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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. [PMID: 38923038 DOI: 10.1002/aah.10218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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2
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [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: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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Wani LA, Jawa P, Khan JA. Development of one step colorimetric RT-LAMP assays for rapid detection of Apple mosaic virus and Prunus necrotic ringspot virus. J Virol Methods 2023; 316:114729. [PMID: 37031745 DOI: 10.1016/j.jviromet.2023.114729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Apple mosaic virus (ApMV) and Prunus necrotic ringspot virus (PNRSV), belonging to genus Ilarvirus, cause significant losses to rose and other plants of the family Rosaceae. They are easily transmitted through mechanical or vegetative means. In our previous study, the occurrence of ApMV and PNRSV in rose plants was reported. In this study, as a first step towards the development of a colorimetric Reverse Transcriptase - Loop Mediated Isothermal Amplification (RT-LAMP) assay, two primer sets were designed, each containing six primers (F3, B3, FIP, BIP, LF and LB) targeting the coat protein genes of ApMV and PNRSV. After incubation of RT-LAMP reaction mix at an isothermal temperature (65 °C/30min), the amplified products were visually confirmed with the nucleic acid intercalation dye SYBR Green I and the indicator dye Hydroxy-Naphthol Blue. The developed assays were virus specific and showed no cross amplification. Their sensitivity was 103 times higher than that of the corresponding RT-PCRs. The LAMP assays developed in this study are inexpensive, rapid and reliable for the early detection of ApMV and PNRSV, and could therefore be used in plant quarantine to control the risk of their spread.
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Affiliation(s)
- Latief A Wani
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India
| | - Priyanka Jawa
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India
| | - Jawaid A Khan
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India.
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Development and Validation of Rapid Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification for Detection of Rift Valley Fever Virus. Adv Virol 2023; 2023:1863980. [PMID: 36755743 PMCID: PMC9902148 DOI: 10.1155/2023/1863980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause massive loss during its outbreak within a very short period of time. Lack of a highly sensitive, instant reading diagnostic method for RVFV, which is more suitable for on-site testing, is a big gap that needs to be addressed. The aim of this study was to develop a novel one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the rapid detection of RVFV. To achieve this, the selected RVFV M segment nucleotide sequences were aligned using Multiple Sequence Comparison by Log-Expectation (MUSCLE) software in MEGA11 version 11.0.11 program to identify conserved regions. A 211 pb sequence was identified and six different primers to amplify it were designed using NEB LAMP Primer design tool version 1.1.0. The specificity of the designed primers was tested using primer BLAST, and a primer set, specific to RVFV and able to form a loop, was selected. In this study, we developed a single-tube test based on calorimetric RT-LAMP that enabled the visual detection of RVFV within 30 minutes at 65°C. Diagnostic sensitivity and specificity of the newly developed kit were compared with RVFV qRT-PCR, using total RNA samples extracted from 118 blood samples. The colorimetric RT-LAMP assay had a sensitivity of 98.36% and a specificity of 96.49%. The developed RT-LAMP was found to be tenfold more sensitive compared to the RVFV qRT-PCR assay commonly used in the confirmatory diagnosis of RVFV.
