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Zhao N, Liu J, Sun D. Detection of HCV genotypes 1b and 2a by a reverse transcription loop-mediated isothermal amplification assay. J Med Virol 2017; 89:1048-1054. [PMID: 27935066 DOI: 10.1002/jmv.24747] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) genotypes 1b and 2a are the major cause of liver disease in northern China; however, conventional detection tools are labor-consuming, technically demanding, and costly. Here, we assessed the specificity, sensitivity, and clinical utility of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of HCV genotypes 1b and 2a. Firstly, clinical samples were collected from HCV genotype 1b and 2a infected patients and the RNA were extracted. Secondly, specificity of RT-LAMP assay for detection HCV genotypes 1b and 2a were tested against viral genomes of other hepatitis viruses. Sensitivity of RT-LAMP assay was determined using serial dilutions of standard HCV genotypes 1b and 2a. The amplified products were detected by both electrophoresis and calcein/Mn2+ -dependent visual methods. Finally, we compared the clinical detection rate of RT-LAMP to that of real-time PCR. RT-LAMP assay showed high specificity to detect HCV genotypes 1b and 2b since there was no cross-reactivity with other hepatitis viruses. Sensitivity of RT-LAMP was 100 IU/mL for both genotypes detected by either electrophoresis or calcein/Mn2+ -dependent visual methods. The detection rate of RT-LAMP assay in clinical samples was also comparable to that of real-time PCR without significant difference between the both assays. This study proposes a newly developed RT-LAMP assay for detection of HCV genotypes 1b and 2a. RT-LAMP is highly specific, sensitive, and simple diagnostic tool which would be useful for screening and early diagnosis of HCV especially in resource-limited environments.
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Affiliation(s)
- Na Zhao
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China.,The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Jinxia Liu
- The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Dianxing Sun
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China
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Molecular Detection and Characterization of Hepatitis C Virus. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lereau M, Fournier-Wirth C, Mayen J, Farre C, Meyer A, Dugas V, Cantaloube JF, Chaix C, Vasseur JJ, Morvan F. Development of Innovative and Versatile Polythiol Probes for Use on ELOSA or Electrochemical Biosensors: Application in Hepatitis C Virus Genotyping. Anal Chem 2013; 85:9204-12. [DOI: 10.1021/ac401941x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Myriam Lereau
- Laboratoire
TransDiag—Sécurité Transfusionnelle et Innovation
Diagnostique, Etablissement Français du Sang Pyrénées-Méditerranée, Montpellier, 34184, France
- Département
des Analogues et Constituants des Acides Nucléiques, Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS Université Montpellier 1 Université Montpellier 2, Montpellier, 34095, France
| | - Chantal Fournier-Wirth
- Laboratoire
TransDiag—Sécurité Transfusionnelle et Innovation
Diagnostique, Etablissement Français du Sang Pyrénées-Méditerranée, Montpellier, 34184, France
| | - Julie Mayen
- Département
des Analogues et Constituants des Acides Nucléiques, Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS Université Montpellier 1 Université Montpellier 2, Montpellier, 34095, France
| | - Carole Farre
- Département
Laboratoire des Sciences Analytiques, Institut des Sciences Analytiques, UMR 5280 CNRS Université de Lyon, Université Lyon 1, Villeurbanne, 69100, France
| | - Albert Meyer
- Département
des Analogues et Constituants des Acides Nucléiques, Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS Université Montpellier 1 Université Montpellier 2, Montpellier, 34095, France
| | - Vincent Dugas
- Département
Laboratoire des Sciences Analytiques, Institut des Sciences Analytiques, UMR 5280 CNRS Université de Lyon, Université Lyon 1, Villeurbanne, 69100, France
| | - Jean-François Cantaloube
- Laboratoire
Emergence et Co-évolution Virale, Etablissement Français du Sang Alpes-Méditerranée, Marseille, 13005, France
| | - Carole Chaix
- Département
Laboratoire des Sciences Analytiques, Institut des Sciences Analytiques, UMR 5280 CNRS Université de Lyon, Université Lyon 1, Villeurbanne, 69100, France
| | - Jean-Jacques Vasseur
- Département
