Parasites, Hosts and Diseases

"SNP"

Original Articles

A LAMP-SNP Assay Detecting C580Y Mutation in Pfkelch13 Gene from Clinically Dried Blood Spot Samples: Thunchanok Khammanee, Nongyao Sawangjaroen, Hansuk Buncherd, Aung Win Tun, Supinya Thanapongpichat; Korean J Parasitol 2021;59(1):15-22.
Published online February 19, 2021; DOI: https://doi.org/10.3347/kjp.2021.59.1.15

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.

Citations

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Colorimetric loop-mediated isothermal amplification (cLAMP) assay for the genotyping of a thrombophilia genetic risk factor, MTHFR (C677T)
Reham Altwayan, Huseyin Tombuloglu, Moneerah Alsaeed, Abdulrahman Alhusil
Analytical Methods.2025; 17(21): 4432. CrossRef
Advancing artemisinin resistance monitoring using a high sensitivity ddPCR assay for Pfkelch13 mutation detection in Asia
Suttipat Srisutham, Aungkana Saejeng, Nardlada Khantikul, Rungniran Sugaram, Raweewan Sangsri, Arjen M. Dondorp, Nicholas P. J. Day, Mallika Imwong
Scientific Reports.2025;[Epub] CrossRef
Loop-mediated isothermal amplification (LAMP): A promising tool for rapid, point-of-care diagnosis of parasitic diseases in low-income countries
Kevin Polpitiya, Madhavi Hewadikaram
Molecular and Biochemical Parasitology.2025; 264: 111704. CrossRef
A Biotinylated cpFIT-PNA Platform for the Facile Detection of Drug Resistance to Artemisinin in Plasmodium falciparum
Odelia Tepper, Daniel H. Appella, Hongchao Zheng, Ron Dzikowski, Eylon Yavin
ACS Sensors.2024; 9(3): 1458. CrossRef
Interference reduction isothermal nucleic acid amplification strategy for COVID-19 variant detection
Guodong Li, Chung-Nga Ko, Zikang Wang, Feng Chen, Wanhe Wang, Dik-Lung Ma, Chung-Hang Leung
Sensors and Actuators B: Chemical.2023; 377: 133006. CrossRef
Super-assembly of integrated gold magnetic assay with loop-mediated isothermal amplification for point-of-care testing
Jianping Liang, Jie Zeng, Xiaojuan Huang, Tengteng Zhu, Yonglong Gong, Chen Dong, Xiangrong Wang, Lingzhi Zhao, Lei Xie, Kang Liang, Qiongxiang Tan, Yali Cui, Biao Kong, Wenli Hui
Nano Research.2023; 16(1): 1242. CrossRef
Engineered Biosensors for Diagnosing Multidrug Resistance in Microbial and Malignant Cells
Niharika G. Jha, Daphika S. Dkhar, Sumit K. Singh, Shweta J. Malode, Nagaraj P. Shetti, Pranjal Chandra
Biosensors.2023; 13(2): 235. CrossRef
Application of loop-mediated isothermal amplification combined with lateral flow assay visualization of Plasmodium falciparum kelch 13 C580Y mutation for artemisinin resistance detection in clinical samples
Wannida Sanmoung, Nongyao Sawangjaroen, Suwannee Jitueakul, Hansuk Buncherd, Aung Win Tun, Supinya Thanapongpichat, Mallika Imwong
Acta Tropica.2023; 246: 106998. CrossRef
Visual single nucleotide polymorphism (SNP) detection for ALDH2 genotyping based on multiplex ligation probe amplification (MLPA) and lateral flow assay
Dan Yin, Xiaolan Li, Li Mai, Ruxin Wang, Sitian Tang, Liyi Hu
Microchemical Journal.2023; 194: 109329. CrossRef
Application of multiple binding sites for LAMP primers across P. falciparum genome improves detection of the parasite from whole blood samples
Cavin Mgawe, Clement Shilluli, Steven Nyanjom, Eddy Odari, Jacqueline C. Linnes, Bernard N. Kanoi, Jesse Gitaka, Lucy Ochola
Frontiers in Malaria.2023;[Epub] CrossRef
Single nucleotide polymorphism genotyping of ALDH2 gene based on asymmetric PCR and fluorescent probe-mediated melting curves
Limei Zhang, Dan Liu, Baolin Li, Jingling Xie, Jinbo Liu, Zhang Zhang
Analytical Biochemistry.2022; 642: 114509. CrossRef
Prevalence of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency among Malaria Patients in Southern Thailand: 8 Years Retrospective Study
Thunchanok Khammanee, Nongyao Sawangjaroen, Hansuk Buncherd, Aung Win Tun, Supinya Thanapongpichat
The Korean Journal of Parasitology.2022; 60(1): 15. CrossRef
Current Epidemiological Characteristics of Imported Malaria, Vector Control Status and Malaria Elimination Prospects in the Gulf Cooperation Council (GCC) Countries
Jamshaid Iqbal, Suhail Ahmad, Ali Sher, Mohammad Al-Awadhi
Microorganisms.2021; 9(7): 1431. CrossRef

