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Tian Y, Chen X, Xu P, Wang Y, Wu X, Wu K, Fu X, Chin Y, Liao Y. Rapid Visual Detection of Elite Erect Panicle Dense and Erect Panicle 1 Allele for Marker-Assisted Improvement in Rice ( Oryza sativa L.) Using the Loop-Mediated Isothermal Amplification Method. Curr Issues Mol Biol 2024; 46:498-512. [PMID: 38248334 PMCID: PMC10814556 DOI: 10.3390/cimb46010032] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular-assisted breeding is an effective way to improve targeted agronomic traits. dep1 (dense and erect panicle 1) is a pleiotropic gene that regulates yield, quality, disease resistance, and stress tolerance, traits that are of great value in rice (Oryza sativa L.) breeding. In this study, a colorimetric LAMP (loop-mediated isothermal amplification) assay was developed for the detection of the dep1 allele and tested for the screening and selection of the heavy-panicle hybrid rice elite restorer line SHUHUI498, modified with the allele. InDel (Insertion and Deletion) primers (DEP1_F and DEP1_R) and LAMP primers (F3, B3, FIP, and BIP) for genotyping were designed using the Primer3 Plus (version 3.3.0) and PrimerExplore (version 5) software. Our results showed that both InDel and LAMP markers could be used for accurate genotyping. After incubation at a constant temperature of 65 °C for 60 min with hydroxynaphthol blue (HNB) as a color indicator, the color of the LAMP assay containing the dep1 allele changed to sky blue. The SHUHUI498 rice line that was detected in our LAMP assay displayed phenotypes consistent with the dep1 allele such as having a more compact plant architecture, straight stems and leaves, and a significant increase in the number of effective panicles and spikelets, demonstrating the effectiveness of our method in screening for the dep1 allele in rice breeding.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Xiyi Chen
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
| | - Kun Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, China; (K.W.); (X.F.)
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (Y.T.); (X.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Chengdu 611130, China; (P.X.); (Y.W.); (X.W.)
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Zhang Y, Ke L, Sun T, Liu Y, Wei B, Du M. Rapid Detection of Malaria Based on Hairpin-Mediated Amplification and Lateral Flow Detection. MICROMACHINES 2023; 14:1917. [PMID: 37893354 PMCID: PMC10609466 DOI: 10.3390/mi14101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
Malaria is listed as one of the three most hazardous infectious diseases worldwide. Travelers and migrants passing through exit and entry ports are important sources of malaria pandemics globally. Developing accurate and rapid detection technology for malaria is important. Here, a novel hairpin-mediated amplification (HMA) technique was proposed for the detection of four Plasmodium species, including P. falciparum, P. vivax, P. malariae, and P. ovale. Based on the conserved nucleotide sequence of Plasmodium, specific primers and probes were designed for the HMA process, and the amplicon can be detected using lateral flow detection (LFD); the results can be read visually without specialized equipment. The specificity of HMA-LFD was evaluated using nucleic acids extracted from four different Plasmodium species and two virus species. The sensitivity of HMA-LFD was valued using 10× serial dilutions of plasmid containing the template sequence. Moreover, 78 blood samples were collected to compare HMA-LFD and qPCR. The HMA-LFD results were all positive for four different Plasmodium species and negative for the other two virus species. The sensitivity of HMA-LFD was tested to be near five copies/μL. The analysis of clinical samples indicated that the consistency of HMA-LFD and qPCR was approximately 96.15%. Based on these results, the HMA-LFD assay was demonstrated to be a rapid, sensitive, and specific technique for the detection of Plasmodium and has great advantages for on-site detection in low-resource areas and exit and entry ports.
