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Wang M, Tang Z, Liao M, Cao H, Zhao N. Loop-mediated isothermal amplification for detecting the Ile-2041-Asn mutation in fenoxaprop-P-ethyl-resistant Alopecurus aequalis. PEST MANAGEMENT SCIENCE 2023; 79:711-718. [PMID: 36258292 DOI: 10.1002/ps.7239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Shortawn foxtail (Alopecurus aequalis Sobol.), a competitive grass weed severely infesting overwintering crops worldwide, has evolved resistance to the highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide fenoxaprop-P-ethyl. The Ile-to-Asn substitution at codon position 2041 of ACCase is a dominant resistance mutation that has been associated with fenoxaprop-P-ethyl resistance in A. aequalis. However, its detection based on conventional methods such as polymerase chain reaction (PCR) and gene sequencing is rather labor- and time-consuming. RESULTS In order to facilitate its detection in field populations of A. aequalis, a simple and efficient method with high sensitivity to the Ile-2041-Asn mutation was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed to target a 244-bp fragment of ACCase comprising codon position 2041. Using the special primers and genomic DNA of A. aequalis, the concentrations of reaction components, temperature and time each were optimized. The LAMP reaction for the detection of the Ile-2041-Asn mutation was processed at 65 °C for 45 min followed by 80 °C for 10 min to stop the reaction. The LAMP method developed was 1000-fold more sensitive than the conventional PCR method, and the detection was also practicable when using crude DNA of A. aequalis as a template. CONCLUSION The low cost, simplicity and high sensitivity of the developed LAMP assay make the detection of the Ile-2041-Asn mutation easier and quicker, which may contribute to the monitoring and management of resistance development to fenoxaprop-P-ethyl in A. aequalis. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Mali Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Zhi Tang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Ning Zhao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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Dos Santos CA, Silva LDC, Souza Júnior MND, Mendes GDM, Estrela PFN, de Oliveira KG, de Curcio JS, Resende PC, Siqueira MM, Pauvolid-Corrêa A, Duarte GRM, Silveira-Lacerda EDP. Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers. Sci Rep 2022; 12:11500. [PMID: 35798777 PMCID: PMC9261132 DOI: 10.1038/s41598-022-15368-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/22/2022] [Indexed: 12/19/2022] Open
Abstract
Despite the advance of vaccination worldwide, epidemic waves caused by more transmissible and immune evasive genetic variants of SARS-CoV-2 have sustained the ongoing pandemic of COVID-19. Monitoring such variants is expensive, as it usually relies on whole-genome sequencing methods. Therefore, it is necessary to develop alternatives that could help identify samples from specific variants. Reverse transcription loop-mediated isothermal amplification is a method that has been increasingly used for nucleic acid amplification, as it is cheaper and easier to perform when compared to other molecular techniques. As a proof of concept that can help distinguish variants, we present an RT-LAMP assay capable of detecting samples carrying a group of mutations that can be related to specific SARS-CoV-2 lineages, here demonstrated for the Variant of Concern Gamma. We tested 60 SARS-CoV-2 RNA samples extracted from swab samples and the reaction showed a sensitivity of 93.33%, a specificity of 88.89% and a kappa value of 0.822 for samples with a Ct ≤ 22.93. The RT-LAMP assay demonstrated to be useful to distinguish VOC Gamma and may be of particular interest as a screening approach for variants in countries with poor sequencing coverage.
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Affiliation(s)
- Carlos Abelardo Dos Santos
- Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil
| | - Lívia do Carmo Silva
- Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil
| | | | | | | | | | - Juliana Santana de Curcio
- Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Reference Laboratory for COVID-19 (WHO) of Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Reference Laboratory for COVID-19 (WHO) of Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Elisângela de Paula Silveira-Lacerda
- Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil.