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Establishment of a T_m-shift Method for Detection of Cat-Derived Hookworms: Yeqi Fu, Yunqiu Liu, Asmaa M.I. Abuzeid, Yue Huang, Xue Zhou, Long He, Qi Zhao, Xiu Li, Jumei Liu, Rongkun Ran, Guoqing Li; Korean J Parasitol 2019;57(1):9-15.
Published online February 26, 2019; DOI: https://doi.org/10.3347/kjp.2019.57.1.9

Abstract
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Melting temperature shift (T_m-shift) is a new detection method that analyze the melting curve on real-time PCR thermocycler using SYBR Green I fluorescent dye. To establish a T_m-shift method for the detection of Ancylostoma ceylanicum and A. tubaeforme in cats, specific primers, with GC tail of unequal length attached to their 5 ? end, were designed based on 2 SNP loci (ITS101 and ITS296) of the internal transcribed spacer 1 (ITS1) sequences. The standard curve of T_m-shift was established using the standard plasmids of A. ceylanicum (AceP) and A. tubaeforme (AtuP). The T_m-shift method stability, sensitivity, and accuracy were tested with reference to the standard curve, and clinical fecal samples were also examined. The results demonstrated that the 2 sets of primers based on the 2 SNPs could accurately distinguish between A. ceylanicum and A. tubaeforme. The coefficient of variation (CV) of T_m-values of AceP and AtuP was 0.07% and 0.06% in ITS101 and was 0.06% and 0.08% in ITS296, respectively. The minimum detectable DNA concentration was 5.22×10-6 and 5.28×10-6 ng/μl samples of AceP and AtuP, respectively. The accuracy of T_m-shift method reached 100% based on examination of 10 hookworm DNA samples with known species. In the clinical detection of hookworm in 69 stray cat fecal sample, the T_m-shift detection results were consistent with the microscopic examination and successfully differentiated between the 2-hookworm species. In conclusion, the developed method is a rapid, sensitive and accurate technique and can provide a promising tool for clinical detection and epidemiological investigation of cat-derived hookworms.

Citations

Citations to this article as recorded by

Genetic characterization of zoonotic hookworms infecting wild felids in northern India
Thangam Venkatesan, Rasmita Panda, Anil Kumar Nehra, Hira Ram, M. Karikalan, Devendra Prasad Pateer, Rajat Garg, A. M. Pawde
BMC Veterinary Research.2025;[Epub] CrossRef
A novel A > G polymorphism in the intron 2 of TBX3 gene is significantly associated with body size in donkeys
Gang Wang, Mei Li, Jun Zhou, Xiaoya An, Fuxia Bai, Yuan Gao, Jie Yu, Haijing Li, Chuzhao Lei, Ruihua Dang
Gene.2021; 785: 145602. CrossRef
Cutaneous Larva Migrans
Alfonso J. Rodriguez-Morales, Natalia González-Leal, Maria Camila Montes-Montoya, Lorena Fernández-Espíndola, D. Katterine Bonilla-Aldana, José María Azeñas- Burgoa, Juan Carlos Diez de Medina, Verónica Rotela-Fisch, Melany Bermudez-Calderon, Kovy Arteaga
Current Tropical Medicine Reports.2021; 8(3): 190. CrossRef

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4 Web of Science
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Influencing Factors for Cure of Clonorchiasis by Praziquantel Therapy: Infection Burden and CYP3A5 Gene Polymorphism: Chung Hyeon Kim, Jeong-Keun Lee, Byung-Suk Chung, Shunyu Li, Min-Ho Choi, Sung-Tae Hong; Korean J Parasitol 2011;49(1):45-49.
Published online March 18, 2011; DOI: https://doi.org/10.3347/kjp.2011.49.1.45