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Affiliation(s)
- Yang Zhang
- Comprehensive Technical Service Center of Xuzhou Customs, Xuzhou Customs, Xuzhou 221000, China;
| | - Lihui Ke
- Department of Thoracic Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China;
| | - Tao Sun
- Nanjing Customs, Nanjing 210001, China;
| | - Yang Liu
- Department of Health and Quarantine, Nanjing Customs, Nanjing 210001, China;
| | - Bo Wei
- Department of Thoracic Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China;
| | - Minghua Du
- Department of Emergency, The First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
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Tian Y, Ye W, Liang X, Xu P, Wu X, Fu X, Chin Y, Liao Y. Rapid Visual Detection of High Nitrogen-Use Efficiency Gene OsGRF4 in Rice ( Oryza sativa L.) Using Loop-Mediated Isothermal Amplification Method. Genes (Basel) 2023; 14:1850. [PMID: 37895199 PMCID: PMC10606894 DOI: 10.3390/genes14101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The GROWTH-REGULATING FACTOR4 (OsGRF4) allele is an important target for the development of new high nitrogen-use efficiency (NUE) rice lines that would require less fertilizers. Detection of OsGRF4 through PCR (polymerase chain reaction)-based assay is cumbersome and needs advanced laboratory skills and facilities. Hence, a method for conveniently and rapidly detecting OsGRF4 on-field is a key requirement for further research and applications. In this study, we employed cleaved amplified polymorphic sequences (CAPs) and loop-mediated isothermal amplification (LAMP) techniques to develop a convenient visual detection method for high NUE gene OsGRF4NM73 (OsGRF4 from the rice line NM73). The TC→AA mutation at 1187-1188 bp loci was selected as the target sequence for the OsGRF4NM73 allele. We further employed this method of identification in 10 rice varieties that carried the OsGRF4 gene and results revealed that one variety (NM73) carries the target OsGRF4NM73 allele, while other varieties did not possess the osgrf4 genotype. The optimal LAMP reaction using hydroxynaphthol blue (HNB), a chromogenic indicator, was carried out at 65 °C for 60 min, and the presence of OsGRF4NM73 allele was confirmed by color changes from violet to sky blue. The results of this study showed that the LAMP method can be conveniently and accurately used to detect the OsGRF4NM73 gene in rice.
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Affiliation(s)
- Yonghang Tian
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Wenwei Ye
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xiangshuai Liang
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
| | - Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xianjun Wu
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
| | - Xiangdong Fu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China;
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya 572022, China; (X.L.); (Y.C.)
- Marine Food Engineering Technology Research Center of Hainan Province, No. 1 Yucai Road, Sanya 572022, China
| | - Yongxiang Liao
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu 611130, China; (W.Y.); (P.X.); (X.W.)
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Noninvasive Approach of Plasmodium falciparum Molecular Detection for Malaria Surveillance in Malaria Endemic Areas in Cameroon. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3600354. [PMID: 36408284 PMCID: PMC9668469 DOI: 10.1155/2022/3600354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
Background Accurate, cost-effective, and noninvasive alternative molecular methods are needed for detecting low malaria parasitemia. The currently-used nested polymerase chain reaction (nPCR) requires blood as well as skilled personnel in order to minimise the risk of bloodborne disease transmission. Therefore, this study is aimed at assessing the accuracy of a noninvasive and more affordable malaria diagnosis with saliva using the loop-mediated isothermal amplification (LAMP) technique. Methods A cross-sectional study was conducted in the Centre and Southwest regions of Cameroon. Matched blood and saliva samples collected from symptomatic and asymptomatic participants were tested for malaria using rapid diagnostic tests, microscopy, PCR, and LAMP. Statistics were performed using R studio software at 95% confidence interval. Results A total of 100 participants (65% symptomatic and 35% asymptomatic) aged between 1 and 74 years with a balanced gender distribution ratio of 1.08 were included in our study. The prevalence of malaria was 61%, 57%, 59%, 42%, 35%, 17%, and 16% for blood-RDT, blood-PCR, blood-LAMP, blood-RT-LAMP, saliva-PCR, saliva-RT-LAMP, and saliva-LAMP, respectively. Both saliva and blood showed a sensitivity of 43.90% and respective specificities of 68.75% and 57.62%. When using RT-LAMP, sensitivities of 49.38% and 48.21% and specificities of 94.11% and 66.67% were recorded for saliva and blood, respectively. Sensitivities of 70.23% and 73.49% and specificities of 62.5% and 76.47% were recorded, respectively, for saliva-LAMP and saliva-RT-LAMP when compared to saliva-PCR as the gold standard. Saliva-LAMP and saliva-RT-LAMP had a fair agreement (к = 0.221 and 0.352, respectively) with saliva-PCR. Homemade LAMP and RT-LAMP technologies match the WHO recommendations and after proper validation in a larger sample size, could serve for malaria diagnosis in developing countries.
