1
|
Nimse SB, Song KS, Warkad SD, Kim T. A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization. BIOSENSORS-BASEL 2021; 11:bios11080265. [PMID: 34436067 PMCID: PMC8391390 DOI: 10.3390/bios11080265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022]
Abstract
Highly sensitive (high SBR) and highly specific (high SNP discrimination ratio) DNA hybridization is essential for a biosensor with clinical application. Herein, we propose a method that allows detecting multiple pathogens on a single platform with the SNP discrimination ratios over 160:1 in the dynamic range of 101 to 104 copies per test. The newly developed SWAT method allows achieving highly sensitive and highly specific DNA hybridizations. The detection and discrimination of the MTB and NTM strain in the clinical samples with the SBR and SNP discrimination ratios higher than 160:1 indicate the high clinical applicability of the SWAT.
Collapse
Affiliation(s)
- Satish Balasaheb Nimse
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
| | - Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; (K.-S.S.); (S.D.W.)
| | | | - Taisun Kim
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
- Correspondence:
| |
Collapse
|
2
|
Yang X, Ding T, Huang H, Xu Y, Yu J, Chen Z. Development and validation of a simple and rapid method for hepatitis C virus genotyping based on one-step RT-qPCR. Exp Ther Med 2020; 20:2284-2290. [PMID: 32765706 DOI: 10.3892/etm.2020.8912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus (HCV) infections caused by different subtypes require different treatments; therefore, rapid and cost-effective genotyping methods for the diagnosis of HCV are greatly needed. In the present study, a new method to diagnose HCV subtypes that depends on a one-step quantitative reverse transcription PCR (RT-qPCR) and TaqMan fluorescence probe technique is described. Five pairs of primers and five probes were designed, which were able to detect five genotypes in three reaction tubes. One reaction was used to detect the 1b subtype, one was used to detect the 2a and 6a subtypes, and the other was used to detect the 3a and 3b subtypes. Rigorous performance validation was implemented for five aspects: Precision, sensitivity, accuracy, specificity and anti-interference. The HCV subtype that infected 289 patients was evaluated in the present study via RT-qPCR and verified by sequencing. The results revealed that the 1b subtype accounted for 45% of infections, the 2a subtype accounted for 9% of infections, the 3a subtype accounted for 13% of infections, the 3b subtype accounted for 18% of infections, and the 6a subtype accounted for 15% of infections. The analytical sensitivity for the detection of each of the five HCV subtypes was 1,000 IU/ml. The new method performed well in the performance validation mentioned above, indicating its effectiveness as a HCV genotyping method. RT-qPCR has mitigated some of the former challenges of existing HCV genotyping methods, including the time commitment, expense, and inaccuracy of such methods. The performance validation of this new method showed that RT-qPCR is reliable enough to be widely applied in China for HCV genotyping.
Collapse
Affiliation(s)
- Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Haifeng Huang
- Triplex International Biosciences (China) Co., Ltd., Xiamen, Fujian 361000, P.R. China
| | - Yang Xu
- Department of First Generation Sequencing, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang 310030, P.R. China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| |
Collapse
|
3
|
Ikonnikova AY, Zasedateleva OA, Surzhikov SA, Pozhitnova VO, Fesenko DO, Stomakhin AA, Zasedatelev AS, Nasedkina TV. Structural Destabilization of Intramolecular Duplexes Improves the Results of DNA Hybridization Analysis. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s000635091806012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
4
|
Gryadunov DA, Shaskolskiy BL, Nasedkina TV, Rubina AY, Zasedatelev AS. The EIMB Hydrogel Microarray Technology: Thirty Years Later. Acta Naturae 2018; 10:4-18. [PMID: 30713758 PMCID: PMC6351029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Indexed: 11/26/2022] Open
Abstract
Biological microarrays (biochips) are analytical tools that can be used to implement complex integrative genomic and proteomic approaches to the solution of problems of personalized medicine (e.g., patient examination in order to reveal the disease long before the manifestation of clinical symptoms, assess the severity of pathological or infectious processes, and choose a rational treatment). The efficiency of biochips is predicated on their ability to perform multiple parallel specific reactions and to allow one to study the interactions of biopolymer molecules, such as DNA, proteins, glycans, etc. One of the pioneers of microarray technology was the Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences (EIMB), with its suggestion to immobilize molecular probes in the three-dimensional structure of a hydrophilic gel. Since the first experiments on sequencing by hybridization on oligonucleotide microarrays conducted some 30 years ago, the hydrogel microarrays designed at the EIMB have come a long and successful way from basic research to clinical laboratory diagnostics. This review discusses the key aspects of hydrogel microarray technology and a number of state-ofthe-art approaches for a multiplex analysis of DNA and the protein biomarkers of socially significant diseases, including the molecular genetic, immunological, and epidemiological aspects of pathogenesis.
