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Yang N, Zhang H, Han X, Liu Z, Lu Y. Advancements and applications of loop-mediated isothermal amplification technology: a comprehensive overview. Front Microbiol 2024; 15:1406632. [PMID: 39091309 PMCID: PMC11292733 DOI: 10.3389/fmicb.2024.1406632] [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: 03/25/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a novel method for nucleic acid detection known for its isothermal properties, high efficiency, sensitivity, and specificity. LAMP employs 4 to 6 primers targeting 6 to 8 regions of the desired sequence, allowing for amplification at temperatures between 60 and 65°C and the production of up to 109 copies within a single hour. The product can be monitored by various methods such as turbidimetry, fluorometry, and colorimetry. However, it faces limitations such as the risk of non-specific amplification, challenges in primer design, unsuitability for short gene sequences, and difficulty in multiplexing. Recent advancements in polymerase and primer design have enhanced the speed and convenience of the LAMP reaction. Additionally, integrating LAMP with technologies like rolling circle amplification (RCA), recombinase polymerase amplification (RPA), and CRISPR-Cas systems has enhanced its efficiency. The combination of LAMP with various biosensors has enabled real-time analysis, broadening its application in point-of-care testing (POCT). Microfluidic technology has further facilitated the automation and miniaturization of LAMP assays, allowing for the simultaneous detection of multiple targets and preventing contamination. This review highlights advancements in LAMP, focusing on primer design, polymerase engineering, and its integration with other technologies. Continuous improvements and integration of LAMP with complementary technologies have significantly enhanced its diagnostic capabilities, making it a robust tool for rapid, sensitive, and specific nucleic acid detection with promising implications for healthcare, agriculture, and environmental monitoring.
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Affiliation(s)
- Nan Yang
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Han Zhang
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Xiu Han
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Zhifeng Liu
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Lu
- Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China
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Tao J, Yan H, Chen S, Du J, Zhou S, Guo H, Lu L, Fang J, Jin X, Wang Z, Ying H, Han W, Dai F. Establishment and application of a loop-mediated isothermal amplification-lateral flow dipstick (LAMP-LFD) method for detecting Clostridium piliforme. Vet Med Sci 2024; 10:e1318. [PMID: 37922247 PMCID: PMC10949940 DOI: 10.1002/vms3.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023] Open
Abstract
BACKGROUND Clostridium piliforme (causative agent of Tyzzer disease) infects various animals, including primates, and hence a threat to animal and human health worldwide. At present, it is detected using traditional methods, such as path morphology, polymerase chain reaction and enzyme-linked immunosorbent assay. Therefore, it is necessary to develop convenient, efficient visual molecular biological methods for detecting C. piliforme. OBJECTIVES To establish a method with good specificity, high sensitivity and simple operation for the detection of C. piliforme. METHODS In this study, we designed internal and external primers based on the conserved 23S rRNA region of C. piliforme to develop a biotin-labelled diarrhoea-suffered loop-mediated isothermal amplification (LAMP) system for detecting of C. piliforme and assessed the specificity, sensitivity and repeatability of the LAMP system. RESULTS The LAMP system did not exhibit cross-reactivity with 24 other common pathogenic species, indicating that it had good specificity. The minimum concentration of sensitivity was 1 × 10-7 ng/μL. Mouse models (Meriones unguiculatus) of Tyzzer disease were established and a LAMP-lateral flow dipstick (LAMP-LFD) was developed for detecting C. piliforme. The detection rate of C. piliforme was 5.08% in clean-grade animals and 9.96% in specific-pathogen-free-grade animals from Jiangsu, Zhejiang and Shanghai. In addition, the detection rates of C. piliforme were 10.1%, 8.6% and 20%, in animals from Hangzhou, Wenzhou and Shaoxing, respectively. The detection rate of C. piliforme was higher in experimental animals used in schools than in those used in companies and research institutes. CONCLUSIONS The LAMP-LFD method established in this study can be used to detect C. piliforme in animals handled in laboratory facilities of universities, pharmaceutical enterprises and research and development institutions.