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5
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Cao G, Qiu Y, Long K, Xiong Y, MeimeiShi, JunYang, Li Y, Nie F, Huo D, Hou C. Carbon nanodots combined with loop-mediated isothermal amplification (LAMP) for detection of African swine fever virus (ASFV). Mikrochim Acta 2022; 189:342. [PMID: 35997837 PMCID: PMC9396581 DOI: 10.1007/s00604-022-05390-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/19/2022] [Indexed: 12/03/2022]
Abstract
The spread of African swine fever virus (ASFV) caused huge economic costs, so early detection is particularly important. Here, we established a fluorescence biosensor based on carbon nanodots (CNDs) and loop-mediated isothermal amplification (LAMP) to ultra-sensitively detect ASFV. LAMP with high efficiency produced a large amount of pyro phosphoric acid and caused pH change in a short time. CNDs with strong light stability had a large fluorescence response at the emission wavelength of 585.5 nm to small pH change by the excitation wavelength of 550 nm. The biosensor realized “turn-off–on” mode for ASFV detection with the detection limit as low as 15.21 copies μL−1. In addition, the biosensor had high accuracy in the actual sample assay. Therefore, the biosensor achieved rapid, sensitive, low-cost, and simple detection for ASFV. Moreover, the biosensor broadened the detection pathway of LAMP as a tool with great development prospect.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yue Qiu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Keyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China
| | - MeimeiShi
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Chongqing Customs, Chongqing Customs Technology Center, Chongqing, 400020, People's Republic of China
| | - JunYang
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Chongqing Customs, Chongqing Customs Technology Center, Chongqing, 400020, People's Republic of China
| | - Yingguo Li
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Chongqing Customs, Chongqing Customs Technology Center, Chongqing, 400020, People's Republic of China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing), Chongqing Customs, Chongqing Customs Technology Center, Chongqing, 400020, People's Republic of China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China. .,Chongqing Key Laboratory of Bio-Perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, People's Republic of China.
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Urrutia-Cabrera D, Liou RHC, Wang JH, Chan J, Hung SSC, Hewitt AW, Martin KR, Edwards TL, Kwan P, Wong RCB. Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes. Sci Rep 2021; 11:22493. [PMID: 34795308 PMCID: PMC8602269 DOI: 10.1038/s41598-021-01472-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has infected millions worldwide, therefore there is an urgent need to increase our diagnostic capacity to identify infected cases. Although RT-qPCR remains the gold standard for SARS-CoV-2 detection, this method requires specialised equipment in a diagnostic laboratory and has a long turn-around time to process the samples. To address this, several groups have recently reported the development of loop-mediated isothermal amplification (LAMP) as a simple, low cost and rapid method for SARS-CoV-2 detection. Herein we present a comparative analysis of three LAMP-based assays that target different regions of the SARS-CoV-2: ORF1ab RdRP, ORF1ab nsp3 and Gene N. We perform a detailed assessment of their sensitivity, kinetics and false positive rates for SARS-CoV-2 diagnostics in LAMP or RT-LAMP reactions, using colorimetric or fluorescent detection. Our results independently validate that all three assays can detect SARS-CoV-2 in 30 min, with robust accuracy at detecting as little as 1000 RNA copies and the results can be visualised simply by color changes. Incorporation of RT-LAMP with fluorescent detection further increases the detection sensitivity to as little as 100 RNA copies. We also note the shortcomings of some LAMP-based assays, including variable results with shorter reaction time or lower load of SARS-CoV-2, and false positive results in some experimental conditions and clinical saliva samples. Overall for RT-LAMP detection, the ORF1ab RdRP and ORF1ab nsp3 assays have faster kinetics for detection but varying degrees of false positives detection, whereas the Gene N assay exhibits no false positives in 30 min reaction time, which highlights the importance of optimal primer design to minimise false-positives in RT-LAMP. This study provides validation of the performance of LAMP-based assays as a rapid, highly sensitive detection method for SARS-CoV-2, which have important implications in development of point-of-care diagnostics for SARS-CoV-2.
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Affiliation(s)
- Daniel Urrutia-Cabrera
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Roxanne Hsiang-Chi Liou
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Jiang-Hui Wang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Jianxiong Chan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Australia
| | - Sandy Shen-Chi Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Keith R Martin
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Thomas L Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Australia
| | - Raymond Ching-Bong Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia. .,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia. .,Shenzhen Eye Hospital, Shenzhen University School of Medicine, Shenzhen, China.
