, Li R, Zhang Y, Zhang W, Hu S, Li Z. Visual and label-free ASFV and PCV2 detection by CRISPR-Cas12a combined with G-quadruplex. Front Vet Sci 2022; 9:1036744. [PMID: 36524221 PMCID: PMC9745048 DOI: 10.3389/fvets.2022.1036744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/07/2022] [Indexed: 09/29/2023] Open
Abstract
African swine fever (ASF) and postweaning multisystemic wasting syndrome (PMWS) are acute infectious diseases caused by the African swine fever virus (ASFV) and porcine circovirus type 2 (PCV2). At present, there are no effective vaccines for the prevention of ASFV. PMWS, which is harmful to the domestic and even the world pig industry, is difficult to cure and has a high mortality. So, developing simple, inexpensive, and accurate analytical methods to detect and effectively diagnose ASFV and PCV2 can be conducive to avoid ASFV and PCV2 infection. CRISPR has become a potentially rapid diagnostic tool due to recent discoveries of the trans-cleavage properties of CRISPR type V effectors. Herein, we report the visual detection based on CRISPR-Cas12a (cpf1), which is more convenient than fluorescence detection. Through in vitro cleavage target DNA activation, Cas12a can trans-cleavage ssDNA G-quadruplex. TMB/H2O2 and Hemin cannot be catalyzed by cleavaged G-DNA to produce green color products. This protocol is useful for the detection of ASFV and PCV2 with high sensitivity. This method can enable the development of visual and label-free ASFV and PCV2 detection and can be carried out in the field without relying on instruments or power. This method can complete nucleic acid detection at 37 °C without using other instruments or energy. Our research has expanded the application of Cas12a and laid the foundation for the field's rapid detection of viral nucleic acid in future.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Rong Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weida Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Sishun Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
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4
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Visual and Rapid Detection of Porcine Epidemic Diarrhea Virus (PEDV) Using Reverse Transcription Loop-Mediated Isothermal Amplification Method. Animals (Basel) 2022; 12:ani12192712. [PMID: 36230453 PMCID: PMC9558507 DOI: 10.3390/ani12192712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/20/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) can cause severe infectious porcine epidemic diarrhea (PED) and infect different ages of pigs, resulting in sickness and death among suckling pigs. For PEDV detection, finding an effective and rapid method is a priority. In this study, we established an effective reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for PEDV detection. Three sets of primers, specific for eight different sequences of the PEDV N gene, were designed in this study. The optimized RT-LAMP amplification program was as follows: 59 min at 61.9 °C and 3 min at 80 °C. The RT-LAMP results were confirmed with the addition of SYBR Green I fluorescence dye and with the detection of a ladder-like band by conventional gel electrophoresis analysis, which demonstrated a significant agreement between the two methods. The LOD of PEDV by RT-LAMP was 0.0001 ng/μL. Compared with RT-LAMP, the traditional RT-PCR method is 100-fold less sensitive. The RT-LAMP results had no cross-reaction with porcine parvovirus (PPV), porcine circovirus type 1 (PCV1), porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), rotavirus (RV), transmissible gastroenteritis virus (TGEV) and porcine reproductive and respiratory syndrome virus (PRRSV). Consequently, the newly developed RT-LAMP method could provide an accurate and reliable tool for PEDV diagnosis.
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Kim DY, Kim HR, Park JH, Kwon NY, Kim JM, Kim JK, Park JH, Lee KK, Kim SH, Kim WI, Lyoo YS, Park CK. Detection of a novel porcine circovirus 4 in Korean pig herds using a loop-mediated isothermal amplification assay. J Virol Methods 2021; 299:114350. [PMID: 34748817 DOI: 10.1016/j.jviromet.2021.114350] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 01/19/2023]
Abstract
A novel porcine circovirus 4 has been recently identified in China and Korea. A sensitive and specific diagnostic method is urgently required to detect the virus in field samples. We developed a loop-mediated isothermal amplification (LAMP) the assay for the visual detection of PCV4 and evaluated its sensitivity, specificity, and applicability in clinical samples. This assay's results can be directly visualized by the naked eye using hydroxynaphthol blue after incubation for 40 min at 64 °C. The assay specifically amplified PCV4 DNA and no other viral nucleic acids. The sensitivity of the assay was <50 DNA copies/reaction, which was 10 times more sensitive than conventional polymerase chain reaction (cPCR) and comparable to real-time PCR (qPCR). Clinical evaluation revealed that the PCV4 detection rate in individual pig samples and at the farm level was 39.3 % (57/145) and 45.7 % (32/70), respectively, which were higher than cPCR (46 samples, 24 farms) and qPCR (52 samples, 29 farms) results. Cumulatively, owing to the advantages of high sensitivity and specificity, direct visual monitoring of the results, no possibility for cross-contamination, and being a low-cost equipment, the developed LAMP assay will be a valuable tool for the detection of the novel PCV4 in clinical samples, even in resource-limited laboratories.