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Development of a LAMP-Based Molecular Species Diagnosis Method for Four Major Agricultural Pests in the Genus Spodoptera (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12100883. [PMID: 34680652 PMCID: PMC8541213 DOI: 10.3390/insects12100883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Four major Spodoptera pests, S. exigua, S. frugiperda, S. litura, and S. littoralis, are widely distributed polyphagous pests affecting various crops. Despite different distribution areas, these four species cause serious damage to agriculture worldwide. As these species are morphologically similar at the larval stage, diagnostic methods have been developed and utilized for their identification. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for rapid and effective species diagnosis, along with PCR, to identify Korean field-collected or overseas samples. The optimal conditions for the LAMP assay were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency in S. exigua, whereas increased non-specific amplification was found in other species. A broad range of DNA concentrations was observed in the LAMP assay, and the minimum detectable DNA concentration was 1 pg. The DNA release method for LAMP involved incubation of larval or adult tissue samples for 5 min at 95 °C, without a DNA extraction step. Considering the gradual diversification invasive pest incidence, this simple and accurate LAMP assay can be used for intensive field monitoring of invasive pests and integrated management of these species. Abstract Molecular-based species identification tools are helpful to identify tiny insect and lepidopteran pests that show morphological similarities in the larval stage and are essential for quarantine as well as agricultural research. Here, we focused on four major Spodoptera pests: S. exigua, S. frugiperda, S. litura, and S. littoralis. S. exigua and S. litura mitochondrial genome sequences were newly identified and species-specific sequence regions were identified in the cytochrome c oxidase subunit II and III regions. Species primers were designed and applied in loop-mediated isothermal amplification (LAMP) and PCR to identify Korean field-collected or overseas samples. The optimal incubation conditions for LAMP were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency for S. exigua, and the nonspecific amplification for other species. The LAMP assay could detect a wide range of DNA concentrations, with the range 1 ng–1 pg in dependence of four LAMP primers. The DNA-releasing technique, without DNA extraction, in the LAMP assay involved larval or adult tissue sample incubation at 95 °C for 5 min. The entire process takes approximately 70 min. This new molecular diagnostic method is simple and accurate, with application in the field and laboratory and for monitoring and ecological studies.
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Orondo PW, Nyanjom SG, Atieli H, Githure J, Ondeto BM, Ochwedo KO, Omondi CJ, Kazura JW, Lee MC, Zhou G, Zhong D, Githeko AK, Yan G. Insecticide resistance status of Anopheles arabiensis in irrigated and non-irrigated areas in western Kenya. Parasit Vectors 2021; 14:335. [PMID: 34174946 PMCID: PMC8235622 DOI: 10.1186/s13071-021-04833-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria control in Kenya is based on case management and vector control using long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS). However, the development of insecticide resistance compromises the effectiveness of insecticide-based vector control programs. The use of pesticides for agricultural purposes has been implicated as one of the sources driving the selection of resistance. The current study was undertaken to assess the status and mechanism of insecticide resistance in malaria vectors in irrigated and non-irrigated areas with varying agrochemical use in western Kenya. METHODS The study was carried out in 2018-2019 in Homa Bay County, western Kenya. The bioassay was performed on adults reared from larvae collected from irrigated and non-irrigated fields in order to assess the susceptibility of malaria vectors to different classes of insecticides following the standard WHO guidelines. Characterization of knockdown resistance (kdr) and acetylcholinesterase-inhibiting enzyme/angiotensin-converting enzyme (Ace-1) mutations within Anopheles gambiae s.l. species was performed using the polymerase chain reaction (PCR) method. To determine the agricultural and public health insecticide usage pattern, a questionnaire was administered to farmers, households, and veterinary officers in the study area. RESULTS Anopheles arabiensis was the predominant species in the irrigated (100%, n = 154) area and the dominant species in the non-irrigated areas (97.5%, n = 162), the rest being An. gambiae sensu stricto. In 2018, Anopheles arabiensis in the irrigated region were susceptible to all insecticides tested, while in the non-irrigated region reduced mortality was observed (84%) against deltamethrin. In 2019, phenotypic mortality was decreased (97.8-84% to 83.3-78.2%). In contrast, high mortality from malathion (100%), DDT (98.98%), and piperonyl butoxide (PBO)-deltamethrin (100%) was observed. Molecular analysis of the vectors from the irrigated and non-irrigated areas revealed low levels of leucine-serine/phenylalanine substitution at position 1014 (L1014S/L1014F), with mutation frequencies of 1-16%, and low-frequency mutation in the Ace-1R gene (0.7%). In addition to very high coverage of LLINs impregnated with pyrethroids and IRS with organophosphate insecticides, pyrethroids were the predominant chemical class of pesticides used for crop and animal protection. CONCLUSION Anopheles arabiensis from irrigated areas showed increased phenotypic resistance, and the intensive use of pesticides for crop protection in this region may have contributed to the selection of resistance genes observed. The susceptibility of these malaria vectors to organophosphates and PBO synergists in pyrethroids offers a promising future for IRS and insecticide-treated net-based vector control interventions. These findings emphasize the need for integrated vector control strategies, with particular attention to agricultural practices to mitigate mosquito resistance to insecticides.
