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Oh C, Xun G, Lane ST, Petrov VA, Zhao H, Nguyen TH. Portable, single nucleotide polymorphism-specific duplex assay for virus surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168701. [PMID: 37992833 DOI: 10.1016/j.scitotenv.2023.168701] [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: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
The Argonaute protein from the archaeon Pyrococcus furiosus (PfAgo) is a DNA-guided nuclease that targets DNA with any sequence. We designed a virus detection assay in which the PfAgo enzyme cleaves the reporter probe, thus generating fluorescent signals when amplicons from a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay contain target sequences. We confirmed that the RT-LAMP-PfAgo assay for the SARS-CoV-2 Delta variant produced significantly higher fluorescent signals (p < 0.001) when a single nucleotide polymorphism (SNP), exclusive to the Delta variant, was present, compared to the samples without the SNP. Additionally, the duplex assay for Pepper mild mottle virus (PMMOV) and SARS-CoV-2 detection produced specific fluorescent signals (FAM or ROX) only when the corresponding sequences were present. Furthermore, the RT-LAMP-PfAgo assay does not require dilution to reduce the impact of environmental inhibitors. The limit of detection of the PMMOV assay, determined with 30 wastewater samples, was 28 gc/μL, with a 95 % confidence interval of [11,103]. Finally, using a point-of-use device, the RT-LAMP-PfAgo assay successfully detected PMMOV in wastewater samples. Based on our findings, we conclude that the RT-LAMP-PfAgo assay can be used as a portable, SNP-specific duplex assay, which will significantly improve virus surveillance in wastewater.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA.
| | - Guanhua Xun
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Vassily Andrew Petrov
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
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2
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Pan X, Wang X, Yu J, Yu M, Cao H, Yong M, Song T, Qi Z, Du Y, Zhang R, Liu Y. Loop-Mediated Isothermal Amplification for Rapid Detection of Mating Types of Villosiclava virens. PLANT DISEASE 2022; 106:1128-1133. [PMID: 34739329 DOI: 10.1094/pdis-09-21-1943-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice false smut (RFS), caused by Villosiclava virens, is an important fungal disease in panicles of rice. V. virens is a heterothallic ascomycete controlled by two opposite idiomorphs, MAT1-1 and MAT1-2. Previous study showed that sexual reproduction of V. virens plays an important role in the epidemic of RFS. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay to detect the mating type of V. virens easily and rapidly by using specific primers based on the mating type genes MAT1-1-2 and MAT1-2-1, respectively. The LAMP assay used only a water/dry bath and could recognize the mating type of V. virens in just 45 min. The LAMP assay was so sensitive that it could detect small amounts of V. virens genomic DNA (as low as 2.0 pg of MAT1-1 and 200.0 pg of MAT1-2) and was 10 times more sensitive than PCR. In addition, we demonstrated the application of mating type via LAMP assay by assessing the genomic DNA of V. virens isolated from rice fields. The high efficiency and specificity of this LAMP assay suggest that it can be used as a rapid testing tool in mating type recognition of V. virens isolates in the field.
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Affiliation(s)
- Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xiao Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Mingli Yong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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3
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Suther C, Stoufer S, Zhou Y, Moore MD. Recent Developments in Isothermal Amplification Methods for the Detection of Foodborne Viruses. Front Microbiol 2022; 13:841875. [PMID: 35308332 PMCID: PMC8930189 DOI: 10.3389/fmicb.2022.841875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 11/15/2022] Open
Abstract
Foodborne and enteric viruses continue to impose a significant public health and economic burden globally. As many of these viruses are highly transmissible, the ability to detect them portably, sensitively, and rapidly is critical to reduce their spread. Although still considered a gold standard for detection of these viruses, real time polymerase chain reaction (PCR)-based technologies have limitations such as limited portability, need for extensive sample processing/extraction, and long time to result. In particular, the limitations related to the susceptibility of real time PCR methods to potential inhibitory substances present in food and environmental samples is a continuing challenge, as the need for extensive nucleic acid purification prior to their use compromises the portability and rapidity of such methods. Isothermal amplification methods have been the subject of much investigation for these viruses, as these techniques have been found to be comparable to or better than established PCR-based methods in portability, sensitivity, specificity, rapidity, and simplicity of sample processing. The purpose of this review is to survey and compare reports of these isothermal amplification methods developed for foodborne and enteric viruses, with a special focus on the performance of these methods in the presence of complex matrices.