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Benié EMA, Silué KD, Ding XC, Yeo I, Assamoi JB, Tuo K, Gnagne AP, Esso LJCE, Coulibaly JT, Assi SB, Bonfoh B, Yavo W, N’Goran EK. Accuracy of a rapid diagnosis test, microscopy and loop-mediated isothermal amplification in the detection of asymptomatic Plasmodium infections in Korhogo, Northern Côte d’Ivoire. Malar J 2022; 21:111. [PMID: 35366883 PMCID: PMC8976314 DOI: 10.1186/s12936-022-04133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Background Highly sensitive and accurate malaria diagnostic tools are essential to identify asymptomatic low parasitaemia infections. This study evaluated the performance of histidine-rich protein 2 (HRP-2) based rapid diagnostic tests (RDTs), microscopy and loop-mediated isothermal amplification (LAMP) for the detection of asymptomatic Plasmodium spp. infections in Northern Côte d’Ivoire, using nested polymerase chain reaction (nPCR) as reference. Methods A household-based survey was carried out in July 2016, in the health district of Korhogo, involving 1011 adults without malaria symptom nor history of fever during the week before recruitment. The fresh capillary blood samples were collected to detect Plasmodium infections using on HRP-2-based RDTs, microscopy and LAMP and stored as dried blood spots (DBS). A subset of the DBS (247/1011, 24.4%) was randomly selected for nPCR analyses. Additionally, venous blood samples, according to LAMP result (45 LAMP positive and 65 LAMP negative) were collected among the included participants to perform the nested PCR used as the reference. Results The prevalence of asymptomatic Plasmodium spp. infections determined by RDT, microscopy, and LAMP were 4% (95% confidence interval (CI) 2.8–5.3), 5.2% (95% CI 3.9–6.6) and 18.8% (95% CI 16.4–21.2), respectively. Considering PCR on venous blood as reference, performed on 110 samples, the sensibility and specificity were, respectively, 17.8% (95% CI 6.1–29.4) and 100% for RDT, 20.0% (95% CI 7.8–32) and 100% for microscopy, and 93.3% (95% CI 85.7–100) and 95.4% (95% CI 92.2–100) for LAMP. Conclusion In Northern Côte d’Ivoire, asymptomatic Plasmodium infection was found to be widely distributed as approximately one out of five study participants was found to be Plasmodium infected. LAMP appears currently to be the only available diagnostic method that can identify in the field this reservoir of infections and should be the method to consider for potential future active case detection interventions targeting elimination of these infections.
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Martín-Ramírez A, Lanza-Suárez M, Muñoz-García C, Hisam SR, Perez-Ayala A, Rubio JM. Usefulness of Malachite-Green LAMP for Diagnosis of Plasmodium and Five Human Malaria Species in a Nonendemic Setting. Am J Trop Med Hyg 2022; 106:tpmd211151. [PMID: 35292597 PMCID: PMC9128691 DOI: 10.4269/ajtmh.21-1151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
Molecular methods are necessary to detect low-density malaria infections. The purpose of this study was to assess the diagnostic performance of six malachite-green loop-mediated amplification method (MG-LAMP) assays (MG-LAMP-Pf, MG-LAMP-Pv, MG-LAMP-Po, MG-LAMP-Pm, MG-LAMP-Pk, and MG-LAMP-Pspp) for the species-specific detection of each human Plasmodium, including P. knowlesi, and the Plasmodium genus compared with the nested-multiplex malaria polymerase chain reaction (NM-PCR), using 161 malaria-positive and 274 malaria-negative samples. MG-LAMP-Pspp assay detected the five human Plasmodium species and each species-specific MG-LAMP assay detected only its corresponding species. Sensitivity, specificity, and predictive values of MG-LAMP assays, compared with NM-PCR, were > 90%, except in the case of the MG-LAMP-Pm assay, which dropped to 47%. Limit of detection for MG-LAMP-Pspp assay ranged from 0.1 parasites/µL for P. falciparum to 16.9 parasites/µL for P. malariae samples, and it was similar for the rest of MG-LAMP assays except for the MG-LAMP-Pm assay. Turnaround time was estimated to be 2 hours and 35 minutes for one MG-LAMP assay and 4 hours and 15 minutes if all species-specific MG-LAMP is set up, whereas for the NM-PCR, turnaround time was ∼6 hours and 15 minutes. Costs per determination ranged from 1 to 6 euros for MG-LAMP assays and 5 euros for NM-PCR. Therefore, MG-LAMP assays appear to have good concordance compared with the reference method, except for the MG-LAMP-Pm assay. They can detect low parasitemia and identify malaria species, with lower costs and shorter time to obtain results, and they are suitable tools to be used in endemic and non-endemic countries for malaria detection.