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Affiliation(s)
- Pauline Winnie Orondo
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya. .,International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya.
| | - Steven G Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Harrysone Atieli
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya.,School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - John Githure
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya
| | - Benyl M Ondeto
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya
| | - Kevin O Ochwedo
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya
| | - Collince J Omondi
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya
| | - James W Kazura
- Center for Global Health & Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, USA
| | - Guofa Zhou
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, USA
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, USA
| | - Andrew K Githeko
- International Center of Excellence for Malaria Research, Tom Mboya University College of Maseno University, Homa Bay, Kenya. .,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya.
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, USA.
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Khammanee T, Sawangjaroen N, Buncherd H, Tun AW, Thanapongpichat S. A LAMP-SNP Assay Detecting C580Y Mutation in Pfkelch13 Gene from Clinically Dried Blood Spot Samples. THE KOREAN JOURNAL OF PARASITOLOGY 2021; 59:15-22. [PMID: 33684983 PMCID: PMC7939969 DOI: 10.3347/kjp.2021.59.1.15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/19/2021] [Indexed: 11/23/2022]
Abstract
Artemisinin resistance (ART) has been confirmed in Greater Mekong Sub-region countries. Currently, C580Y mutation on Pfkelch13 gene is known as the molecular marker for the detection of ART. Rapid and accurate detection of ART in field study is essential to guide malaria containment and elimination interventions. A simple method for collection of malaria-infected blood is to spot the blood on filter paper and is fast and easy for transportation and storage in the field study. This study aims to evaluate LAMP-SNP assay for C580Y mutation detection by introducing an extra mismatched nucleotide at the 3’ end of the FIP primer. The LAMP-SNP assay was performed in a water bath held at a temperature of 56°C for 45 min. LAMP-SNP products were interpreted by both gel-electrophoresis and HNB-visualized changes in color. The method was then tested with 120 P. falciparum DNA from dried blood spot samples. In comparing the LAMP-SNP assay results with those from DNA sequencing of the clinical samples, the 2 results fully agreed to detect C580Y. The sensitivity and specificity of the LAMP-SNP assay showed 100%. There were no cross-reactions with other Plasmodium species and other Pfkelch13 mutations. The LAMP-SNP assay performed in this study was rapid, reliable, and useful in detecting artemisinin resistance in the field study.
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Affiliation(s)
- Thunchanok Khammanee
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Nongyao Sawangjaroen
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Supinya Thanapongpichat
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
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Cibecchini G, Cecere P, Tumino G, Morcia C, Ghizzoni R, Carnevali P, Terzi V, Pompa PP. A Fast, Naked-Eye Assay for Varietal Traceability in the Durum Wheat Production Chain. Foods 2020; 9:foods9111691. [PMID: 33228015 PMCID: PMC7699333 DOI: 10.3390/foods9111691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023] Open
Abstract
The development of a colorimetric mono-varietal discriminating assay, aimed at improving traceability and quality control checks of durum wheat products, is described. A single nucleotide polymorphism (SNP) was identified as a reliable marker for wheat varietal discrimination, and a rapid test for easy and clear identification of specific wheat varieties was developed. Notably, an approach based on the loop-mediated isothermal amplification reaction (LAMP) as an SNP discrimination tool, in combination with naked-eye visualization of the results, was designed and optimized. Our assay was proven to be effective in the detection of adulterated food products, including both substitution and mixing with different crop varieties.
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Affiliation(s)
- Giulia Cibecchini
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
- Department of Chemistry and Industrial Chemistry, University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Paola Cecere
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
| | - Giorgio Tumino
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | - Caterina Morcia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | - Roberta Ghizzoni
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | | | - Valeria Terzi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
- Correspondence: (V.T.); (P.P.P.)
| | - Pier Paolo Pompa
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
- Correspondence: (V.T.); (P.P.P.)