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Affiliation(s)
- Cassandra Suther
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Medicine, University of Connecticut Health, Farmington, CT, United States
| | - Sloane Stoufer
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health, Farmington, CT, United States
| | - Matthew D. Moore
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
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4
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Zhu Y, Wu X, Gu A, Dobelle L, Cid C, Li J, Hoffmann MR. Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:862-873. [PMID: 34967203 PMCID: PMC8751019 DOI: 10.1021/acs.est.1c04623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 05/06/2023]
Abstract
Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.
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Affiliation(s)
- Yanzhe Zhu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xunyi Wu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Alan Gu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Leopold Dobelle
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Clément
A. Cid
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jing Li
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Michael R. Hoffmann
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
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5
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Sensitive Detection of Chicken Meat in Commercial Processed Food Products Based on One-Step Colourimetric Loop-Mediated Isothermal Amplification. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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6
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Hasan H, Nasirudeen NA, Ruzlan MAF, Mohd Jamil MA, Ismail NAS, Wahab AA, Ali A. Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers. CHILDREN (BASEL, SWITZERLAND) 2021; 8:1112. [PMID: 34943308 PMCID: PMC8700514 DOI: 10.3390/children8121112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022]
Abstract
Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.
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Affiliation(s)
- Haziqah Hasan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Nor Ashika Nasirudeen
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Alif Farhan Ruzlan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Aiman Mohd Jamil
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Noor Akmal Shareela Ismail
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Asrul Abdul Wahab
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Adli Ali
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
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7
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Zhou S, Huang Q, Yu M, Li Y, Zheng X, Xiu Y. Rapid visual detection of Aeromonas salmonicida by loop-mediated isothermal amplification with hydroxynaphthol blue dye. JOURNAL OF FISH DISEASES 2021; 44:1993-2001. [PMID: 34411329 DOI: 10.1111/jfd.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
To make crucial prevention, reduce fish losses and minimize the economic damage of diseases on the fish farm owners, a rapid detection of fish pathogens is mandatory. In this study, a loop-mediated isothermal amplification assay combined with hydroxynaphthol blue dye (LAMP-HNB) was developed and used for the rapid detection of Aeromonas salmonicida that caused significant economic losses in fish farming. Firstly, a pair of outer and inner primers specific for conserved fragment of vapA gene in A. salmonicida were designed and synthesized. Secondly, by optimizing the reaction conditions including reaction temperature, time, Mg2+ concentration, dNTP concentration and primer ratio, a LAMP-HNB assay was successfully established for the detection of A. salmoncida. Thirdly, the assay showed good specificity with no false-positive and false-negative results, and good sensitivity with the detection limit of 3.077 × 10-6 ng/μl, which was 102 times more sensitive than the conventional PCR. Finally, the LAMP-HNB assay was validated by the fish samples inoculated with different concentrations of A. salmoncida. This is the first development of rapid visual detection of A. salmonicida based on LAMP-HNB assay, which has great application prospect and market for diagnostic testing, health certification and active surveillance programmers.