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Affiliation(s)
- Da-Young Kim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hye-Ryung Kim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Hyun Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea; DIVA Bio Incorporation, Daegu, 41519, Republic of Korea
| | - Na-Young Kwon
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong-Min Kim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Kyeom Kim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ji-Hoon Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyoung-Ki Lee
- Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Seong-Hee Kim
- Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Young S Lyoo
- College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea.
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6
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Chen Z, Mao S, Zhang W, Fan X, Wu W, Liu C, Zhao K, Lu R. Rapid Visual Detection Method for Barley Yellow Mosaic Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). PLANT DISEASE 2021; 105:2658-2663. [PMID: 33320043 DOI: 10.1094/pdis-06-20-1216-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Barley yellow mosaic disease, caused mainly by Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus, is a devastating disease of barley and is a threat to Eurasian barley production. Early detection is essential for effective management of the pathogens and to assure food security. In this study, a simple, rapid, specific, sensitive, and visual method was developed to detect BaYMV using loop-mediated isothermal amplification (LAMP). Two pairs of oligonucleotide primers (inner and outer primers) were designed to amplify the gene encoding the coat protein of BaYMV. The optimal conditions for the LAMP method were determined, and a one-step reverse transcription (RT)-LAMP method was also developed. Subsequently, the fastest processing time for RT-LAMP was determined. Among eight plant viruses examined using the LAMP method, only BaYMV was detectable, suggesting that the assay was highly specific. The RT-LAMP method was 10 times more sensitive than the RT-PCR method in the sensitivity test. To further shorten the virus detection process, a dye was added to the RT-LAMP products, and positive reactions were simply read by the naked eye via a color change (from orange to light green) under visible light. Barley samples from the middle and lower reaches of the Yangtze River basin, where BaYMV broke out very seriously in 1970s, were detected by the newly established RT-LAMP method. The results showed that all samples were positive for BaYMV, indicating the potential risk of the virus in these areas. This newly established LAMP/RT-LAMP method could be a promising tool for barley protection and food security control.
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Affiliation(s)
- Zhiwei Chen
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Shuihua Mao
- School of Life Science, Taizhou University, Taizhou 317000, China
| | - Wan Zhang
- Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu 215008, China
| | - Xiaorui Fan
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Wu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chenghong Liu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Kai Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Ruiju Lu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
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7
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Li Y, Yu Z, Jiao S, Liu Y, Ni H, Wang Y. Development of a recombinase-aided amplification assay for rapid and sensitive detection of porcine circovirus 3. J Virol Methods 2020; 282:113904. [PMID: 32470487 DOI: 10.1016/j.jviromet.2020.113904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
Porcine circovirus type 3 (PCV3) is a novel member of the genus Circovirus, first detected in the United States in 2016, with subsequent reports in many countries. PCV3 infections have caused serious economic losses in the pig industry. Alternative rapid and sensitive assays for PCV3 detection are needed for clinical diagnosis, especially in laboratories not equipped with more sophisticated equipment. Here, a real-time recombinase-aided amplification assay (RAA) was developed for PCV3 detection. Specific primers and probes targeting the conserved region of the capsid gene of PCV3 were designed. The assay was performed at 39 °C for 30 min using specialized equipment. Furthermore, 36 clinical samples were used to evaluate the RAA. The analytical sensitivity of the RAA for PCV3 was 38 copies per reaction at 95% probability level, using a probit regression model. There was no cross-reactivity with other DNA viruses belonging to the Circoviridae and Parvoviridae families. The detection rate agreed with that obtained by an established real-time PCR assay with a kappa value of 1.0. Our results demonstrated that this new RAA could be used for the rapid, accurate, and sensitive detection of PCV3.