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7
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Wong Tzeling JM, Engku Nur Syafirah EAR, Irekeola AA, Yusof W, Aminuddin Baki NN, Zueter A, Harun A, Chan YY. One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei. Anal Chim Acta 2021; 1171:338682. [PMID: 34112436 DOI: 10.1016/j.aca.2021.338682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.
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Affiliation(s)
- Jilien Michelle Wong Tzeling
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - E A R Engku Nur Syafirah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, PMB 4412, Offa Kwara State, Nigeria.
| | - Wardah Yusof
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Nurul Najian Aminuddin Baki
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - AbdelRahman Zueter
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Department of Medical Laboratory Sciences, Faculty of Applied Health Sciences, The Hashemite University, 13133, Zarqa, Jordan.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Li J, Liang W, Xu S, Shi J, Zhou X, Liu B, Yu L, Xiong J, Si G, He D. Rapid and sensitive detection of Senecavirus A by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick method. PLoS One 2019; 14:e0216245. [PMID: 31048910 PMCID: PMC6497277 DOI: 10.1371/journal.pone.0216245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/16/2019] [Indexed: 11/19/2022] Open
Abstract
Senecavirus A (SVA) is a critical pathogen causing vesicular lesions in sows and acute death of newborn piglets, resulting in very large economic losses in the pig industry. To restrict the transmission of SVA, an establishment of an effective diagnostic method is crucial for the prevention and control of the disease. However, traditional detection methods often have many drawbacks. In this study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was combined with a lateral flow dipstick (LFD) to detect SVA. The resulting RT-LAMP-LFD assay was performed at 60°C for 50 min and then directly judged on an LFD visualization strip. This method shows high specificity and sensitivity to SVA. The detection limit of RT-LAMP was 4.56x10-8 ng/μL RNA, approximately 11 copies/μL RNA, and it was 10 times more sensitive than RT-PCR. This detection method’s positive rate for clinical samples is comparable to that of RT-PCR. This method is time saving and highly efficient and is thus expected to be used to diagnose SVA infections in this field.
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Affiliation(s)
- Jinhui Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Weifang Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shuaifei Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jian Shi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xia Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bowen Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Li Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jingfeng Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guangbin Si
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dongsheng He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
- * E-mail:
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9
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Arunrut N, Kiatpathomchai W, Ananchaipattana C. Development and evaluation of real‐time loop mediated isothermal amplification assay for rapid and sensitive detection ofSalmonellaspp. in chicken meat products. J Food Saf 2018. [DOI: 10.1111/jfs.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Narong Arunrut
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Chiraporn Ananchaipattana
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
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Hashimoto Y, Hatayama Y, Kojima N, Morishita S, Matsumoto S, Hosoda Y, Hara A, Motokura T. Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia-Retinoic Acid Receptor α mRNA. Yonago Acta Med 2016; 59:262-269. [PMID: 28070163 PMCID: PMC5214692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/06/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Acute promyelocytic leukemia (APL) is a disease characterized by expression of Promyelocytic Leukemia-Retinoic Acid Receptor α (PML-RARα) chimeric mRNA. Although APL is curable, early death due to hemorrhage is a major problem. Here, we report the development of a simple and rapid diagnostic method for APL based on reverse transcription loop-mediated isothermal amplification (RT-LAMP). METHODS An RT-LAMP primer set was designed to detect three types of PML-RARα mRNA in a single reaction. Serial dilutions of plasmid DNA containing bcr1, bcr2, or bcr3 PML-RARα sequences and RNA extracted from bone marrow aspirates of 6 patients with APL were used to compare the results of RT-LAMP and nested PCR assays. RESULTS Plasmid DNA was amplified by RT-LAMP, for which the reaction time was > 4 h shorter and the lower detection limit was higher than for nested RT-PCR. Six of 7 samples tested positive by both methods. CONCLUSION We developed an RT-LAMP assay for simple and rapid PML-RARα mRNA detection that may be clinically useful for point-of-care testing and APL diagnosis.