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Affiliation(s)
- Shun Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qing Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Mingming Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Ying Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xujia Zheng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yunji Xiu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
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8
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Kaur N, Thota N, Toley BJ. A stoichiometric and pseudo kinetic model of loop mediated isothermal amplification. Comput Struct Biotechnol J 2020; 18:2336-2346. [PMID: 32994892 PMCID: PMC7493047 DOI: 10.1016/j.csbj.2020.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 01/15/2023] Open
Abstract
Loop mediated isothermal amplification (LAMP) is one of the most popular isothermal DNA amplification techniques for research and commercial applications, enabling amplification of both DNA and RNA (with the assistance of reverse transcriptase). The LAMP mechanism is powered by strategic primer design and a strand displacement polymerase, generating products that fold over, creating loops. LAMP leads to generation of products of increasing length over time. These products containing multiple loops are conventionally called cauliflower structures. Existing literature on LAMP provides extremely limited understanding of progression of cascades of reactions involved in the reaction and it is believed that cauliflower structures of increasing length constitute a majority of the product formed in LAMP. This study presents a first of its kind stoichiometric and pseudo kinetic model to comprehend LAMP reactions in deeper depth by (i) classifying LAMP reaction products into uniquely identifiable categories, (ii) generating a condensed reaction network to depict millions of interconnected reactions occurring during LAMP, and (iii) elucidating the pathways for amplicon generation. Despite the inherent limitations of conventional stoichiometric modelling for polymerization type reactions (the network rapidly becomes too large and intractable), our model provides new theoretical understanding of the LAMP reaction pathway. The model shows that while longer length products are formed, it is the smaller length recycle amplicons that contribute more towards the exponential increase in the amount of double stranded DNA. Prediction of concentration of different types of LAMP amplicons will also contribute substantially towards informing design of probe-based assays.
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Affiliation(s)
- Navjot Kaur
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012 India
| | - Nikhil Thota
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012 India
| | - Bhushan J Toley
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012 India
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9
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Chomean S, Pholyiam K, Thamwarokun A, Kaset C. Development of Visual Detection of α-Thalassemia-1 (the - - SEA Deletion) Using pH-Sensitive Loop-Mediated Isothermal Amplification. Hemoglobin 2018; 42:171-177. [PMID: 30192689 DOI: 10.1080/03630269.2018.1488723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Detection of α-thalassemia-1 (α-thal-1) carriers provides valuable insight for genetic consulting in prevention and control programs for couples who are at risk of conceiving a fetus with severe thalassemia, both Hb Bart's hydrops fetalis and hemolytic Hb H disease. The traditional method is complicated, time-consuming and requires high instrument cost and expertise. Loop-mediated isothermal amplification (LAMP) based on pH-sensitive dye technology, shows all the characteristics required of a real-time analysis with simple operation for potential use in the clinical diagnosis of high incidence α-thal-1 [Southeast Asian (SEA) or - -SEA deletion]. Four primers specific for six distinct regions of the α-globin gene deletion were designed and analyzed by LAMP using the pH-indicator dye, phenol red. The amplification of the - -SEA deletion changed the color of phenol red from pink to orange. The diagnostic ability of detection of the - -SEA deletion by pH-sensitive LAMP was validated using both known and unknown blood samples and compared to the conventional polymerase chain reaction (PCR) method. Color inspection of pH-sensitive LAMP products could clearly identify the - -SEA deletion. There was no cross reaction with a normal α-globin gene, α-thal-1 Thai (- -THAI deletion), α-thal-2 [-α3.7 (rightward) and -α4.2 (leftward) deletion] and β-thalassemia (β-thal). Detection of the SEA deletion by pH-sensitive LAMP was consistent as compared to conventional PCR. The pH-sensitive LAMP method developed for this deletion carrier diagnosis has high sensitivity, specificity, simplicity, and requires simple instrumentation that makes it applicable for resource-limited laboratories in rural areas of developing countries.