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Affiliation(s)
- Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Zhaorong Yu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Suli Jiao
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Yuhui Liu
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Hongxia Ni
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Yong Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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8
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Liu Y, Meng H, Shi L, Li L. Sensitive detection of porcine circovirus 3 by droplet digital PCR. J Vet Diagn Invest 2019; 31:604-607. [PMID: 31046639 DOI: 10.1177/1040638719847686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus 3 (PCV-3) is a newly emerging virus that poses a potential threat to the swine industry. We developed a sensitive assay utilizing droplet digital PCR (ddPCR) to detect PCV-3. Specificity of the assay was confirmed by the failure of amplification of DNA of other relevant viruses. The detection limit for ddPCR was 1 copy/μL, 10 times greater sensitivity than TaqMan real-time PCR (rtPCR). Both methods showed a high degree of linearity, although TaqMan rtPCR showed less sensitivity than ddPCR for clinical detection. Our findings indicate that ddPCR might offer faster and improved analytical sensitivity for PCV-3 detection.
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Affiliation(s)
- Yuqi Liu
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Hecheng Meng
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Lei Shi
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
| | - Lili Li
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China (Liu, Shi, Li).,School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China (Meng)
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9
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Liu Y, Meng H, Shi L, Li L. Development of a droplet digital polymerase chain reaction for sensitive and simultaneous identification of porcine circovirus type 2 and 3. J Virol Methods 2019; 270:34-37. [PMID: 31026559 DOI: 10.1016/j.jviromet.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/28/2022]
Abstract
In this study, a sensitive assay for simultaneous detection of porcine circovirus type 2 (PCV2) and type 3 (PCV3) was established using droplet digital PCR (ddPCR). Pairs of primers and probes were specifically designed to amplify PCV2 and PCV3. Specificity of the assay was confirmed by the failure of amplification of DNA of other relevant viruses. The detection limit for ddPCR was 2 copies/μL for PCV2 and 1 copy/μL for PCV3, a 3- and 10-fold greater sensitivity than TaqMan real-time PCR, respectively. Both methods showed a high degree of linearity, although TaqMan real-time PCR showed less sensitivity than ddPCR for clinical detection. In summary, the results demonstrated that the established ddPCR is an effective alternative method for the precise simultaneous quantification of PCV2 and PCV3 in clinical samples, especially in detecting lower concentrations of co-infected samples.
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Affiliation(s)
- Yuqi Liu
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Lei Shi
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
| | - Lili Li
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China.
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Wang H, Cong F, Zeng F, Lian Y, Liu X, Luo M, Guo P, Ma J. Development of a real time reverse transcription loop-mediated isothermal amplification method (RT-LAMP) for detection of a novel swine acute diarrhea syndrome coronavirus (SADS-CoV). J Virol Methods 2018; 260:45-48. [PMID: 29936095 PMCID: PMC7113678 DOI: 10.1016/j.jviromet.2018.06.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 12/20/2022]
Abstract
A novel swine acute diarrhea syndrome Coronavirus (SADS-CoV) that causes severe diarrhea in suckling piglets was identified in southern China in 2017. A simple and rapid detection test was developed for this virus using real-time RT-LAMP based on the conserved N gene of the virus. The method had a detection limit of 1.0 × 101 copies/μL with no cross-reactions with classical swine fever virus, porcine and respiratory syndrome virus NA, porcine and respiratory syndrome virus EU, transmissible gastroenteritis coronavirus, foot and mouth disease virus, porcine epidemic diarrhea virus (S-INDEL and non-S-INDEL), swine influenza virus subtype H1N1, porcine circovirus type 2, seneca valley virus, porcine parvovirus, porcine deltacoronavirus and rotavirus. This method was also reproducible. Twenty of 24 clinical samples were identified as SADS-CoV RNA-positive by the real-time RT-LAMP and the results were consistent with that of the real time RT-PCR method. This new method for detecting SADS-CoV is specific and sensitive for the detection of SADS-CoV.
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Affiliation(s)
- Huanan Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China; Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Fanwen Zeng
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China; Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Yuexiao Lian
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China; Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Xiangnan Liu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China; Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Manlin Luo
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China.
| | - Pengju Guo
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou, 510642, China.