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Affiliation(s)
- Alexandra Martín-Ramírez
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Lanza-Suárez
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlota Muñoz-García
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
| | - Shamilah R. Hisam
- Parasitology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health Malaysia, Setia Alam, Selangor, Malaysia
| | - Ana Perez-Ayala
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - José M. Rubio
- Malaria and Emerging Parasitic Diseases Laboratory, National Microbiology Centre, Instituto de Salud Carlos III, Madrid, Spain
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Performance and Application of Commercially Available Loop-Mediated Isothermal Amplification (LAMP) Kits in Malaria Endemic and Non-Endemic Settings. Diagnostics (Basel) 2021; 11:diagnostics11020336. [PMID: 33670618 PMCID: PMC7922894 DOI: 10.3390/diagnostics11020336] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive molecular tool suitable for use as a near point-of-care test for the diagnosis of malaria. Recent meta-analyses have detailed high sensitivity and specificity of malaria LAMP when compared to microscopy, rapid diagnostic tests, and polymerase chain reaction in both endemic and non-endemic settings. Despite this, the use of malaria LAMP has primarily been limited to research settings to date. In this review, we aim to assess to what extent commercially available malaria LAMP kits have been applied in different settings, and to identify possible obstacles that may have hindered their use from being adopted further. In order to address this, we conducted a literature search in PubMed.gov using the search terms (((LAMP) OR (Loop-mediated isothermal amplification)) AND ((Malaria) OR (Plasmodium))). Focusing primarily on studies employing one of the commercially available kits, we then selected three key areas of LAMP application for further review: the performance and application of LAMP in malaria endemic settings including low transmission areas; LAMP for malaria screening during pregnancy; and malaria LAMP in returning travelers in non-endemic settings.
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Magneto-optical diagnosis of symptomatic malaria in Papua New Guinea. Nat Commun 2021; 12:969. [PMID: 33579923 PMCID: PMC7881035 DOI: 10.1038/s41467-021-21110-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/07/2021] [Indexed: 11/20/2022] Open
Abstract
Improved methods for malaria diagnosis are urgently needed. Here, we evaluate a novel method named rotating-crystal magneto-optical detection (RMOD) in 956 suspected malaria patients in Papua New Guinea. RMOD tests can be conducted within minutes and at low cost. We systematically evaluate the capability of RMOD to detect infections by directly comparing it with expert light microscopy, rapid diagnostic tests and polymerase chain reaction on capillary blood samples. We show that compared to light microscopy, RMOD exhibits 82% sensitivity and 84% specificity to detect any malaria infection and 87% sensitivity and 88% specificity to detect Plasmodium vivax. This indicates that RMOD could be useful in P. vivax dominated elimination settings. Parasite density correlates well with the quantitative magneto-optical signal. Importantly, residual hemozoin present in malaria-negative patients is also detectable by RMOD, indicating its ability to detect previous infections. This could be exploited to reveal transmission hotspots in low-transmission settings. Here Arndt et al. establish rotating-crystal magneto-optical detection (RMOD) as a near-point-of-care diagnostic tool for malaria detection and report a sensitivity and specificity of 82% and 84%, respectively, as validated by analyzing a clinical population in a high transmission setting in Papua New Guinea.