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Rapid detection of rifampicin-resistant Mycobacterium tuberculosis, based on isothermal DNA amplification and DNA chromatography. J Microbiol Methods 2020; 177:106062. [PMID: 32950563 DOI: 10.1016/j.mimet.2020.106062] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022]
Abstract
Rapid and easy detection of nucleotide point mutations in bacterial pathogens associated with drug resistance is essential for the proper use of antimicrobials. Here, we developed a rapid and simple method for the detection of mutations using Loop-mediated isothermal amplification (LAMP) combined with the single-tag hybridization (STH) chromatographic printed array strips (PAS) method. This procedure is able to detect four mutations (C1349 T, A1295C, G1303 T, A1304 T) in Rifampicin Resistance Determining Region (RRDR) of rifampicin-resistant Mycobacterium tuberculosis (RR-TB), simultaneously. LAMP reactions contained a LAMP primer and eight allele-specific primers for each mutation. The allele-specific primers products were detected by nucleic acid chromatography using PAS. Four detection lines were detected there, one of which was detected at different positions depend on the wild type and the mutant type. We carried out the four mutations detection using 31 genomic DNA (2 A1295T, 1 G1303 T, 6 A1304 T, 22 C1349 T) from clinical isolate. The mutations have been confirmed by sequence analysis. The detection results were completely consistent with the sequence analysis. In the present study, four mutations could be detected, but only 60% of RR-TB could be detected with these four. It is expected that the detection rate will increase by adding more mutant primers. The combined LAMP and STH chromatographic PAS method is a simple and rapid method for detecting point mutations in clinical isolates as a point-of-care testing (POCT) technique. In addition, it does not require special equipment and can meet the demand in areas where drug-resistant bacteria are endemic, such as developing countries.
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Gill P, Hadian Amree A. AS-LAMP: A New and Alternative Method for Genotyping. Avicenna J Med Biotechnol 2020; 12:2-8. [PMID: 32153732 PMCID: PMC7035465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In recent decades, different methods have been introduced for the genotyping of Single Nucleotide Polymorphisms (SNPs) and mutations in nucleic acid sequences. These methods have several applications ranging from agriculture to medicine. The Loop-mediated isothermal amplification (LAMP) method was first introduced by Notomi et al. Since then, different methods derived from LAMP have been extensively applied in detecting pathogens. The LAMP method is an isothermal technique that amplifies the target DNA segment using four different primers that have been uniquely designed for recognizing six distinct zones on the objective gene; the process of reaction continues at a constant temperature via a strand displacement reaction. Amplifying and detecting the targeted zone can be accomplished in one stage. Although the LAMP method is mostly used for pathogen detection, several studies have used this method for genotyping. The present article reviewed various studies that used the LAMP method for SNP detection. The outcomes indicated that the LAMP technique could be a reliable and alternative technique for genotyping. Further studies are recommended to use this approach for genotyping.
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Affiliation(s)
- Pooria Gill
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Arash Hadian Amree
- Student Research Committee, Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran,Corresponding author: Arash Hadian Amree, M.D., Ph.D. Candidate, Student Research Committee, Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran, Tel: +98 9111548344, Fax: +98 11 33361626, E-mail:
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Vontas J, Mavridis K. Vector population monitoring tools for insecticide resistance management: Myth or fact? PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 161:54-60. [PMID: 31685197 DOI: 10.1016/j.pestbp.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/10/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Insecticide resistance is a large and growing problem for the control of mosquito disease vectors. The World Health Organization (WHO) established the Global Plan for Insecticide Resistance Management (GPIRM) in 2012. In that context, both classical and molecular tools, as well as entomological databases and decision support platforms have been developed and used for IRM. Despite major advances in the molecular elucidation of resistance mechanisms and the development of diagnostic tools, their impact on disease control programs has been limited. In most cases diagnostic tools provide a retrospective examination of changes imposed by insecticides rather than a prospective analysis to guide vector control strategies. The uncertainty of the predictive value of markers, the assay robustness and the common misconceptions in resistance diagnosis terminology are continuing challenges in monitoring vector resistance. Furthermore, an often logistics, as opposed to systematic scientific evidence, based approach to decision for the use of the very few alternative chemicals in vector control, has reduced the value of resistance monitoring in practice. The current deployment of new insecticidal active ingredients should necessitate the application of companion diagnostics (CDx) and the development of modern ways for interpretation and management of the data by trained programme managers. This will establish their real value for use in decision-making, in line with evidence based choice of chemicals in agriculture and medical applications.