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11
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Zheng S, Wu X, Shi J, Peng Z, Gao M, Xin C, Liu Y, Wang S, Xu S, Han H, Yu J, Sun W, Cong X, Li J, Wang J. Rapid specific and visible detection of porcine circovirus type 3 using loop-mediated isothermal amplification (LAMP). Transbound Emerg Dis 2018; 65:597-601. [PMID: 29504259 DOI: 10.1111/tbed.12835] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/30/2022]
Abstract
In this study, a rapid and specific assay for the detection of porcine circovirus type 3 (PCV3) was established using loop-mediated isothermal amplification (LAMP). Four primers were specifically designed to amplify PCV3. The LAMP assay was effectively optimized to amplify PCV3 by water bath at 60°C for 60 min. The detection limit was approximately 1 × 101 copy in this LAMP assay. Compared to porcine circovirus type 2 (PCV2), both gE and gD genes of pseudorabies virus (PRV) and porcine parvovirus (PPV), the LAMP assay showed a high specific detection of PCV3. A visible detection method was developed using SYBR Green I to recognize the results rapidly. Based on the detection of 20 clinical tissue samples, the LAMP assay was more practical and convenient than classical PCR due to its simplicity, high sensitivity, rapidity, specificity, visibility and cost efficiency.
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Affiliation(s)
- S Zheng
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,Qingdao Agricultural University, Qingdao, China
| | - X Wu
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Shi
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Z Peng
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - M Gao
- Shandong Normal University, Jinan, China
| | - C Xin
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,Qingdao Agricultural University, Qingdao, China
| | - Y Liu
- Shandong Normal University, Jinan, China
| | - S Wang
- Shandong Normal University, Jinan, China
| | - S Xu
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - H Han
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Yu
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - W Sun
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - X Cong
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Li
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Wang
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
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12
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Park YR, Kim HR, Kim SH, Lee KK, Lyoo YS, Yeo SG, Park CK. Loop-mediated isothermal amplification assay for the rapid and visual detection of novel porcine circovirus 3. J Virol Methods 2018; 253:26-30. [DOI: 10.1016/j.jviromet.2017.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/11/2017] [Accepted: 12/22/2017] [Indexed: 10/18/2022]
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13
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Zhang P, Wang L, Li Y, Jiang P, Wang Y, Wang P, Kang L, Wang Y, Sun Y, Jiang Y. Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection. Vet Res 2018; 49:18. [PMID: 29448950 PMCID: PMC5815207 DOI: 10.1186/s13567-018-0512-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/01/2018] [Indexed: 12/17/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) is the primary cause of post-weaning multisystemic wasting syndrome (PMWS) and other PCV-associated diseases. According to our previous RNA-sequencing analysis, the differences in the susceptibility to PCV2 infection depended on the genetic differences between the Laiwu (LW) and Yorkshire × Landrace crossbred (YL) pigs, but the cellular microRNA (miRNA) that are differentially expressed between the LW and YL pigs before and after PCV2 infection remain to be determined. In this study, high-throughput sequencing was performed to determine the abundance and differential expression of miRNA in lung tissues from PCV2-infected and PCV2-uninfected LW and YL pigs. In total, 295 known and 95 novel miRNA were identified, and 23 known and 25 novel miRNA were significantly differentially expressed in the PCV2-infected vs. PCV2-uninfected LW pigs and/or the PCV2-infected vs. PCV2-uninfected YL pigs. The expression levels of ssc-miR-122, ssc-miR-192, ssc-miR-451, ssc-miR-486, and ssc-miR-504 were confirmed by quantitative real-time PCR (qRT-PCR). Analysis of the potential targets of the four up-regulated miRNA (i.e., ssc-miR-122, ssc-miR-192, ssc-miR-451 and ssc-miR-486) identified pathways and genes that may be important for disease resistance. Among the up-regulated miRNA, ssc-miR-122 can repress the protein expression and viral DNA replication of PCV2 and down-regulate the expression of the nuclear factor of activated T-cells 5 (NFAT5) and aminopeptidase puromycin sensitive (NPEPPS) by binding to their 3′ untranslated region (3′UTR) in PK15 cells. Therefore, ssc-miR-122 may indirectly suppress PCV2 infection by targeting genes related to the host immune system, such as NFAT5 and NPEPPS.
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Affiliation(s)
- Ping Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Liyuan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Yanping Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Ping Jiang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanchao Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Pengfei Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Yuding Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China.
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, Shandong, China.