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Rogier E, Hamre KES, Joseph V, Plucinski MM, Presume J, Romilus I, Mondelus G, Elisme T, van den Hoogen L, Lemoine JF, Drakeley C, Ashton RA, Chang MA, Existe A, Boncy J, Stresman G, Druetz T, Eisele TP. Conventional and High-Sensitivity Malaria Rapid Diagnostic Test Performance in 2 Transmission Settings: Haiti 2017. J Infect Dis 2020; 221:786-795. [PMID: 31630194 DOI: 10.1093/infdis/jiz525] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 01/24/2023] Open
Abstract
Accurate malaria diagnosis is foundational for control and elimination, and Haiti relies on histidine-rich protein 2 (HRP2)-based rapid diagnostic tests (RDTs) identifying Plasmodium falciparum in clinical and community settings. In 2017, 1 household and 2 easy-access group surveys tested all participants (N = 32 506) by conventional and high-sensitivity RDTs. A subset of blood samples (n = 1154) was laboratory tested for HRP2 by bead-based immunoassay and for P. falciparum 18S rDNA by photo-induced electron transfer polymerase chain reaction. Both RDT types detected low concentrations of HRP2 with sensitivity estimates between 2.6 ng/mL and 14.6 ng/mL. Compared to the predicate HRP2 laboratory assay, RDT sensitivity ranged from 86.3% to 96.0% between tests and settings, and specificity from 90.0% to 99.6%. In the household survey, the high-sensitivity RDT provided a significantly higher number of positive tests, but this represented a very small proportion (<0.2%) of all participants. These data show that a high-sensitivity RDT may have limited utility in a malaria elimination setting like Haiti.
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Affiliation(s)
- Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen E S Hamre
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vena Joseph
- Center for Applied Malaria Research and Evaluation, Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Mateusz M Plucinski
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacquelin Presume
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Ithamare Romilus
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Gina Mondelus
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Tamara Elisme
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Lotus van den Hoogen
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jean Frantz Lemoine
- Programme National de Contrôle de la Malaria, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ruth A Ashton
- Center for Applied Malaria Research and Evaluation, Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Michelle A Chang
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alexandre Existe
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Jacques Boncy
- Laboratorie National de Santé Publique, Ministère de la Santé Publique et de la Population, Port-au-Prince, Haiti
| | - Gillian Stresman
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Thomas Druetz
- Center for Applied Malaria Research and Evaluation, Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA.,Department of Social and Preventive Medicine, University of Montreal School of Public Health, Montreal, Quebec, Canada
| | - Thomas P Eisele
- Center for Applied Malaria Research and Evaluation, Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
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Picot S, Cucherat M, Bienvenu AL. Systematic review and meta-analysis of diagnostic accuracy of loop-mediated isothermal amplification (LAMP) methods compared with microscopy, polymerase chain reaction and rapid diagnostic tests for malaria diagnosis. Int J Infect Dis 2020; 98:408-419. [PMID: 32659450 DOI: 10.1016/j.ijid.2020.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/01/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Diagnosis is a challenging issue for eliminating malaria. Loop-mediated isothermal amplification (LAMP) could be an alternative to conventional methods. This study aimed to evaluate the diagnostic accuracy of LAMP for malaria compared with microscopy, polymerase chain reaction (PCR) and rapid diagnostic tests (RDTs). METHODS AND DESIGN MEDLINE, Web of Science and Scopus were searched from inception to 1 July 2019. Prospective and retrospective, randomised and non-randomised, mono-center and multi-center studies, including symptomatic or asymptomatic patients, that reported one LAMP method and one comparator (microscopy, RDT or PCR) were included. PROSPERO registration number: CRD42017075186. RESULTS Sixty-six studies published between 2006 and 2019 were included, leading to the analysis of 30,641 LAMP tests. The pooled sensitivity of LAMP remained between 96% and 98%, whichever the comparator. The pooled specificity of LAMP was around 95%, but was a little higher if the best PCR studies were considered. The AUC was found to be >0.98, whichever the subgroup of studies was considered. Diagnostic odds ratio (DOR) was found to be around 1000 for all subgroups, except for Plasmodium vivax. CONCLUSION This meta-analysis confirmed that the LAMP method is robust for diagnosing malaria, both in symptomatic and asymptomatic people. Thus, the impact of LAMP for controlling malaria is expected to be important.
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Affiliation(s)
- Stephane Picot
- Malaria Research Unit, SMITh, ICBMS UMR 5246 CNRS-INSA-CPE-Université de Lyon, Campus Lyon-Tech La Doua, 69622 Villeurbanne Cedex, France; Institut de Parasitologie et Mycologie Médicale, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Michel Cucherat
- Service de Pharmacotoxicologie, Hospices Civils de Lyon, Laboratoire de Biométrie et Biologie Évolutive, CNRS, UMR5558, Université Lyon 1, Lyon, France
| | - Anne-Lise Bienvenu
- Malaria Research Unit, SMITh, ICBMS UMR 5246 CNRS-INSA-CPE-Université de Lyon, Campus Lyon-Tech La Doua, 69622 Villeurbanne Cedex, France; Service Pharmacie, Groupement Hospitalier Nord, Hospices Civils de Lyon, France; Service d'Hématologie, Groupement Hospitalier Nord, Hospices Civils de Lyon, France.