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Affiliation(s)
- John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Greece.
| | - Konstantinos Mavridis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece
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Status of Insecticide Resistance and Its Mechanisms in Anopheles gambiae and Anopheles coluzzii Populations from Forest Settings in South Cameroon. Genes (Basel) 2019; 10:genes10100741. [PMID: 31554225 PMCID: PMC6827028 DOI: 10.3390/genes10100741] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/02/2019] [Accepted: 09/13/2019] [Indexed: 01/29/2023] Open
Abstract
A key factor affecting malaria vector control efforts in Cameroon is the rapid expansion of insecticide resistance in Anopheles gambiae s.l (An. gambiae) populations; however, mechanisms involved in insecticide resistance in forest mosquito populations are still not well documented yet. The present study was conducted to screen molecular mechanisms conferring insecticide resistance in An. gambiae s.l. populations from the South Cameroon forest region. WHO bioassays were conducted with F0 An. gambiae females aged three to four days from forest (Sangmelima, Nyabessan, and Mbandjock) and urban sites (Yaoundé (Bastos and Nkolondom)), against pyrethroids (permethrin 0.75% and deltamethrin 0.05%) and carbamates (bendiocarb 0.1%). Members of the An. Gambiae s.l. species complex were identified using molecular diagnostic tools. TaqMan assays were used to screen for target site mutations. The expression profiles of eight genes implicated in insecticide resistance were assessed using RT-qPCR. Cuticle hydrocarbon lipids were measured to assess their potential implication in insecticide resistance. Both An. Gambiae and An. coluzzii were detected. An. gambiae was highly prevalent in Sangmelima, Nyabessan, Mbandjock, and Nkolondom. An. coluzzii was the only species found in the Yaoundé city center (Bastos). Low mortality rate to both pyrethroids and bendiocarb was recorded in all sites. High frequency of L1014F allele (75.32–95.82%) and low frequencies of L1014S (1.71–23.05%) and N1575Y (5.28–12.87%) were recorded. The G119S mutation (14.22–35.5%) was detected for the first time in An. gambiae populations from Cameroon. This mutation was rather absent from An. coluzzii populations. The detoxification genes Cyp6m2, Cyp9k1, Cyp6p4, Cyp6z1, as well as Cyp4g16 which catalyzes epicuticular hydrocarbon biosynthesis, were found to be overexpressed in at least one population. The total cuticular hydrocarvbon content, a proxy of cuticular resistance, did not show a pattern associated with pyrethroid resistance in these populations. The rapid emergence of multiple resistance mechanisms in An. Gambiae s.l. population from the South Cameroon forest region is of big concern and could deeply affect the sustainability of insecticide-based interventions strategies in this region.
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Gill P, Amree AH. Allele-Specific Loop-Mediated Isothermal Amplification for the Detection of IVSII-I G>A Mutation On β-Globin Gene. Open Access Maced J Med Sci 2019; 7:1582-1587. [PMID: 31210804 PMCID: PMC6560289 DOI: 10.3889/oamjms.2019.285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Thalassemia is one of the most common genetic health problems in the world. More than 200 different mutations have been identified in the beta-globin gene and among the 24 β-globin gene mutations in β-thalassemia carriers in the north of Iran IVSII-I G>A mutation has the highest frequency. Using fast, inexpensive, simple and reliable methods for the detection of the mutations in β-thal carriers is very important in prenatal diagnosis, and introduction of alternative methods to the existing ones can help to simplify the detection of mutations. Since its introduction, different methods derived from LAMP have been widely used for SNPs detection. AIM This study was aimed to design a new method for the detection of IVSII-I G>A mutation on β-globin gene based on AS - LAMP technique. METHODS Primer explorer V5 software was used for the design of LAMP primers. Three sets of primers were designed. In the first set, the BIP primers were exactly complementary to the normal and mutant alleles. In the second set, 1 nucleotide (T) was inserted at the 5' end of BIP primers, and in the last set, one nucleotide at the 5' end of BIP primer was changed. The other required primers for the LAMP reaction (FIP, B3, and F3) were the same for all 3 sets of primers. The LAMP reaction was applied on three DNA samples (Wild type, Heterozygote and Homozygote for IVSII-I G>A mutation) and synthetic DNA. RESULTS The results of the present study showed that LAMP reaction using three sets of primers could not successfully detect the IVSII-I G > A mutation among subjects DNA sample and synthetic DNA. CONCLUSION Although several studies have successfully used ARMS-LAMP method to detect the SNPs, and other studies use a variety of methods to identify IVSII-I G>A mutation, the present study was unable to differentiate between a normal allele and IVSII-I G>A mutation. Hence further studies are recommended to consider redesigning of primer set, DNA concentration and using commercial LAMP Master Mix to detect the mutation.