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14
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Development of Isothermal Recombinase Polymerase Amplification Assay for Rapid Detection of Porcine Circovirus Type 2. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8403642. [PMID: 28424790 PMCID: PMC5382309 DOI: 10.1155/2017/8403642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 11/17/2022]
Abstract
Porcine circovirus virus type II (PCV2) is the etiology of postweaning multisystemic wasting syndrome (PMWS), porcine dermatitis, nephropathy syndrome (PDNS), and necrotizing pneumonia. Rapid diagnosis tool for detection of PCV2 plays an important role in the disease control and eradication program. Recombinase polymerase amplification (RPA) assays using a real-time fluorescent detection (PCV2 real-time RPA assay) and RPA combined with lateral flow dipstick (PCV2 RPA LFD assay) were developed targeting the PCV2 ORF2 gene. The results showed that the sensitivity of the PCV2 real-time RPA assay was 102 copies per reaction within 20 min at 37°C and the PCV2 RPA LFD assay had a detection limit of 102 copies per reaction in less than 20 min at 37°C. Both assays were highly specific for PCV2, with no cross-reactions with porcine circovirus virus type 1, foot-and-mouth disease virus, pseudorabies virus, porcine parvovirus, porcine reproductive and respiratory syndrome virus, and classical swine fever virus. Therefore, the RPA assays provide a novel alternative for simple, sensitive, and specific identification of PCV2.
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15
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Development of Loop-Mediated Isothermal Amplification Assay Based on 6b Gene Sequence for Rapid Detection of Pasteurella multocida B:2. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0713-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Chander Y, Koelbl J, Puckett J, Moser MJ, Klingele AJ, Liles MR, Carrias A, Mead DA, Schoenfeld TW. A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP). Front Microbiol 2014; 5:395. [PMID: 25136338 PMCID: PMC4117986 DOI: 10.3389/fmicb.2014.00395] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/14/2014] [Indexed: 11/13/2022] Open
Abstract
Meeting the goal of providing point of care (POC) tests for molecular detection of pathogens in low resource settings places stringent demands on all aspects of the technology. OmniAmp DNA polymerase (Pol) is a thermostable viral enzyme that enables true POC use in clinics or in the field by overcoming important barriers to isothermal amplification. In this paper, we describe the multiple advantages of OmniAmp Pol as an isothermal amplification enzyme and provide examples of its use in loop-mediated isothermal amplification (LAMP) for pathogen detection. The inherent reverse transcriptase activity of OmniAmp Pol allows single enzyme detection of RNA targets in RT-LAMP. Common methods of nucleic acid amplification are highly susceptible to sample contaminants, necessitating elaborate nucleic acid purification protocols that are incompatible with POC or field use. OmniAmp Pol was found to be less inhibited by whole blood components typical in certain crude sample preparations. Moreover, the thermostability of the enzyme compared to alternative DNA polymerases (Bst) and reverse transcriptases allows pretreatment of complete reaction mixes immediately prior to amplification, which facilitates amplification of highly structured genome regions. Compared to Bst, OmniAmp Pol has a faster time to result, particularly with more dilute templates. Molecular diagnostics in field settings can be challenging due to the lack of refrigeration. The stability of OmniAmp Pol is compatible with a dry format that enables long term storage at ambient temperatures. A final requirement for field operability is compatibility with either commonly available instruments or, in other cases, a simple, inexpensive, portable detection mode requiring minimal training or power. Detection of amplification products is shown using lateral flow strips and analysis on a real-time PCR instrument. Results of this study show that OmniAmp Pol is ideally suited for low resource molecular detection of pathogens.
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Affiliation(s)
| | | | | | | | | | - Mark R Liles
- Department of Biological Sciences, Auburn University Auburn, AL, USA
| | - Abel Carrias
- Department of Biological Sciences, Auburn University Auburn, AL, USA
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Saffie NE, Abdullah J, Rahman ZA, Hussin A, Ismail A, Mohamed M. Establishment of an in-House Loop-Mediated Isothermal Amplification (LAMP) for a Rapid Detection of S
almonella
Typhi and S
almonella
Paratyphi A at Low-Resource Settings. J Food Saf 2014. [DOI: 10.1111/jfs.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Zaidah A. Rahman
- School of Medical Sciences; Universiti Sains Malaysia; Kubang Kerian Kelantan 16150 Malaysia
| | - Azura Hussin
- Hospital Raja Perempuan Zainab II; Kota Bharu Kelantan Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine (INFORMM)
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18
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Salar R, Gahlawat S, Siwach P, Duhan J, Gahlawat SK. Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review. BIOTECHNOLOGY: PROSPECTS AND APPLICATIONS 2013. [PMCID: PMC7122297 DOI: 10.1007/978-81-322-1683-4_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.