des Analogues et Constituants des Acides Nucléiques, Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS Université Montpellier 1 Université Montpellier 2, Montpellier, 34095, France
| | - François Morvan
- Département
des Analogues et Constituants des Acides Nucléiques, Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS Université Montpellier 1 Université Montpellier 2, Montpellier, 34095, France
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Molecular Detection and Characterization of Hepatitis C Virus. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mao H, Zhang H, Zhang H, Zhao J, Lu Z, Jin G, Gu S, Wang H, Wang Y. Clinical evaluation of a colorimetric oligonucleotide chip for genotyping hepatitis C virus. Clin Biochem 2009; 43:214-9. [PMID: 19786007 DOI: 10.1016/j.clinbiochem.2009.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 09/12/2009] [Accepted: 09/15/2009] [Indexed: 12/09/2022]
Abstract
INTRODUCTION Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. It is associated with the development of end-stage liver disease and hepatocellular carcinoma. Studies have shown that determination of hepatitis C virus (HCV) genotypes is clinically important for prediction of the clinical course and the outcome of antiviral therapy. The aim of this study was to evaluate a colorimetric oligonucleotide chip, which can be used for the rapid and economical detection of the genotypes/subtypes of hepatitis C virus. DESIGN AND METHODS A total of 860 serum specimens were tested by an oligonucleotide chip genotyping test. Partial genotype results were compared with those obtained by sequencing method and INNOLiPA HCV II assay. The relative sensitivities of the methods were assessed by using the 5'NCR amplicon from the HCV RNA fluorescent amplicor HCV tests and Light Cycler. RESULTS Of 860 serum specimens tested for their genotypes/subtypes by the oligonucleotide array, 607 HCV positive serum samples could be typed by the sequencing method and 60 of 607 HCV positive serum specimens were typed by INNOLiPA HCV II method. Identification of genotype/subtypes by nucleotide sequencing and INNOLiPA HCV II assay showed respective coincidence rates of 99.8% and 96.7% with the HCV oligonucleotide chip results. And the colorimetric method exhibited 99.8% of relative sensitivity compared with the fluorescent amplicor HCV tests. CONCLUSION To our knowledge this oligonucleotide chip genotyping method offers a fast and convenient way to determine the genotype in large-scale settings. The tests can be easily adapted by a clinical diagnostic laboratory.
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Affiliation(s)
- Hongju Mao
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, PR China.
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Sethi D, Kumar A, Gupta KC, Kumar P. A facile method for the construction of oligonucleotide microarrays. Bioconjug Chem 2009; 19:2136-43. [PMID: 18939860 DOI: 10.1021/bc800241k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, the oligonucleotide-based microarray technique has emerged as a powerful and promising tool for various molecular biological studies. Here, a facile protocol for the construction of an oligonucleotide microarray is demonstrated that involves immobilization of oligonucleotide-trimethoxysilyl conjugates onto virgin glass microslides. The projected immobilization strategy reflects high immobilization efficiency ( approximately 36-40%) and signal-to-noise ratio ( approximately 98), and hybridization efficiency ( approximately 32-35%). Using the proposed protocol, aminoalkyl, mercaptoalkyl, and phosphorylated oligonucleotides were immobilized onto virgin glass microslides. Briefly, modified oligonucleotides were reacted first with 3-glycidyloxypropyltriethoxysilane (GOPTS), and subsequently, the resultant conjugates were directly immobilized onto the virgin glass surface by making use of silanization chemistry. The constructed microarrays were then used for discrimination of base mismatches. On subjecting to different pH and thermal conditions, the microarray showed sufficient stability. Application of this chemistry to manufacture oligonucleotide probe-based microarrays for detection of bacterial meningitis is demonstrated. Single-step reaction for the formation of conjugates with the commercially available reagent (GOPTS), omission of capping step and surface modification, and efficient immobilization of oligonucleotides onto the virgin glass surface are the key features of the proposed strategy.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Delhi, India
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