Collapse
Affiliation(s)
- D. A. Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - B. L. Shaskolskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - T. V. Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - A. Yu. Rubina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - A. S. Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| |
Collapse
|
5
|
Manee N, Thongbaiphet N, Pasomsub E, Chantratita W. Clinical evaluation of a newly developed automated massively parallel sequencing assay for hepatitis C virus genotyping and detection of resistance-association variants. Comparison with a line probe assay. J Virol Methods 2017; 249:31-37. [PMID: 28851606 DOI: 10.1016/j.jviromet.2017.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 07/13/2017] [Accepted: 08/21/2017] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis and hepatocellular carcinoma. Recently, HCV was classified into 6 major genotypes (GTs) and 67 subtypes (STs). Efficient genotyping has become an essential tool for prognosis and indicating suitable treatment, prior to starting therapy in all HCV-infected individuals. The widely used genotyping assays have limitation with regard to genotype accuracy. This study was a comparative evaluation of exact HCV genotyping in a newly developed automated-massively parallel sequencing (MPS) system, versus the established Line probe assay 2.0 (LiPA), substantiated by Sanger sequencing, using 120 previously identified-HCV RNA positive specimens. LiPA gave identical genotypes in the majority of samples tested with MPS. However, as much as 25% of LiPA did not identify subtypes, whereas MPS did, and 0.83% of results were incompatible. Interestingly, only MPS could identify mixed infections in the remaining cases (1.67%). In addition, MPS could detect Resistance-Associated Variants (RAVs) simultaneously in GT1 in 56.82% of the specimens, which were known to affect drug resistance in the HCV NS3/NS4A and NS5A genomic regions. MPS can thus be deemed beneficial for guiding decisions on HCV therapy and saving costs in the long term when compared to traditional methods.
Collapse
Affiliation(s)
- Narathon Manee
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Nipa Thongbaiphet
- Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Ekawat Pasomsub
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Wasun Chantratita
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| |
Collapse
|
6
|
Kubanov AA, Leinsoo AT, Chestkov AV, Dementieva EI, Shaskolskiy BL, Solomka VS, Gryadunov DA, Deryabin DG. Drug resistance mutations and susceptibility phenotypes of Neisseria gonorrhoeae isolates in Russia. Mol Biol 2017. [DOI: 10.1134/s0026893317030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Tong YQ, Liu B, Liu H, Zheng HY, Gu J, Liu H, Song EJ, Song C, Li Y. Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population. Clin Microbiol Infect 2015; 21:874.e9-874.e21. [PMID: 26055416 DOI: 10.1016/j.cmi.2015.05.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/10/2015] [Accepted: 05/26/2015] [Indexed: 12/21/2022]
Abstract
Nucleotide sequencing of the phylogenetically informative region of NS5B remains the gold standard for hepatitis C virus (HCV) genotyping. Here we developed a new methodology for sequencing new NS5B regions to increase the accuracy and sensitivity of HCV genotyping and subtyping. The eight new primers were identified by scanning the full-length NS5B regions from 1127 HCV genomic sequences found in HCV databases. The ability of each pair of primers to amplify HCV subtypes was scored, and the new primers were able to amplify the NS5B region better than the previously used primers, therefore more accurately subtyping HCV strains. Sequencing the DNA amplified by the new primer pairs can specifically and correctly detect the five standard HCV subtypes (1a, 2a, 3b, 6a and 1b). We further examined patient samples and found that the new primers were able to identify HCV subtypes in clinical samples with high sensitivity. This method was able to detect all subtypes of HCV in 567 clinical samples. Importantly, three novel HCV subtypes (1b-2a, 1b-2k and 6d-6k) were identified in the samples, which have not been previous reported in China. In conclusion, sequencing the NS5B region amplified by the new NS5B primers is a more reliable method of HCV genotyping and a more sensitive diagnostic tool than sequencing using the previously described primers, and could identify new HCV subtypes. Our research is useful for clinical diagnosis, guidance of clinical treatment, management of clinical patients, and studies on the epidemiology of HCV.