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Affiliation(s)
- Yuki Hashimoto
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Yuki Hatayama
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Nao Kojima
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Shota Morishita
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Satoko Matsumoto
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Yuzuru Hosoda
- †Department of Hematology, Tottori University Hospital, Yonago 683-8504, Japan; ‡Division of Clinical Laboratory Medicine, Department of Pathophysiological and Therapeutic Science, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Ayako Hara
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan
| | - Toru Motokura
- Division of Clinical Laboratory, Tottori University Hospital, Yonago 683-8504, Japan; †Department of Hematology, Tottori University Hospital, Yonago 683-8504, Japan; ‡Division of Clinical Laboratory Medicine, Department of Pathophysiological and Therapeutic Science, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
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11
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Choopara I, Arunrut N, Kiatpathomchai W, Dean D, Somboonna N. Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue. Lett Appl Microbiol 2016; 64:51-56. [PMID: 27689353 DOI: 10.1111/lam.12675] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/17/2016] [Accepted: 09/26/2016] [Indexed: 12/01/2022]
Abstract
We developed an assay comprising crude DNA lysis by simple heat treatment coupled loop-mediated isothermal amplification with hydroxynaphthol blue for Chlamydia trachomatis detection (petty patent pending), and evaluated the developed assay for its feasibility as a one-step point-of-care detection on 284 endocervical swab specimens from clinically symptomatic C. trachomatis and healthy subjects. This assay is sensitive to 0·04 pg of ompA, specific with six primers targeting C. trachomatis ompA region, rapid (45 min total assay time), inexpensive (approx. 3 USD/reaction), does not require sophisticated instrumentation, and has comparable assay effectiveness (95% specificity, 90-100% sensitivity) to bacterial DNA isolation by a commercial kit coupled with polymerase chain reaction and gel electrophoresis (98-100% specificity, 87-100% sensitivity) based on the clinical samples test. The test result could be read by naked eye through the colour change from violet (negative) to sky blue (positive) for C. trachomatis-infected specimens. Further, this assay uses all safe chemical reagents and is hence safe to the users. SIGNIFICANCE AND IMPACT OF THE STUDY Chlamydia trachomatis is the major bacterial sexually transmitted disease worldwide. The clinical symptoms are broad, and chronic C. trachomatis infections could lead to blindness, ectopic pregnancy, sterility in males and females, and a higher risk of the development of cervical cancer. The result indicates the potential usefulness of our crude DNA lysis coupled loop-mediated isothermal amplification with hydroxynaphthol blue for a simple, rapid, specific, sensitive and cost-effective assay for C. trachomatis detection from suspected specimens. This assay offers an alternative in the clinical diagnosis of C. trachomatis in resource-limited health-care facilities and clinical laboratories in developing countries, and in field tests.