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11
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Imai K, Tarumoto N, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Ohno H, Murakami T, Maesaki S, Suzuki Y, Yamagishi J, Maeda T. An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer. Malar J 2018; 17:217. [PMID: 29843734 PMCID: PMC5975513 DOI: 10.1186/s12936-018-2362-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 05/22/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. RESULTS A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. CONCLUSIONS An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Lucky Ronald Runtuwene
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Yuki Eshita
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Faculty of Medicine, Oita University, 1-1 Hasama-machi, Yufu, Oita, 879-5593, Japan.,Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Thung Phaya, Ratchathewi, Bangkok, 10400, Thailand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichiro Maeda
- Division of Biomedical Sciences, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Josef Tuda
- Department of Parasitology, Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Hideaki Ohno
- Department of Infectious Diseases and Infection Control, Saitama Medical Center, Saitama Medical University, 1981 Kamoda, Kawagoe, Saitama, 350-8550, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Junya Yamagishi
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan. .,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.
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12
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Curtis KA, Morrison D, Rudolph DL, Shankar A, Bloomfield LSP, Switzer WM, Owen SM. A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood. J Virol Methods 2018; 255:91-97. [PMID: 29474813 DOI: 10.1016/j.jviromet.2018.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Isothermal nucleic acid amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are suitable for the development of a rapid, low-cost NAT that can be used at the POC. For demonstration of utility for global use, studies are needed to validate the performance of RT-LAMP for the detection of divergent subtypes. In this study, we designed and evaluated multiplexed HIV-1 integrase RT-LAMP primers to detect subtypes within group M, along with an RNase P positive internal processing and amplification control. Using a panel of 26 viral isolates representing the major circulating subtypes, we demonstrated detection of all isolates of subtypes A1, C, D, F1, F2, G, CRF01_AE, CRF02_AG, and two unique recombinant forms (URFs). A whole blood panel created with one representative isolate of each subtype was successfully amplified with the group M HIV-1 integrase and RNase P internal control primers. The group M HIV-1 RT-LAMP assay was further evaluated on 61 plasma specimens obtained from persons from Cameroon and Uganda. The sequence-conserved group M HIV-1 RT-LAMP primers, coupled to a low-cost amplification device, may improve diagnosis of acute infection at the POC and provide timely confirmation of HIV status.
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Affiliation(s)
- Kelly A Curtis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Daphne Morrison
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Donna L Rudolph
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura S P Bloomfield
- Stanford University School of Medicine, Stanford, CA, USA; Emmett Interdisciplinary Program in Environment and Resources, Stanford, CA, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Michele Owen
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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13
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Lee PLM. DNA amplification in the field: move over PCR, here comes LAMP. Mol Ecol Resour 2017; 17:138-141. [PMID: 28211246 DOI: 10.1111/1755-0998.12548] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 05/26/2016] [Indexed: 11/28/2022]
Abstract
It would not be an exaggeration to say that among molecular technologies, it is PCR (polymerase chain reaction) that underpins the discipline of molecular ecology as we know it today. With PCR, it has been possible to target the amplification of particular fragments of DNA, which can then be analysed in a multitude of ways. The capability of PCR to amplify DNA from a mere handful of copies further means that conservationists and ecologists are able to sample DNA unobtrusively and with minimal disturbance to the environment and the organisms of interest. However, a key disadvantage of PCR-based methods has been the necessity for a generally non-portable, laboratory setting to undertake the time-consuming thermocycling protocols. LAMP (loop-mediated isothermal amplification) offers a logistically simpler protocol: a relatively rapid DNA amplification reaction occurs at one temperature, and the products are visualized with a colour change within the reaction tubes. In the first field application of LAMP for an ecological study, Centeno-Cuadros et al. () demonstrates how LAMP can be used to determine the sex of three raptor species. By enabling DNA amplification in situ and in 'real-time', LAMP promises to revolutionize how molecular ecology is practised in the field.