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Affiliation(s)
- Junhao Tao
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Huiqiong Yan
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Sisi Chen
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Jiangtao Du
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Shasang Zhou
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Honggang Guo
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Lingqun Lu
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
| | - Jie Fang
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Xiaoyin Jin
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Zhiyuan Wang
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Huazhong Ying
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
| | - Wei Han
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
| | - Fangwei Dai
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
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Aksono EB, Lamid M, Rimayanti R, Hamid IS, Effendi MH, Rantam FA, Widjiati W, Mufasirin M, Puspitasari H, Fitria M, Fajar NS, Suwanti LT, Nusdianto N, Zaidan AH, Kanai Y, Sucipto TH. Designing one-step reverse transcriptase loop-mediated isothermal amplification for serotype O foot-and-mouth disease virus detection during the 2022 outbreak in East Java, Indonesia. Vet World 2023; 16:1889-1896. [PMID: 37859973 PMCID: PMC10583884 DOI: 10.14202/vetworld.2023.1889-1896] [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: 03/28/2023] [Accepted: 08/23/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim Various methods can detect foot-and-mouth disease (FMD) in cows, but they necessitate resources, time, costs, laboratory facilities, and specific clinical specimen submission, often leading to FMD virus (FMDV) diagnosis delays. The 2022 FMD outbreak in East Java, Indonesia, highlighted the need for an easy, inexpensive, rapid, and accurate detection approach. This study aims to devise a one-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) technique and phylogenetic analysis to detect the serotype O FMDV outbreak in East Java. Materials and Methods Swab samples were collected from the foot vesicles, nasal secretions, and saliva of five suspected FMDV-infected cows in East Java between June and July 2022. The RT-LAMP design used hydroxy naphthol blue dye or SYBR Green I dye, with confirmatory analysis through reverse transcriptase polymerase chain reaction (RT-PCR) targeting 249 base pairs. PCR products underwent purification, sequencing, and nucleotide alignment, followed by phylogenetic analysis. Results The RT-LAMP method using hydroxy naphthol blue dye displayed a positive reaction through a color shift from purple to blue in the tube. Naked-eye observation in standard light or ultraviolet (UV) light at 365 nm, with SYBR Green I stain, also revealed color change. Specifically, using SYBR Green I dye, UV light at 365 nm revealed a color shift from yellow to green, signifying a positive reaction. Nucleotide alignment revealed mutations and deletion at the 15th sequence in the JT-INDO-K3 isolate from the East Java FMDV outbreak. Despite differing branches, the phylogenetic tree placed it in the same cluster as serotype O FMDV from Malaysia and Mongolia. Conclusion JT-INDO-K3 exhibited distinctions from Indonesian serotype O FMDV isolates and those documented in GenBank. Then, the RT-LAMP method used in this study has a detection limit 10 times higher latter than the conventional RT-PCR limit, without any cross-reactivity among strains.
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Affiliation(s)
- Eduardus Bimo Aksono
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Institute of Life Science, Technology and Engineering, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Mirni Lamid
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Rimayanti Rimayanti
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Iwan Sahrial Hamid
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Mustofa Helmi Effendi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Fedik Abdul Rantam
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Widjiati Widjiati
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Mufasirin Mufasirin
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Heni Puspitasari
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Munawaroh Fitria
- Department of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia
| | - Nur Syamsiatul Fajar
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Lucia Tri Suwanti
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Nusdianto Nusdianto
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Andi Hamim Zaidan
- Institute of Life Science, Technology and Engineering, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Yuta Kanai
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Teguh Hari Sucipto
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
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Ghazaleh RA, Al-Sawalhe M, Odeh IA, El Ibrahim J, Al-Turman B, Makhamreh J. Host range, severity and trans boundary transmission of Orf virus (ORFV). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 112:105448. [PMID: 37217030 DOI: 10.1016/j.meegid.2023.105448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/03/2023] [Accepted: 04/30/2023] [Indexed: 05/24/2023]
Abstract
Contagious ecthyma in small ruminants is a zoonotic disease caused by Orf virus (ORFV) in the genus Parapoxvirus that can be deadly to its natural hosts. It causes significant losses worldwide, and commonly infects humans. However, the literature about its comparative severity in sheep and goat hosts is misleading; and while contagious ecthyma has been shown to occur in camels and transmit to humans, there is confusion as to whether ORFV is responsible. Camels are important from a 'One Health' perspective as they have been implicated as a reservoir host for the virus causing Middle East Respiratory Syndrome (MERS), which has a case fatality rate of 35% in humans. We compared ORFV gene sequences and mortality data from the West Bank in Palestine, where ORFV has not been reported previously, with data from the region. Surprisingly, we found that infections of camels that had been attributed to ORFV were more closely related to a different member of the genus Parapoxvirus. Two Middle East ORFVs isolated from humans were unrelated and sat alongside sheep and goat derived sequences on two distinct ORFV lineages of a maximum likelihood B2L gene tree. One of the viral lineages bifurcated to produce a monophyletic group of goat-derived ORFVs characterized uniquely by a glycine at amino acid reside 249. We found that serine is the ancestral allele shared between ORFV infections of sheep and also two closely related Parapoxviruses (PCPV and CCEV), indicating that the glycine allele represents a more recent shift in virus host range adaptation to goats. Furthermore, and contrary to some reports that ORFV is more severe in goats than in sheep, we observed median mortality of up to 24.5% in sheep, but none in goats. We also identified trans-boundary spread of ORFV between the West Bank and Israel.