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Affiliation(s)
- Sirinart Chomean
- a Department of Medical Technology, Faculty of Allied Health Science s, Thammasat University , Klong Luang , Pathum Thani Province , Thailand
| | - Kanokporn Pholyiam
- a Department of Medical Technology, Faculty of Allied Health Science s, Thammasat University , Klong Luang , Pathum Thani Province , Thailand
| | - Areenuch Thamwarokun
- a Department of Medical Technology, Faculty of Allied Health Science s, Thammasat University , Klong Luang , Pathum Thani Province , Thailand
| | - Chollanot Kaset
- a Department of Medical Technology, Faculty of Allied Health Science s, Thammasat University , Klong Luang , Pathum Thani Province , Thailand
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Yang X, Al-Attala MN, Zhang Y, Zhang AF, Zang HY, Gu CY, Gao TC, Chen Y, Al-Attala MN, Ali F, Li YF, Yao J, Zhu JG. Rapid Detection of Ustilaginoidea virens from Rice using Loop-Mediated Isothermal Amplification Assay. PLANT DISEASE 2018; 102:1741-1747. [PMID: 30125168 DOI: 10.1094/pdis-01-18-0065-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ustilaginoidea virens is an important fungus that causes rice false smut disease. This disease significantly reduces both grain yield and quality. Various methods have been developed for the detection of U. virens but most of these methods need sophisticated equipment such as a thermal cycler. Here, we present a loop-mediated isothermal amplification (LAMP) assay for the specific detection of U. virens. This assay used a specific region of the UvG-β1 gene (212-bp region) to design six LAMP primers. The LAMP assay was optimized by the combination of rapidity, simplicity, and high sensitivity for the detection of about 1 pg of target genomic DNA in the reaction whereas, with polymerase chain reaction (PCR), there was no amplification of DNA with concentrations less than 1 ng. Among the genomic DNA of 22 fungus species and two strains of U. virens, only the tube containing the DNA of U. virens changed to yellowish green with SYBR Green I. The color change was indicative of DNA amplification. No DNA was amplified from either the other 22 fungus species or the negative control. Moreover, 20 spikelets and 22 rice seed samples were used for the detection of rice false smut via LAMP. The results were comparable with conventional PCR. We conclude that gene UvG-β1 coupled with LAMP assay, can be used for the detection and identification of U. virens gene via LAMP.
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Affiliation(s)
- Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Mohamed N Al-Attala
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Yong Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Yu Chen
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Mohamed N Al-Attala
- Plant Pathology Unit, Plant Protection Department, Desert Research Center, Cairo 11753, Egypt
| | - Farman Ali
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences; and Department of Agriculture, Abdul Wali Khan University Mardan, Pakistan
| | - Yun-Fei Li
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Jian Yao
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Jin-Guo Zhu
- Hunan Entry-Exit Inspection and Quarantine Bureau, Changsha 410004, China
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11
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Hata A, Kitajima M, Haramoto E, Lee S, Ihara M, Gerba CP, Tanaka H. Next-generation amplicon sequencing identifies genetically diverse human astroviruses, including recombinant strains, in environmental waters. Sci Rep 2018; 8:11837. [PMID: 30087387 PMCID: PMC6081416 DOI: 10.1038/s41598-018-30217-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
Human astroviruses are associated with gastroenteritis and known to contaminate water environments. Three different genetic clades of astroviruses are known to infect humans and each clade consists of diverse strains. This study aimed to determine the occurrence and genetic diversity of astrovirus strains in water samples in different geographical locations, i.e., influent and effluent wastewater samples (n = 24 each) in Arizona, U.S., and groundwater (n = 37) and river water (n = 14) samples collected in the Kathmandu Valley, Nepal, using next-generation amplicon sequencing. Astrovirus strains including rare types (types 6 and 7 classical human astroviruses), emerging type (type 5 VA-astroviruses), and putative recombinants were identified. Feline astrovirus strains were collaterally identified and recombination between human and feline astroviruses was suggested. Classical- and VA-astroviruses seemed to be prevalent during cooler months, while MLB-astroviruses were identified only during warmer months. This study demonstrated the effectiveness of next-generation amplicon sequencing for identification and characterization of genetically diverse astrovirus strains in environmental water.
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Affiliation(s)
- Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan. .,Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Hokkaido, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, Japan
| | - Suntae Lee
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
| | - Charles P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, Arizona, USA
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
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12
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Rapid and simple identification of carbapenemase genes, bla
NDM, bla
OXA-48, bla
VIM, bla
IMP-14 and bla
KPC groups, in Gram-negative bacilli by in-house loop-mediated isothermal amplification with hydroxynaphthol blue dye. World J Microbiol Biotechnol 2017; 33:130. [DOI: 10.1007/s11274-017-2295-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
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13
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Zhou N, Lin X, Wang S, Wang H, Bi Z, Wang P, Chen P, Tao Z, Song L, Song Y, Xu A. Molecular characterization of classic human astrovirus in eastern China, as revealed by environmental sewage surveillance. J Appl Microbiol 2016; 120:1436-44. [DOI: 10.1111/jam.13109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 01/20/2023]
Affiliation(s)
- N. Zhou
- School of Public Health; Shandong University; Jinan China
| | - X. Lin
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - S. Wang
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - H. Wang
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - Z. Bi
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - P. Wang
- School of Public Health; Shandong University; Jinan China
| | - P. Chen
- School of Public Health; Shandong University; Jinan China
| | - Z. Tao
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - L. Song
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - Y. Song
- School of Public Health; Shandong University; Jinan China
| | - A. Xu
- School of Public Health; Shandong University; Jinan China
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
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14
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Rodriguez-Manzano J, Karymov MA, Begolo S, Selck DA, Zhukov D, Jue E, Ismagilov RF. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones. ACS NANO 2016; 10:3102-13. [PMID: 26900709 PMCID: PMC4819493 DOI: 10.1021/acsnano.5b07338] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests.