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Affiliation(s)
- Patricia L M Lee
- Deakin University, Geelong, Vic., Australia.,School of Life and Environmental Sciences, Centre for Integrative Ecology, Warrnambool Campus, Princes Hwy, Sherwood Park, PO Box 423, Warrnambool, Vic., 3280, Australia
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14
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Imai K, Tarumoto N, Misawa K, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Murakami T, Maesaki S, Suzuki Y, Yamagishi J, Maeda T. A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer. BMC Infect Dis 2017; 17:621. [PMID: 28903726 PMCID: PMC5598014 DOI: 10.1186/s12879-017-2718-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination. In this study, we demonstrate a new diagnostic procedure for human malaria using loop mediated isothermal amplification (LAMP) and the MinION™ nanopore sequencer. METHODS We generated specific LAMP primers targeting the 18S-rRNA gene of all five human Plasmodium species including two P. ovale subspecies (P. falciparum, P. vivax, P. ovale wallikeri, P. ovale curtisi, P. knowlesi and P. malariae) and examined human blood samples collected from 63 malaria patients in Indonesia. Additionally, we performed amplicon sequencing of our LAMP products using MinION™ nanopore sequencer to identify each Plasmodium species. RESULTS Our LAMP method allowed amplification of all targeted 18S-rRNA genes of the reference plasmids with detection limits of 10-100 copies per reaction. Among the 63 clinical samples, 54 and 55 samples were positive by nested PCR and our LAMP method, respectively. Identification of the Plasmodium species by LAMP amplicon sequencing analysis using the MinION™ was consistent with the reference plasmid sequences and the results of nested PCR. CONCLUSIONS Our diagnostic method combined with LAMP and MinION™ could become a simple and accurate tool for the identification of human Plasmodium species, even in resource-limited situations.
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Affiliation(s)
- Kazuo Imai
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kazuhisa Misawa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Lucky Ronald Runtuwene
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Yuki Eshita
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Faculty of Medicine, Oita University, 1-1 Hasama-machi, Yufu, Oita, 879-5593, Japan.,Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Thung Phaya, Ratchathewi, Bangkok, 10400, Thailand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichiro Maeda
- Division of Biomedical Sciences, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Josef Tuda
- Department of Parasitology, Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Manado, Bahu, 95115, Indonesia
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Junya Yamagishi
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan. .,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.
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15
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Cuadros J, Martin Ramírez A, González IJ, Ding XC, Perez Tanoira R, Rojo-Marcos G, Gómez-Herruz P, Rubio JM. LAMP kit for diagnosis of non-falciparum malaria in Plasmodium ovale infected patients. Malar J 2017; 16:20. [PMID: 28061871 PMCID: PMC5219760 DOI: 10.1186/s12936-016-1669-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/22/2016] [Indexed: 01/15/2023] Open
Abstract
Background Microscopy and rapid diagnosis tests have a limited sensitivity in diagnosis of malaria by Plasmodium ovale. The LAMP kit (LoopAMP®) can be used in the field without special equipment and could have an important role in malaria control programmes in endemic areas and for malaria diagnosis in returned travellers. The performance of the Pan primer of the kit in detecting malaria by P. ovale was compared with the results of standard nPCR in samples of patients returning from P. ovale endemic areas. Methods Plasmodium ovale positive samples (29, tested by PCR and/or microscopy) and malaria negative specimens (398, tested by microscopy and PCR) were collected in different hospitals of Europe from June 2014 to March 2016 and frozen at −20 °C. Boil and spin method was used to extract DNA from all samples and amplification was performed with LoopAMP® MALARIA kit (Eiken Chemical, Japan) in an automated turbidimeter (Eiken 500). The results of LAMP read by turbidimetry and with the naked eye were compared. Results The kit showed a sensitivity of 100% and a specificity of 97.24% with positive and negative predictive values of 72.5 and 100%, respectively. Naked eyed readings were in accordance with turbidimetry readings (sensitivity, 92.5%, specificity, 98.96% and positive and negative predictive values, respectively, 90.24 and 99.22%). The limit of detection of LAMP assay for P. ovale was between 0.8 and 2 parasites/µl. Conclusions The Pan primer of the Malaria kit LoopAMP® can detect P. ovale at very low-levels and showed a predictive negative value of 100%. This tool can be useful in malaria control and elimination programmes and in returned travellers from P. ovale endemic areas. Naked eye readings are equivalent to automated turbidimeter readings in specimens obtained with EDTA. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1669-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Cuadros
- Department of Clinical Microbiology and Parasitology, Hospital Príncipe de Asturias, 28805, Alcalá de Henares, Madrid, Spain.