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Affiliation(s)
- Pooria Gill
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Sari, Iran.,Nano Medicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Arash Hadian Amree
- Hemoglobinopathy Institute, Thalassemia Research Center, Mazandaran University of Medical Science, Sari, Iran
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Filipenko ML, Oscorbin IP, Khrapov EA, Shamovskaya DA, Cherednichenko AG, Shvartz Y. Detection of Ser450Leu mutation in rpoB gene of Mycobacterium tuberculosis by allele-specific loop-mediated isothermal DNA amplification method. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify genetic mutations a rather time-consuming and expensive method of polymerase chain reaction (PCR) is widely used. The aim of the present work was to evaluate the possibility of using the two schemes of the method of allele-specific isothermal loop amplification (LAMP) to detect the TCG/TTG (S450L) mutation in the rpoB gene of Mycobacterium tuberculosis. 48 clinical isolates of M. tuberculosis and 11 samples of sputum were used, randomized and obtained in the microbiological laboratory of the city of Novosibirsk from incident patients. It is shown that the use of an analysis scheme using the allele-specific primer FIP compared to F3 has the best resolution: the difference between the amplification time of the mutation and the wild type allele was 22 ± 2,4 versus 13 ± 4,1 minutes (p = 0,0011). When using 100 DNA genomic equivalents a true positive signal (amplification of the rpoB gene with a mutation using the corresponding allele-specific primer) was detected after 29,4 ± 3,4 minutes. A positive signal was visualized after adding SYBR Green I to the reaction, both when illuminated with daylight and when using a UV transilluminator. Using the developed method the DNA sample of 20 RIFR isolates from M. tuberculosis was analyzed containing the Ser450Leu mutation in the rpoB gene, 10 RIFR isolates containing other mutations in the rpoB gene and 18 RIFs isolates without any mutations; the presence of mutations in the samples was determined using classical Sanger sequencing. The sensitivity and specificity of LAMP for detecting a Ser450Leu mutation in the rpoB gene was 100%. This approach allows the use of crude lysates of mycobacteria as DNA, which reduces the total analysis time to 1,5 hour.
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Affiliation(s)
- ML Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - IP Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - EA Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - DA Shamovskaya
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - YaSh Shvartz
- Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
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Ren Y, Li Y, Duan X, Wang H, Wang H, Li Z. One-Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop-Mediated Isothermal Amplification (mLAMP). ChemistrySelect 2019. [DOI: 10.1002/slct.201802693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yiqian Ren
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Yanru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Honghong Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Hui Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
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14
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Malpartida-Cardenas K, Rodriguez-Manzano J, Yu LS, Delves MJ, Nguon C, Chotivanich K, Baum J, Georgiou P. Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers. Anal Chem 2018; 90:11972-11980. [PMID: 30226760 PMCID: PMC6195307 DOI: 10.1021/acs.analchem.8b02416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 101 copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Michael J Delves
- Department of Life Sciences, Imperial College London , South Kensington Campus , SW7 2AZ , London , United Kingdom
| | - Chea Nguon
- National Centre for Parasitology , Entomology and Malaria Control , Phnom Penh 12302 , Cambodia
| | - Kesinee Chotivanich
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine , Mahidol University , Bangkok 10400 , Thailand
| | - Jake Baum
- Department of Life Sciences, Imperial College London , South Kensington Campus , SW7 2AZ , London , United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London , SW7 2AZ , United Kingdom
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15
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Ayukawa Y, Hanyuda S, Fujita N, Komatsu K, Arie T. Novel loop-mediated isothermal amplification (LAMP) assay with a universal QProbe can detect SNPs determining races in plant pathogenic fungi. Sci Rep 2017; 7:4253. [PMID: 28652587 PMCID: PMC5484703 DOI: 10.1038/s41598-017-04084-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is grouped into three races based on their pathogenicity to different host cultivars. Rapid detection and discrimination of Fol races in field soils is important to prevent tomato wilt disease. Although five types of point mutations in secreted in xylem 3 (SIX3) gene, which are characteristic of race 3, have been reported as a molecular marker for the race, detection of these point mutations is laborious. The aim of this study is to develop a rapid and accurate method for the detection of point mutations in SIX3 of Fol. Loop-mediated isothermal amplification (LAMP) of SIX3 gene with the universal QProbe as well as two joint DNAs followed by annealing curve analysis allowed us to specifically detect Fol and discriminate race 3 among other races in about one hour. Our developed method is applicable for detection of races of other plant pathogenic fungi as well as their pesticide-resistant mutants that arise through point mutations in a particular gene.
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Affiliation(s)
- Yu Ayukawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Saeri Hanyuda
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Naoko Fujita
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
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