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15
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Khorosheva EM, Karymov MA, Selck DA, Ismagilov RF. Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP. Nucleic Acids Res 2016; 44:e10. [PMID: 26358811 PMCID: PMC4737171 DOI: 10.1093/nar/gkv877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions.
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Affiliation(s)
- Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Mikhail A Karymov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
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16
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Matson DO, Vesikari T, Dennehy P, Dallas MD, Goveia MG, Itzler RF, Ciarlet M. Analysis by rotavirus gene 6 reverse transcriptase-polymerase chain reaction assay of rotavirus-positive gastroenteritis cases observed during the vaccination phase of the Rotavirus Efficacy and Safety Trial (REST). Hum Vaccin Immunother 2015; 10:2267-75. [PMID: 25424931 DOI: 10.4161/hv.29176] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During the vaccination phase of the Rotavirus Efficacy and Safety Trial (REST), the period between the administration of dose 1 through 13 days after the administration of dose 3, there were more wild-type rotavirus gastroenteritis (RVGE) cases among vaccine recipients compared with placebo recipients using the protocol-specified microbiological plaque assay in the clinical-efficacy cohort, a subset of subjects where vaccine efficacy against RVGE of any severity was assessed. In this study, a rotavirus genome segment 6-based reverse transcriptase-polymerase chain reaction assay was applied post hoc to clarify the accuracy of type categorization of all these RVGE cases in vaccine recipients during the vaccination phase of REST. The assay characterized 147 (90%) of 163 re-assayed RVGE cases or rotavirus-associated health care contacts as type-determinable: either wild-type or vaccine-type rotavirus strains. In the clinical-efficacy cohort (N = 5673), 19 (18.8%) of 101 samples from RVGE cases contained wild-type rotavirus, 70 (69.3%) vaccine virus, and 12 (11.9%) were indeterminable. In the large-scale cohort (N = 68,038), 10 (34.5%) of 29 samples from RVGE-related health care contacts contained wild-type rotavirus strains, 15 (51.7%) vaccine-type rotavirus strains, and 4 (13.8%) were indeterminable. Of the 33 samples from RVGE cases in placebo recipients, all were confirmed to contain wild-type rotaviruses. Altogether, this post-hoc re-evaluation showed that the majority (75%) of type-determinable RVGE cases or health care contacts that occurred during the vaccination phase of REST in vaccine recipients were associated with vaccine-type rotavirus strains rather than wild-type rotavirus strains.
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Affiliation(s)
- David O Matson
- a Department of Pediatrics; Eastern Virginia Medical School; Norfolk, VA USA
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17
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Mohandas SS, Muthuchelvan D, Pandey AB, Biswas SK, Chand K, Venkatesan G, Choudhary D, Ramakrishnan MA, Mondal B. Development of reverse transcription loop mediated isothermal amplification assay for rapid detection of bluetongue viruses. J Virol Methods 2015; 222:103-5. [PMID: 26073661 DOI: 10.1016/j.jviromet.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 05/23/2015] [Accepted: 06/08/2015] [Indexed: 02/01/2023]
Abstract
A single-step reverse transcription loop mediated isothermal amplification (RT-LAMP) assay targeting NS1 - a highly conserved gene among BTV serotypes was optimized and validated with seven serotypes: BTV-1, BTV-2, BTV-9, BTV-10, BTV-16, BTV-21 and BTV-23. The relative sensitivity of the assay was 0.3 TCID50 and no cross reactivity could be observed with foot and mouth disease, peste-des-petits-ruminants, goatpox, sheeppox and orf viruses. The established assay was also assessed by screening of clinical samples and the result is comparable with conventional RT-PCR. The RT-LAMP assay described here could be an additional tool to the existing assays for diagnosis/surveillance of BTV.