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Affiliation(s)
- R.K. Salar
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - S.K. Gahlawat
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - P. Siwach
- grid.448811.0Department of Biotechnology, Chaudhary Devi lal University, Sirsa, Haryana India
| | - J.S. Duhan
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
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Wang C, Pang VF, Lee F, Liao PC, Huang YL, Lin YL, Lai SS, Jeng CR. Development and evaluation of a loop-mediated isothermal amplification method for rapid detection and differentiation of two genotypes of porcine circovirus type 2. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2013; 47:363-70. [PMID: 23845855 DOI: 10.1016/j.jmii.2013.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 04/19/2013] [Accepted: 05/08/2013] [Indexed: 11/26/2022]
Abstract
BACKGROUND Porcine circovirus type 2 (PCV2) is one of the major swine viral diseases and has caused significant economic loss to pig producers. PCV2 has been divided into two major genotypes: PCV2a, PCV2b. A loop-mediated isothermal amplification (LAMP) method was developed for the detection and differentiation of PCV2a and PCV2b in clinical samples. METHODS LAMP-specific primer sets were designed based on six PCV2a and six PCV2b reference isolates. To determine the analytical specificity of LAMP, DNA samples extracted from 36 porcine virus isolates were tested by LAMP, including eight PCV2a, 11 PCV2b, four PCV type 1, two porcine parvovirus, three pseudorabies virus, and eight porcine reproductive and respiratory virus. To evaluate the analytical sensitivity of the assay, 10-fold serial dilutions of PCV2a and PCV2b recombinant plasmids were performed to prepare the dilutions at concentration from 10(6) to 1 copy(ies)/μL, and each dilution was tested by both LAMP and nested polymerase chain reaction (nested PCR). A total of 168 clinical samples were analyzed by both LAMP and nested PCR, and the relative sensitivity and specificity of LAMP compared to nested PCR were calculated. RESULTS Using different primer sets of LAMP, LAMP could be completed within 50 minutes. This method was found to be highly analytically specific for PCV2a and PCV2b; only the target gene was detected without cross-reaction. The analytical sensitivity of LAMP for PCV2a and PCV2b were 10 copies/μL, demonstrating analytical sensitivity comparable to that obtained using nested PCR. In addition, the sensitivity and specificity of LAMP relative to those of nested PCR were 97.7% and 100.0%, respectively. The percentage of observed agreement was 98.2%, and the κ statistic was 0.949. CONCLUSION LAMP is a rapid, specific, and sensitive diagnostic method for the detection and differentiation of PCV2a and PCV2b in clinical samples.
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Affiliation(s)
- Chun Wang
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Chung-Cheng Road, Tamsui, New Taipei City 251, Taiwan; Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Victor Fei Pang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Fan Lee
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Chung-Cheng Road, Tamsui, New Taipei City 251, Taiwan
| | - Pei-Chih Liao
- Animal Disease Control Centre of Yunlin County, No. 517, Sec. 2, Yunlin Road, Douliou City, Yunlin County 640, Taiwan
| | - Yu-Liang Huang
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Chung-Cheng Road, Tamsui, New Taipei City 251, Taiwan
| | - Yeou-Liang Lin
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Chung-Cheng Road, Tamsui, New Taipei City 251, Taiwan
| | - Shiow-Suey Lai
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan.
| | - Chian-Ren Jeng
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan.
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20
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Yang BC, Wang FX, Zhang SQ, Song N, Li JX, Yang ZQ, Wen YJ, Wu H. Comparative evaluation of conventional polymerase chain reaction (PCR), with loop-mediated isothermal amplification and SYBR green I-based real-time PCR for the quantitation of porcine circovirus-1 DNA in contaminated samples destined for vaccine production. J Virol Methods 2013; 191:1-8. [PMID: 23538038 DOI: 10.1016/j.jviromet.2013.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 10/27/2022]
Abstract
Porcine circovirus type1 (PCV1), described initially as a contaminant of a porcine kidney cell line, is ubiquitous within the swine population The presence of PCV1 in porcine cell lines can lead to contamination during both human and porcine vaccine production. Therefore, a rapid, specific, sensitive and practical method is needed for the detection of PCV1 in bio-products. The aim of this study was to compare three assays in their ability to accurately quantify PCV1 virus in biological samples, namely loop-mediated isothermal amplification (LAMP), SYBR green I-based real-time polymerase chain reaction (PCR) and conventional PCR. All assays yielded successful quantitation of PCV1 DNA and differentiated between PCV1-free and-contaminated cells. In addition, the results were specific for PCV1, since amplification of samples containing closely-related PCV2 or other pathogenic swine viruses yielded negative results. The lowest detection threshold of 10(2) copies was displayed by the SYBR green I-based real-time PCR assay. In addition, this assay was the most effective in detecting PCV1 contamination in a set of commercially available porcine vaccines. Therefore we conclude that SYBR green I-based real-time PCR is specific and sensitive for detecting PCV1 in biological samples and maybe used for quality control of vaccine and biomaterial production.