Abstract
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Chemotherapy of clonorchiasis with praziquantel (PZQ) is effective but about 15% of treated cases have been reported uncured. The present study investigated correlation of single nucleotide polymorphisms (SNPs) of the cytochrome P450 gene, CYP3A5 and cure of clonorchiasis. A total of 346 egg passing residents were subjected and treated by 3 doses of 25 mg/kg PZQ. Reexamination recognized 33 (9.5%) uncured and 313 cured. Numbers of eggs per gram of feces (EPGs) before treatment were significantly lower in the cured group than in the uncured group (2,011.2±3,600.0 vs 4,998.5±7,012.0, P<0.001). DNAs of the subjects were screened for SNPs at 7 locations of CYP3A5 using PCR. In the uncured group, the SNP frequencies at g.-20555G>A and g.27526C>T of CYP3A5 were 15.2% and 9.1% while those were 3.8% and 1.0%, respectively, in the cured group. The cure rate was significantly lower in the cases with SNP at g.27526C>T and EPGs≥1,000. In conclusion, EPGs and SNPs of CYP3A5 are factors which influence cure of clonorchiasis by PZQ therapy. It is strongly suggested to recommend 2-day medication for individuals with high EPGs≥1,000.

Citations

Citations to this article as recorded by

Clonorchiasis and opisthorchiasis: epidemiology, transmission, clinical features, morbidity, diagnosis, treatment, and control
Men-Bao Qian, Jennifer Keiser, Jürg Utzinger, Xiao-Nong Zhou, Graeme N. Forrest
Clinical Microbiology Reviews.2024;[Epub] CrossRef
Efficacy and Safety of Tribendimidine Against Clonorchis sinensis
Men-Bao Qian, Peiling Yap, Yi-Chao Yang, Hai Liang, Zhi-Hua Jiang, Wei Li, Yu-Guang Tan, Hui Zhou, Jürg Utzinger, Xiao-Nong Zhou, Jennifer Keiser
Clinical Infectious Diseases.2013; 56(7): e76. CrossRef
Efficacy of Praziquantel against Schistosoma mekongi and Opisthorchis viverrini: A Randomized, Single-Blinded Dose-Comparison Trial
Leonore Lovis, Tippi K. Mak, Khampheng Phongluxa, Phonepasong Ayé Soukhathammavong, Youthanavanh Vonghachack, Jennifer Keiser, Penelope Vounatsou, Marcel Tanner, Christoph Hatz, Jürg Utzinger, Peter Odermatt, Kongsap Akkhavong, Banchob Sripa
PLoS Neglected Tropical Diseases.2012; 6(7): e1726. CrossRef

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63 Download
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Mini Review

Large-scale Genotyping and Genetic Mapping in Plasmodium Parasites: Xin-zhuan Su, Hongying Jiang, Ming Yi, Jianbing Mu, Robert M. Stephens; Korean J Parasitol 2009;47(2):83-91.
Published online May 26, 2009; DOI: https://doi.org/10.3347/kjp.2009.47.2.83

Abstract
PDF

The completion of many malaria parasite genomes provides great opportunities for genomewide characterization of gene expression and high-throughput genotyping. Substantial progress in malaria genomics and genotyping has been made recently, particularly the development of various microarray platforms for large-scale characterization of the Plasmodium falciparum genome. Microarray has been used for gene expression analysis, detection of single nucleotide polymorphism (SNP) and copy number variation (CNV), characterization of chromatin modifications, and other applications. Here we discuss some recent advances in genetic mapping and genomic studies of malaria parasites, focusing on the use of high-throughput arrays for the detection of SNP and CNV in the P. falciparum genome. Strategies for genetic mapping of malaria traits are also discussed.

Citations

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Experimental evidence for hybridization of closely related lineages in Plasmodium relictum
Vaidas Palinauskas, Rasa Bernotienė, Rita Žiegytė, Staffan Bensch, Gediminas Valkiūnas
Molecular and Biochemical Parasitology.2017; 217: 1. CrossRef
Genetic diversity of Plasmodium falciparum in human malaria cases in Mali
Cécile Nabet, Safiatou Doumbo, Fakhri Jeddi, Salimata Konaté, Tommaso Manciulli, Bakary Fofana, Coralie L’Ollivier, Aminata Camara, Sandra Moore, Stéphane Ranque, Mahamadou A. Théra, Ogobara K. Doumbo, Renaud Piarroux
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Genetic structure of Plasmodium vivax using the merozoite surface protein 1 icb5-6 fragment reveals new hybrid haplotypes in southern Mexico
René Cerritos, Lilia González-Cerón, José A Nettel, Ana Wegier
Malaria Journal.2014;[Epub] CrossRef
Infectious diseases detection by microarray: An overview of clinical relevant infections
Sara Elisa Herrera-Rodriguez, Darwin Elizondo-Quiroga, Ikuri Alvarez-Maya
Journal of Biomedical Science and Engineering.2013; 06(10): 1006. CrossRef