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Affiliation(s)
- Sreekala S Mohandas
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | - Dhanavelu Muthuchelvan
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India.
| | - Awadh Bihari Pandey
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | - Sanchay Kumar Biswas
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | - Karam Chand
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | - Gnanavel Venkatesan
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | - Dheeraj Choudhary
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Uttarakhand 263 138, India
| | | | - Bimalendu Mondal
- Indian Veterinary Research Institute, Kolkata 700 037 West Bengal, India
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18
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Wastewater Analysis Indicates that Genetically Diverse Astroviruses, Including Strains Belonging to Novel Clades MLB and VA, Are Circulating within Japanese Populations. Appl Environ Microbiol 2015; 81:4932-9. [PMID: 25979884 DOI: 10.1128/aem.00563-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/10/2015] [Indexed: 12/25/2022] Open
Abstract
Human astroviruses (HAstVs) are a common etiological agent of infantile gastroenteritis. Recent studies revealed that novel astrovirus (AstV) strains of the MLB clade (MLB-AstVs) and VA clade (VA-AstVs), which are genetically distinct from the classic HAstVs, are circulating in the human population. In the present study, we quantified classic HAstVs as well as carried out a genetic analysis of classic and novel HAstVs in wastewater in Japan. The concentration of classic HAstVs in the influent water samples ranged from 10(4) to 10(5) copies per liter, and the amount removed by wastewater treatment was determined to be 2.4 ± 0.3 log10. Four types of classic HAstV strains (HAstV types 1, 2, 5, and 4/8) as well as novel AstV strains belonging to the MLB-2, VA-1, and VA-2 clades were identified using reverse transcription-PCR (RT-PCR) assays, including assays newly developed for the detection of strains of the MLB and VA clades, followed by cloning and nucleotide sequencing. Our results suggest that genetically diverse AstV strains are circulating among the human population in Japan. The newly developed (semi)nested RT-PCR assays for these novel AstV clades are useful to identify and characterize the novel AstVs in environmental waters.
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19
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Alhassan A, Makepeace BL, LaCourse EJ, Osei-Atweneboana MY, Carlow CKS. A simple isothermal DNA amplification method to screen black flies for Onchocerca volvulus infection. PLoS One 2014; 9:e108927. [PMID: 25299656 PMCID: PMC4191976 DOI: 10.1371/journal.pone.0108927] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/09/2014] [Indexed: 11/30/2022] Open
Abstract
Onchocerciasis is a debilitating neglected tropical disease caused by infection with the filarial parasite Onchocerca volvulus. Adult worms live in subcutaneous tissues and produce large numbers of microfilariae that migrate to the skin and eyes. The disease is spread by black flies of the genus Simulium following ingestion of microfilariae that develop into infective stage larvae in the insect. Currently, transmission is monitored by capture and dissection of black flies and microscopic examination of parasites, or using the polymerase chain reaction to determine the presence of parasite DNA in pools of black flies. In this study we identified a new DNA biomarker, encoding O. volvulus glutathione S-transferase 1a (OvGST1a), to detect O. volvulus infection in vector black flies. We developed an OvGST1a-based loop-mediated isothermal amplification (LAMP) assay where amplification of specific target DNA is detectable using turbidity or by a hydroxy naphthol blue color change. The results indicated that the assay is sensitive and rapid, capable of detecting DNA equivalent to less than one microfilaria within 60 minutes. The test is highly specific for the human parasite, as no cross-reaction was detected using DNA from the closely related and sympatric cattle parasite Onchocerca ochengi. The test has the potential to be developed further as a field tool for use in the surveillance of transmission before and after implementation of mass drug administration programs for onchocerciasis.
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Affiliation(s)
- Andy Alhassan
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Benjamin L. Makepeace
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Clotilde K. S. Carlow
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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