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Affiliation(s)
- Bo-Chao Yang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences CAAS, No 4899 Juye Street, Chuangchun 130112, China
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21
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Qiu X, Li T, Zhang G, Cao J, Jin Y, Xing G, Liao M, Zhou J. Development of a loop-mediated isothermal amplification method to rapidly detect porcine circovirus genotypes 2a and 2b. Virol J 2012; 9:318. [PMID: 23270577 PMCID: PMC3573989 DOI: 10.1186/1743-422x-9-318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 12/05/2012] [Indexed: 12/20/2022] Open
Abstract
Background Porcine circovirus type 2 (PCV2), is nowadays associated with a number of diseases known as porcine circovirus-associated diseases (PCVAD), especially postweaning multisystemic wasting syndrome (PMWS). The epidemiological investigation of PCV2 infection was usually conducted by PCR, nested PCR, PCR-RFLP, TaqMan-based assay and nucleotide sequencing. However, there is still no rapid, sensitive and practical method for detecting PCV2 genotypes. As a novel nucleic acid amplification method, the loop-mediated isothermal amplification method (LAMP) has been used to detect a variety of pathogenic microorganisms. Results Herein, a LAMP method is developed to detect the genotypes of PCV2. The diagnostic sensitivity of LAMP is 1 copy/reaction for differentiating genotypes PCV2a and PCV2b. The reaction process was completed at 65°C for 1 hour in a water bath. Cross-reactivity assay shows that this method is specific for PCV2a and PCV2b and no reactive for PCV2c and other swine-origin viruses (i.e. CSFV, PRRSV, BVDV, TGEV and PEDV, etc). Identity between LAMP and nested PCR was 92.3% on 52 field clinical samples. Conclusions LAMP method provides a rapid, sensitive, reliable way to detect PCV2a and PCV2b, and a better means for the large scale investigation of PCV2a and PCV2b infection.
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Affiliation(s)
- Xiaohuo Qiu
- Key Laboratory of Animal Virology of Ministry of Agriculture, College of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China
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22
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Li J, Song D, He W, Bao Y, Lu R, Su G, Wang G, Lu H, Zhao K, Gao F. Rapid detection of orf virus by loop-mediated isothermal amplification based on the DNA polymerase gene. Arch Virol 2012. [PMID: 23183830 DOI: 10.1007/s00705-012-1526-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
At present, there are no effective antiviral treatments available for contagious ecthyma, and rapid diagnosis is therefore critical for effective control of the disease. Recently, the invention of a novel LAMP technique that can rapidly amplify nucleic acids with high specificity and sensitivity under isothermal conditions has overcome some of the deficiencies of nucleic acid-based diagnostic tests and has made on-site diagnosis possible. To establish a flexible loop-mediated isothermal amplification (LAMP) assay for the rapid detection of orf virus, two pairs of primers, including outer primers F3/B3 and inner primers FIP/BIP, were designed to amplify the DNA polymerase gene. Optimal time and temperature conditions for LAMP were found to be 45 min and 62 °C, respectively. The LAMP assay was shown to be specific, with no cross-reactivity with sheeppox virus, goatpox virus, avian molluscum roup virus or vesicular stomatitis virus. Additionally, the sensitivity of the LAMP method was similar to that of real-time PCR and demonstrated greater sensitivity than a conventional polymerase chain reaction (PCR) assay. To assess the utility of LAMP in the detection of orf virus in clinical samples, a total of 35 samples collected from orf virus-infected sheep and goats were tested using the optimized LAMP assay, real-time PCR, and conventional PCR. Of the samples, 26 were found to be positive by LAMP, and 25 (74.3 %) were positive by real-time PCR, whereas only 18 (51.4 %) were positive by conventional PCR. Our results have shown that the LAMP assay developed in this study can be used for the rapid detection of orf virus.