Collapse
Affiliation(s)
- Y-Q Tong
- Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - B Liu
- Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, China
| | - H Liu
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - H-Y Zheng
- Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - J Gu
- Department of Clinical Laboratory, China
| | - H Liu
- Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China
| | - E J Song
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA
| | - C Song
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, USA.
| | - Y Li
- Department of Clinical Laboratory, China; Clinical Molecular Diagnostic Centre, Renmin Hospital of Wuhan University, Wuhan, China.
| |
Collapse
|
8
|
Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA. Sci Rep 2015; 5:8721. [PMID: 25735213 PMCID: PMC4348642 DOI: 10.1038/srep08721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
Collapse
|
9
|
Khadem Ansari MH, Omrani MD, Kheradmand F. Oxidative stress response in patients infected by diverse hepatitis C virus genotypes. HEPATITIS MONTHLY 2015; 15:e22069. [PMID: 25788953 PMCID: PMC4350251 DOI: 10.5812/hepatmon.22069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/12/2014] [Accepted: 02/01/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The molecular mechanism of hepatitis C-virus (HCV) genome-specific pathogenesis remains unclear. Oxidative stress is an important pathophysiological mechanism in chronic HCV infection, but its relation to HCV genotypes has not been thoroughly examined. OBJECTIVES In the present case-control study, the effect of diverse HCV genotypes on oxidative status changes was investigated. PATIENTS AND METHODS From 310 patients examined by enzyme immunoassay and PCR, 160 patients with positive results for HCV with previously determined genotypes were chosen. For the control group, 160 first time blood donors referred to the Regional Blood Transfusion organization of the West Azerbaijan province, northwestern Iran were selected. Oxidative stress markers such as total antioxidant status (TAS), serum levels of reduced (GSH) and oxidized (GSSG) glutathione, Gamma-glutamyl transferase (GGT) and malondialdehyde (MDA) were evaluated in patients infected with diverse HCV genotypes and those in the control group. RESULTS In the patient and control groups, the mean ± SE of TAS, GSH, GSSG, GGT and MDA were 1.04 ± 0.35 vs. 2.68 ± 0.77, 1.25 ± 0.37 vs. 3.12 ± 0.58, 0.20 ± 0.05 vs. 0.08 ± 0.04, 26.82 ± 5.62 vs 8.28 ± 2.03 and 2.56 ± 0.60 vs. 0.93 ± 0.34. All markers had statistical difference between the two groups (P <0.05). Obvious differences were found in oxidant/antioxidant balance among diverse HCV genotypes with an ascending trend in antioxidant levels among patients infected with genotypes 1a/b, 4, 2a/c, 2b, 3a and healthy controls and a vice versa trend in measures of oxidative markers except for malondialdehyde with a variable pattern. CONCLUSIONS More serious disease in HCV genetic subtype 1a/1b might be associated with more severe oxidative stress. Milder damage in subtypes 4, 2a/c, 2b and 3a could be related to lower oxidative response, respectively. A combination of antiviral and antioxidative therapies may enhance the overall response rate of patients with HCV infection, especially with more destructive genotypes.
Collapse
Affiliation(s)
| | - Mir-Davood Omrani
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
| | - Fatemeh Kheradmand
- Cellular and Molecular Research Center, Clinical Biochemistry Department, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, IR Iran
- Corresponding Author: Fatemeh Kheradmand, Cellular and Molecular Research Center, Clinical Biochemistry Department, Faculty of Medicine, Urmia University of Medical Sciences, 11th Km of Sero (Nazloo) Road, Urmia, IR Iran. Tel: +98-4412770397, Fax: +98-4412780800, E-mail:
| |
Collapse
|
10
|
Ansaldi F, Orsi A, Sticchi L, Bruzzone B, Icardi G. Hepatitis C virus in the new era: Perspectives in epidemiology, prevention, diagnostics and predictors of response to therapy. World J Gastroenterol 2014; 20:9633-9652. [PMID: 25110404 PMCID: PMC4123355 DOI: 10.3748/wjg.v20.i29.9633] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/18/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
Despite the great successes achieved in the fields of virology and diagnostics, several difficulties affect improvements in hepatitis C virus (HCV) infection control and eradication in the new era. New HCV infections still occur, especially in some of the poorest regions of the world, where HCV is endemic and long-term sequelae have a growing economic and health burden. An HCV vaccine is still no available, despite years of researches and discoveries about the natural history of infection and host-virus interactions: several HCV vaccine candidates have been developed in the last years, targeting different HCV antigens or using alternative delivery systems, but viral variability and adaption ability constitute major challenges for vaccine development. Many new antiviral drugs for HCV therapy are in preclinical or early clinical development, but different limitations affect treatment validity. Treatment predictors are important tools, as they provide some guidance for the management of therapy in patients with chronic HCV infection: in particular, the role of host genomics in HCV infection outcomes in the new era of direct-acting antivirals may evolve for new therapeutic targets, representing a chance for modulated and personalized treatment management, when also very potent therapies will be available. In the present review we discuss the most recent data about HCV epidemiology, the new perspectives for the prevention of HCV infection and the most recent evidence regarding HCV diagnosis, therapy and predictors of response to it.