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Affiliation(s)
- Robin Abu Ghazaleh
- Palestine-Korea Biotechnology Research Center, Palestine Polytechnic University, P.O. Box 198, Hebron, Palestine.
| | - Mohammed Al-Sawalhe
- Palestine-Korea Biotechnology Research Center, Palestine Polytechnic University, P.O. Box 198, Hebron, Palestine
| | - Insaf Abu Odeh
- Palestine-Korea Biotechnology Research Center, Palestine Polytechnic University, P.O. Box 198, Hebron, Palestine
| | - Jehad El Ibrahim
- Palestine-Korea Biotechnology Research Center, Palestine Polytechnic University, P.O. Box 198, Hebron, Palestine; National Agricultural Research Center (NARC), Jenin, Palestine
| | - Basem Al-Turman
- Palestine-Korea Biotechnology Research Center, Palestine Polytechnic University, P.O. Box 198, Hebron, Palestine
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Simon DS, Yew CW, Kumar VS. Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2. Microorganisms 2023; 11:1233. [PMID: 37317207 PMCID: PMC10223058 DOI: 10.3390/microorganisms11051233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes.
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Affiliation(s)
| | | | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (D.S.S.); (C.-W.Y.)
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Fan Q, Xie Z, Wei Y, Zhang Y, Xie Z, Xie L, Huang J, Zeng T, Wang S, Luo S, Li M. Development of a visual multiplex fluorescent LAMP assay for the detection of foot-and-mouth disease, vesicular stomatitis and bluetongue viruses. PLoS One 2022; 17:e0278451. [PMID: 36480573 PMCID: PMC9731490 DOI: 10.1371/journal.pone.0278451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can be used to amplify target genes at a constant temperature, and it has several advantages, including convenience, specificity and sensitivity. However, due to the special interpretation methods of this technology for reaction results, all the previously reported LAMP detection methods have been restricted to identifying a single target, which limits the application of this technology. In this study, we modified conventional LAMP to include a quencher-fluorophore composite probe complementary to the F1c segment of the inner primer FIP; upon strand separation, a gain in the visible fluorescent signal was observed. The probes could be labeled with different fluorophores, showing different colors at the corresponding wavelengths. Therefore, this multiplex LAMP (mLAMP) assay can simultaneously detect 1-3 target sequences in a single LAMP reaction tube, and the results are more accurate and intuitive. In this study, we comprehensively demonstrated a single-reaction mLAMP assay for the robust detection of three cattle viruses without nonspecific amplification of other related pathogenic cattle viruses. The detection limit of this mLAMP assay was as low as 526-2477 copies/reaction for the recombinant plasmids. It is expected that this mLAMP assay can be widely used in clinical diagnosis.