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Affiliation(s)
- I Choopara
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - N Arunrut
- Bioengineering and Sensing Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - W Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - D Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA.,Joint Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | - N Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Arunrut N, Kampeera J, Sirithammajak S, Sanguanrut P, Proespraiwong P, Suebsing R, Kiatpathomchai W. Sensitive Visual Detection of AHPND Bacteria Using Loop-Mediated Isothermal Amplification Combined with DNA-Functionalized Gold Nanoparticles as Probes. PLoS One 2016; 11:e0151769. [PMID: 27003504 PMCID: PMC4803327 DOI: 10.1371/journal.pone.0151769] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a component cause of early mortality syndrome (EMS) of shrimp. In 2013, the causative agent was found to be unique isolates of Vibrio parahaemolyticus (VPAHPND) that contained a 69 kbp plasmid (pAP1) carrying binary Pir-like toxin genes PirvpA and PirvpB. In Thailand, AHPND was first recognized in 2012, prior to knowledge of the causative agent, and it subsequently led to a precipitous drop in shrimp production. After VPAHPND was characterized, a major focus of the AHPND control strategy was to monitor broodstock shrimp and post larvae for freedom from VPAHPND by nucleic acid amplification methods, most of which required use of expensive and sophisticated equipment not readily available in a shrimp farm setting. Here, we describe a simpler but equally sensitive approach for detection of VPAHPND based on loop-mediated isothermal amplification (LAMP) combined with unaided visual reading of positive amplification products using a DNA-functionalized, ssDNA-labled nanogold probe (AuNP). The target for the special set of six LAMP primers used was the VPAHPND PirvpA gene. The LAMP reaction was carried out at 65°C for 45 min followed by addition of the red AuNP solution and further incubation at 65°C for 5 min, allowing any PirvpA gene amplicons present to hybridize with the probe. Hybridization protected the AuNP against aggregation, so that the solution color remained red upon subsequent salt addition (positive test result) while unprotected AuNP aggregated and underwent a color change from red to blue and eventually precipitated (negative result). The total assay time was approximately 50 min. The detection limit (100 CFU) was comparable to that of other commonly-used methods for nested PCR detection of VPAHPND and 100-times more sensitive than 1-step PCR detection methods (104 CFU) that used amplicon detection by electrophoresis or spectrophotometry. There was no cross reaction with DNA templates derived from non-AHPND bacteria commonly found in shrimp ponds (including other Vibrio species). The new method significantly reduced the time, difficulty and cost for molecular detection of VPAHPND in shrimp hatchery and farm settings.
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Affiliation(s)
- Narong Arunrut
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jantana Kampeera
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarawut Sirithammajak
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Piyachat Sanguanrut
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI road, Bangkok 10400, Thailand
| | - Porranee Proespraiwong
- Aquatic Animal Health Research Center, Charoen Pokphand Foods Pulic CO., LTD. Samutsakorn 74000, Thailand
| | - Rungkarn Suebsing
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
- * E-mail:
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Hu D, Hao L, Zhang J, Yao P, Zhang Q, Lv H, Gong X, Pan X, Cao M, Zhu J, Zhang Y, Feng Y, Wang C. Development of reverse transcription loop-mediated isothermal amplification assays to detect Hantaan virus and Seoul virus. J Virol Methods 2015; 221:68-73. [PMID: 25920565 DOI: 10.1016/j.jviromet.2015.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 04/15/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022]
Abstract
We developed two assays based on one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) to identify Hantaan virus (HTNV) and Seoul virus (SEOV), members of the Hantavirus genus that cause hemorrhagic fever with renal syndrome (HFRS). Our results showed that these assays can be conducted within 30min under isothermal conditions. The detection limit for HTNV was around 10 copies per reaction, similar to detection levels for quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. The detection limit for SEOV was 100 copies per reaction, a sensitivity that was 10-fold lower than that for qRT-PCR assays but 10-fold higher than that for RT-PCR assays. The method we developed was specific for both HTNV and SEOV without any cross-reaction with other pathogens. We conclude that RT-LAMP assays could be useful for the rapid and direct detection of HTNV and SEOV clinically, and for the epidemiological investigation of HFRS.
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Affiliation(s)
- Dan Hu
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Lina Hao
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Jinhai Zhang
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Pingping Yao
- Zhejiang Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Qi Zhang
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Heng Lv
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Xiufang Gong
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Xiuzhen Pan
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Min Cao
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Jin Zhu
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Yun Zhang
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China
| | - Youjun Feng
- Center for Infection & Immunity, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Changjun Wang
- Research Institute for Medicine of Nanjing Command, Nanjing 210002, China.
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Cao D, Hu L, Lin M, Li M, Ye Z, Sun H, Huang J, Yang H, Tian J. Real-time fluorescence Loop-Mediated Isothermal Amplification (LAMP) for rapid and reliable diagnosis of pulmonary tuberculosis. J Microbiol Methods 2015; 109:74-8. [DOI: 10.1016/j.mimet.2014.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 11/27/2022]
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