| | | | - Iveth J González
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Xavier C Ding
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Ramon Perez Tanoira
- Department of Medicine and Laboratory, Gambo Rural General Hospital, Kore, West-Arsi, Gambo, Ethiopia.,Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Gerardo Rojo-Marcos
- Department of Internal Medicine, Hospital Príncipe de Asturias, Madrid, Spain
| | - Peña Gómez-Herruz
- Department of Clinical Microbiology and Parasitology, Hospital Príncipe de Asturias, 28805, Alcalá de Henares, Madrid, Spain
| | - Jose Miguel Rubio
- Malaria and Emergent Protozoa Laboratory, National Center for Microbiology of Majadahonda, Madrid, Spain
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16
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Grimberg BT, Grimberg KO. Hemozoin detection may provide an inexpensive, sensitive, 1-minute malaria test that could revolutionize malaria screening. Expert Rev Anti Infect Ther 2016; 14:879-83. [PMID: 27530228 PMCID: PMC5224914 DOI: 10.1080/14787210.2016.1222900] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/08/2016] [Indexed: 12/25/2022]
Abstract
Malaria remains widespread throughout the tropics and is a burden to the estimated 3.5 billion people who are exposed annually. The lack of a fast and accurate diagnostic method contributes to preventable malaria deaths and its continued transmission. In many areas diagnosis is made solely based on clinical presentation. Current methods for malaria diagnosis take more than 20 minutes from the time blood is drawn and are frequently inaccurate. The introduction of an accurate malaria diagnostic that can provide a result in less than 1 minute would allow for widespread screening and treatment of endemic populations, and enable regions that have gained a foothold against malaria to prevent its return. Using malaria parasites' waste product, hemozoin, as a biomarker for the presence of malaria could be the tool needed to develop this rapid test.
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Affiliation(s)
- Brian T Grimberg
- a School of Medicine - Center for Global Health and Diseases , Case Western Reserve University , Cleveland , OH , USA
| | - Kerry O Grimberg
- b School of Medicine, Department of Radiology , Case Western Reserve University , Cleveland , OH , USA
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17
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Centeno-Cuadros A, Abbasi I, Nathan R. Sex determination in the wild: a field application of loop-mediated isothermal amplification successfully determines sex across three raptor species. Mol Ecol Resour 2016; 17:153-160. [PMID: 27235333 DOI: 10.1111/1755-0998.12540] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 11/26/2022]
Abstract
PCR-based methods are the most common technique for sex determination of birds. Although these methods are fast, easy and accurate, they still require special facilities that preclude their application outdoors. Consequently, there is a time lag between sampling and obtaining results that impedes researchers to take decisions in situ and in real time considering individuals' sex. We present an outdoor technique for sex determination of birds based on the amplification of the duplicated sex-chromosome-specific gene Chromo-Helicase-DNA binding protein using a loop-mediated isothermal amplification (LAMP). We tested our method on Griffon Vulture (Gyps fulvus), Egyptian Vulture (Neophron percnopterus) and Black Kite (Milvus migrans) (family Accipitridae). We introduce the first fieldwork procedure for sex determination of animals in the wild, successfully applied to raptor species of three different subfamilies using the same specific LAMP primers. This molecular technique can be deployed directly in sampling areas because it only needs a voltage inverter to adapt a thermo-block to a car lighter and results can be obtained by the unaided eye based on colour change within the reaction tubes. Primers and reagents are prepared in advance to facilitate their storage at room temperature. We provide detailed guidelines how to implement this procedure, which is simpler (no electrophoresis required), cheaper and faster (results in c. 90 min) than PCR-based laboratory methods. Our successful cross-species application across three different raptor subfamilies posits our set of markers as a promising tool for molecular sexing of other raptor families and our field protocol extensible to all bird species.
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Affiliation(s)
- A Centeno-Cuadros
- Movement Ecology Lab, Department of Ecology, Evolution and Behaviour, Faculty of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio, s/n, Isla de la Cartuja, Seville, 41092, Spain
| | - I Abbasi
- Kuvin Center, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - R Nathan
- Movement Ecology Lab, Department of Ecology, Evolution and Behaviour, Faculty of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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