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Affiliation(s)
- Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- * E-mail:
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
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8
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Zhang J, Hou Q, Ma W, Chen D, Zhang W, Wubshet AK, Ding Y, Li M, Li Q, Chen J, Dai J, Wu G, Zhang Z, Zaberezhny AD, Pejsak Z, Tarasiuk K, Zafar Khan MU, Wang Y, He J, Liu Y. A Naked-Eye Visual Reverse Transcription Loop-Mediated Isothermal Amplification with Sharp Color Changes for Potential Pen-Side Test of Foot-and-Mouth Disease Virus. Viruses 2022; 14:v14091982. [PMID: 36146788 PMCID: PMC9504329 DOI: 10.3390/v14091982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Visual loop-mediated isothermal amplification (LAMP) is qualified to be applied in the field to detect pathogens due to its simplicity, rapidity and cost saving. However, the color changes in currently reported visual reverse transcription LAMP (RT-LAMP) for foot-and-mouth disease virus (FMDV) detection are not so obvious to the naked eye, so interpretation of results is troublesome. In this study, a new naked-eye visual RT-LAMP to detect all seven distinct serotypes of FMDV was established based on the 3D genes by using pH-sensitive neutral red as the indicator, rendering a sharp contrast of color changes between the negative (light orange) and the positive (pink). Analytical sensitivity tests showed that the detection limit of the visual RT-LAMP was 104 copies/µL while those were 103 and 104 copies/µL for the RT-qPCR and conventional RT-PCR methods, respectively. Specificity tests proved that the established visual RT-LAMP assay had no cross-reactivity with other common livestock viruses. Furthermore, the analysis of 59 clinical samples showed 98.31% and 100% concordance with the RT-qPCR and the RT-PCR, respectively. The pan-serotypic FMD visual RT-LAMP assay could be suitable for a pen-side test of all seven serotypes of FMDV because the results could be easily distinguished by the naked eye without the requirement of complicated instruments and professional technicians. Hence, the novel method may have a promising prospect in field tests which exert an important role in monitoring, preventing, and controlling FMD, especially in regions with no PCR or qPCR instrument available.
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Affiliation(s)
- Jie Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Qian Hou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Weimin Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Danian Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Weibing Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Ashenafi Kiros Wubshet
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yaozhong Ding
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Miaomiao Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Qian Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jiao Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Junfei Dai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Guohua Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Ziteng Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China
| | - Alexei D. Zaberezhny
- Federal State Budgetary Institution, All-Russian Research and Technological Institute of Biological Industry (VNITIBP), Moscow 141142, Russia
| | - Zygmunt Pejsak
- Department of Infectious and Parasitic Diseases, University Center of Veterinary Medicine Jagiellonian University—Agriculture Universities, 31-120 Krakow, Poland
| | - Kazimierz Tarasiuk
- Department of Infectious and Parasitic Diseases, University Center of Veterinary Medicine Jagiellonian University—Agriculture Universities, 31-120 Krakow, Poland
| | | | - Yang Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jijun He
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- Correspondence: (J.H.); (Y.L.)
| | - Yongsheng Liu
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China
- Correspondence: (J.H.); (Y.L.)
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Ku J, Chauhan K, Hwang SH, Jeong YJ, Kim DE. Enhanced Specificity in Loop-Mediated Isothermal Amplification with Poly(ethylene glycol)-Engrafted Graphene Oxide for Detection of Viral Genes. BIOSENSORS 2022; 12:bios12080661. [PMID: 36005057 PMCID: PMC9405610 DOI: 10.3390/bios12080661] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the simple, quick, and low-cost detection of various viral genes. LAMP assays are susceptible to generating non-specific amplicons, as high concentrations of DNA primers can give rise to primer dimerization and mismatched hybridizations, resulting in false-positive signals. Herein, we reported that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly enhance the specificity of LAMP, owing to its ability to adsorb single-stranded DNA (ssDNA). By adsorbing surplus ssDNA primers, PEG-nGO minimizes the non-specific annealing of ssDNAs, including erroneous priming and primer dimerization, leading to the enhanced specificity of LAMP. The detection of complementary DNAs transcribed from the hepatitis C virus (HCV) RNA was performed by the PEG-nGO-based LAMP. We observed that the inclusion of PEG-nGO significantly enhances the specificity and sensitivity of the LAMP assay through the augmented difference in fluorescence signals between the target and non-target samples. The PEG-nGO-based LAMP assay greatly facilitates the detection of HCV-positive clinical samples, with superior precision to the conventional quantitative real-time PCR (RT-qPCR). Among the 20 clinical samples tested, all 10 HCV-positive samples are detected as positive in the PEG-nGO-based LAMP, while only 7 samples are detected as HCV-positive in the RT-qPCR. In addition, the PEG-nGO-based LAMP method significantly improves the detection precision for the false-positive decision by 1.75-fold as compared to the LAMP without PEG-nGO. Thus, PEG-nGO can significantly improve the performance of LAMP assays by facilitating the specific amplification of target DNA with a decrease in background signal.