Collapse
|
11
|
Yang YC, Wang DY, Cheng HF, Chuang EY, Tsai MH. A reliable multiplex genotyping assay for HCV using a suspension bead array. Microb Biotechnol 2014; 8:93-102. [PMID: 25042084 PMCID: PMC4321376 DOI: 10.1111/1751-7915.12140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 01/25/2023] Open
Abstract
The genotyping of the hepatitis C virus (HCV) plays an important role in the treatment of HCV because genotype determination has recently been incorporated into the treatment guidelines for HCV infections. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. We therefore developed a multiplex genotyping assay to determine HCV genotypes using a bead array. Synthetic plasmids, genotype panels and standards were used to verify the target-specific primer (TSP) design in the assay, and the results indicated that discrimination efforts using 10 TSPs in a single reaction were extremely successful. Thirty-five specimens were then tested to evaluate the assay performance, and the results were highly consistent with those of direct sequencing, supporting the reliability of the assay. Moreover, the results from samples with mixed HCV genotypes revealed that the method is capable of detecting two different genotypes within a sample. Furthermore, the specificity evaluation results suggested that the assay could correctly identify HCV in HCV/human immunodeficiency virus (HIV) co-infected patients. This genotyping platform enables the simultaneous detection and identification of more than one genotype in a same sample and is able to test 96 samples simultaneously. It could therefore provide a rapid, efficient and reliable method of determining HCV genotypes in the future.
Collapse
Affiliation(s)
- Yi-Chen Yang
- Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan; Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | | | | | | | | |
Collapse
|
12
|
Gryadunov D, Dementieva E, Mikhailovich V, Nasedkina T, Rubina A, Savvateeva E, Fesenko E, Chudinov A, Zimenkov D, Kolchinsky A, Zasedatelev A. Gel-based microarrays in clinical diagnostics in Russia. Expert Rev Mol Diagn 2014; 11:839-53. [DOI: 10.1586/erm.11.73] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dmitry Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Ekaterina Dementieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Vladimir Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Tatiana Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Alla Rubina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Elena Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Eugeny Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Alexander Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | - Danila Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| | | | - Alexander Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
| |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Important factors in reliable determination of hepatitis C virus genotype by use of the 5' untranslated region. J Clin Microbiol 2013; 51:1485-9. [PMID: 23467599 DOI: 10.1128/jcm.03344-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Accurate genotyping of hepatitis C virus (HCV) is important for determining the optimal regimen, dose, and duration of antiviral therapy for chronic HCV infection, as well as for estimating the response rate. The 5' untranslated region (UTR) of HCV RNA is used in commercial genotyping, but the probes and the lengths of the amplicons are proprietary and vary among the assays. In this study, factors involved in the reliable determination of HCV genotypes utilizing the 5' UTR were evaluated. Serum samples from four subjects with chronic HCV infection and disparate results on commercial genotyping and four controls were analyzed. HCV RNA was extracted from serum samples, and the 5' UTR and NS5B region were sequenced. Ten clones from each region were compared to prototype sequences and analyzed for genotype assignment using five programs. The results were compared to those from commercial assays. 5' UTR sequences were sequentially shortened from either the 5' end, the 3' end, or both ends, with genotyping of the resultant fragments. Sequences were obtained for the 5' UTR in all eight subjects and for the NS5B region in five subjects. The genotype assignments were identical between the two regions in the five subjects with complete sequencing. Genotyping by sequencing gave different results than those from the commercial assays in the four experimental samples but agreed in the four controls. Shortening of the sequences affected the results, and the results for sequences of <200 bases were inaccurate. Neither the Hamming distance nor the quasispecies affected the results. Sequencing of the HCV 5' UTR provided reliable genotyping results and resolved discrepancies identified in commercial assays, but genotyping by sequencing was highly dependent upon sequence length.
Collapse
|