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Affiliation(s)
- Jida Li
- College of Animal Science and Veterinary Medicine, Jilin University, 5333 Xi'an road, Changchun, 130062, China
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23
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Reverse transcription loop-mediated isothermal amplification for rapid detection of the newly emerged poultry Flavivirus. Folia Microbiol (Praha) 2012; 58:277-82. [PMID: 23152303 DOI: 10.1007/s12223-012-0204-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
Poultry Flavivirus (PF) was a recently emerged virus with high morbidity rates and mortality rates in China. It is the causative agent of egg drop syndrome at present. Development of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was the most efficient way to prevent and control the PF disease. The assay was performed at 64 °C for 45 min, using six specific primers that recognized eight targets of the PF E gene. The RT-LAMP assay, compared to conventional reverse transcription polymerase chain reaction, has 100-fold-greater sensitivity, with a detection limit of 1 × 10(-3) copies per μL RNA and no cross-reaction with poultry other viruses. The RT-LAMP assay is a valuable tool for detected PF without requiring any sophisticated equipment, and the detection has potential usefulness for clinical diagnosis in the field.
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Tsui CK, Woodhall J, Chen W, Lévesque CA, Lau A, Schoen CD, Baschien C, Najafzadeh MJ, de Hoog GS. Molecular techniques for pathogen identification and fungus detection in the environment. IMA Fungus 2011; 2:177-89. [PMID: 22679603 PMCID: PMC3359816 DOI: 10.5598/imafungus.2011.02.02.09] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/03/2011] [Indexed: 12/25/2022] Open
Abstract
Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here.
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Affiliation(s)
- Clement K.M. Tsui
- Department of Forest Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James Woodhall
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK
| | - Wen Chen
- Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada, K1A OC6
| | - C. André Lévesque
- Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada, K1A OC6
| | - Anna Lau
- Centre for Infectious Diseases and Microbiology and the University of Sydney, Westmead Hospital, Westmead, NSW 2145, Australia
- *Current mailing address: Department of Laboratory Medicine, 10 Center Drive, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cor D. Schoen
- Plant Research International, Business Unit Bio-Interactions and Plant Health, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Christiane Baschien
- Technische Universität Berlin, Environmental Microbiology, Sekr. FR1-2, Franklinstrasse 29, 10587 Berlin, Germany
- **Current mailing address: Federal Environment Agency Germany, Corrensplatz 1, 14195 Berlin, Germany
| | - Mohammad J. Najafzadeh
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - G. Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Li S, Fang M, Zhou B, Ni H, Shen Q, Zhang H, Han Y, Yin J, Chang W, Xu G, Cao G. Simultaneous detection and differentiation of dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus by a combined reverse-transcription loop-mediated isothermal amplification assay. Virol J 2011; 8:360. [PMID: 21777455 PMCID: PMC3149006 DOI: 10.1186/1743-422x-8-360] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 07/21/2011] [Indexed: 11/27/2022] Open
Abstract
Background Rapid identification and differentiation of mosquito-transmitted flaviviruses in acute-phase sera of patients and field-caught vector mosquitoes are important for the prediction and prevention of large-scale epidemics. Results We developed a flexible reverse-transcription loop-mediated isothermal amplification (RT-LAMP) unit for the detection and differentiation of dengue virus serotypes 1-4 (DENV1-4), Japanese encephalitis virus (JEV), and West Nile virus (WNV). The unit efficiently amplified the viral genomes specifically at wide ranges of viral template concentrations, and exhibited similar amplification curves as monitored by a real-time PCR engine. The detection limits of the RT-LAMP unit were 100-fold higher than that of RT-PCR in 5 of the six flaviviruses. The results on specificity indicated that the six viruses in the assay had no cross-reactions with each other. By examining 66 viral strains of DENV1-4 and JEV, the unit identified the viruses with 100% accuracy and did not cross-react with influenza viruses and hantaviruses. By screening a panel of specimens containing sera of 168 patients and 279 pools of field-caught blood sucked mosquitoes, results showed that this unit is high feasible in clinical settings and epidemiologic field, and it obtained results 100% correlated with real-time RT-PCR. Conclusions The RT-LAMP unit developed in this study is able to quickly detect and accurately differentiate the six kinds of flaviviruses, which makes it extremely feasible for screening these viruses in acute-phase sera of the patients and in vector mosquitoes without the need of high-precision instruments.
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Affiliation(s)
- Shuhua Li
- Department of Epidemiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, China
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