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Affiliation(s)
- Jamin Ku
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Khushbu Chauhan
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yong-Joo Jeong
- School of Applied Chemistry, Kookmin University, Seoul 02707, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
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10
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Kim JW, Park KW, Kim M, Lee KK, Lee CS. Highly Specific Loop-Mediated Isothermal Amplification Using Graphene Oxide-Gold Nanoparticles Nanocomposite for Foot-and-Mouth Disease Virus Detection. NANOMATERIALS 2022; 12:nano12020264. [PMID: 35055281 PMCID: PMC8778833 DOI: 10.3390/nano12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of rapid results, isothermal reaction conditions, and high sensitivity. However, this diagnostic system often produces false positive results due to a high rate of non-specific reactions caused by formation of hairpin structures, self-dimers, and mismatched hybridization. The non-specific signals can be due to primers used in the methods because the utilization of multiple LAMP primers increases the possibility of self-annealing of primers or mismatches between primers and templates. In this study, we report a nanomaterial-assisted LAMP method that uses a graphene oxide-gold nanoparticles (AuNPs@GO) nanocomposite to enable the detection of foot-and-mouth disease virus (FMDV) with high sensitivity and specificity. Foot-and-mouth disease (FMD) is a highly contagious and deadly disease in cloven-hoofed animals; hence, a rapid, sensitive, and specific detection method is necessary. The proposed approach exhibited high sensitivity and successful reduction of non-specific signals compared to the traditionally established LAMP assays. Additionally, a mechanism study revealed that these results arose from the adsorption of single-stranded DNA on AuNPs@GO nanocomposite. Thus, AuNPs@GO nanocomposite is demonstrated to be a promising additive in the LAMP system to achieve highly sensitive and specific detection of diverse diseases, including FMD.
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Affiliation(s)
- Jong-Won Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
| | - Kyoung-Woo Park
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Myeongkun Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
| | - Kyung Kwan Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biomedical and Nanopharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Korea
| | - Chang-Soo Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-4-2879-8446
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11
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Jang M, Kim S. Inhibition of Non-specific Amplification in Loop-Mediated Isothermal Amplification via Tetramethylammonium Chloride. BIOCHIP JOURNAL 2022; 16:326-333. [PMID: 35909465 PMCID: PMC9326409 DOI: 10.1007/s13206-022-00070-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 02/02/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) may be used in molecular and point-of-care diagnostics for pathogen detection. The amplification occurs under isothermal conditions using up to six primers. However, non-specific amplification is frequently observed in LAMP. Non-specific amplification has the potential to be triggered by forward and reverse internal primers. And the relatively low reaction temperature (55-65 °C) induces the secondary structure via primer-primer interactions. Primer redesign and probe design have been recommended to solve this problem. LAMP primers have strict conditions, such as Tm, GC contents, primer dimer, and distance between primers compared to conventional PCR primers. Probe design requires specialized knowledge to have high specificity for a target. In polymerase chain reaction (PCR), some chemicals or proteins are used for improving specificity and efficiency. Therefore, we hypothesized that additives can suppress the non-specific amplification. In this study, tetramethylammonium chloride (TMAC), formamide, dimethyl sulfoxide, Tween 20, and bovine serum albumin have been used as LAMP additives. In our study, TMAC was presented as a promising additive for suppressing non-specific amplification in LAMP. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00070-3.
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Affiliation(s)
- MinJu Jang
- grid.256155.00000 0004 0647 2973Department of Bionanotechnology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Sanghyo Kim
- grid.256155.00000 0004 0647 2973Department of Bionanotechnology, Gachon University, Seongnam, 13120 Republic of Korea
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