1
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Ma Y, Wu H, Chen S, Xie C, Hu J, Qi X, Ma X, Chu Y, Shan J, Lu Y, Cui L, Zou B, Zhou G. FEN1-aided recombinase polymerase amplification (FARPA) for one-pot and multiplex detection of nucleic acids with an ultra-high specificity and sensitivity. Biosens Bioelectron 2023; 237:115456. [PMID: 37354713 DOI: 10.1016/j.bios.2023.115456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
Recombinase polymerase amplification (RPA) running at 37-42 °C is fast, efficient and less-implemented; however, the existing technologies of nucleic acid testing based on RPA have some limitations in specificity of single-base recognition and multiplexing capability. Herein, we report a highly specific and multiplex RPA-based nucleic acid detection platform by combining flap endonuclease 1 (FEN1)-catalysed invasive reactions with RPA, termed as FEN1-aided RPA (FARPA). The optimal conditions enable RPA and FEN1-based fluorescence detection to occur automatically and sequentially within a 25-min turnaround time and FARPA exhibits sensitivity to 5 target molecules. Due to the ability of invasive reactions in discriminating single-base variation, this one-pot FARPA is much more specific than the Exo probe-based or CRISPR-based RPA methods. Using a universal primer pair derived from tags in reverse transcription primers, multiplex FARPA was successfully demonstrated by the 3-plex assay for the detection of SARS-CoV-2 pathogen (the ORF1ab, the N gene, and the human RNase P gene as the internal control), the 2-plex assay for the discrimination of SARS-CoV-2 wild-type from variants (Alpha, Beta, Epsilon, Delta, or Omicrons), and the 4-plex assay for the screening of arboviruses (zika virus, tick-borne encephalitis virus, yellow fever virus, and chikungunya virus). We have validated multiplex FARPA with 103 nasopharyngeal swabs for SARS-CoV-2 detection. The results showed a 100% agreement with RT-qPCR assays. Moreover, a hand-held FARPA analyser was constructed for the visualized FARPA due to the switch-like endpoint read-out. This FARPA is very suitable for pathogen screening and discrimination of viral variants, greatly facilitating point-of-care diagnostics.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China; Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Shan Chen
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Chunmei Xie
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingjing Hu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingwen Shan
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yan Lu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Lunbiao Cui
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China.
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2
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Ma Y, Ma X, Bu L, Shan J, Liu D, Zhang L, Qi X, Chu Y, Wu H, Zou B, Zhou G. Flap Endonuclease-Induced Steric Hindrance Change Enables the Construction of Multiplex and Versatile Lateral Flow Strips for DNA Detection. Anal Chem 2022; 94:14725-14733. [PMID: 36223239 DOI: 10.1021/acs.analchem.2c03143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A lateral flow strip (LFS) is an ideal tool for point-of-care testing (POCT), but traditional LFSs cannot be used for multiplex detection. Herein, a multiplex and versatile LFS based on flap endonuclease 1 (FEN1)-induced steric hindrance change (FISH-LFS) is proposed. In this method, multiplex PCR coupled with cascade invasive reactions was employed to yield single-stranded flaps, which were target-specific but independent of target sequences. Then, the amplicons were applied for FISH-LFS, and the single-stranded flaps would be efficiently captured by the complementary LFS-probes at different test lines. As flaps were cleaved from the specially designed hairpin probes, competition among flaps and hairpin probes would occur in capturing the probes at test lines. We enabled the hairpin probes to flow through the test lines while the flaps to stay at the test lines by making use of the difference in steric hindrance between hairpin probes and flaps. The assay is able to detect as low as two copies of blood pathogens (HBV, HCV, and HIV), to pick up as low as 0.1% mutants from wild-type gDNA, and to genotype 200 copies of SARS-CoV-2 variants α and β within 75 min at a conventional PCR engine. As the method is free of dye, a portable PCR engine could be used for a cost-effective multiplex detection on site. Results using an ultrafast mobile PCR system for FISH-LFS showed that as fast as 30 min was achieved for detecting three pathogens (HBV, HCV, and HIV) in blood, very suitable for POCT of pathogen screening. The method is convenient in operation, simple in instrumentation, specific in genotyping, and very easy in setting up multiplex POCT assays.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Li Bu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Jingwen Shan
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Danni Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Likun Zhang
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, State Key Laboratory of Analytical Chemistry for Life Science and Jiangsu Key Laboratory of Molecular Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.,School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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3
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Sheng N, Zou B, Tong H, Lu Y, Xing S, Song Q, Zhou G. Sequence-encoded quantitative invader assay enables highly sensitive hepatitis B virus DNA quantification in a single tube without the use of a calibration curve. Analyst 2019; 144:5775-5784. [PMID: 31460526 DOI: 10.1039/c9an00970a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Absolute quantification of HBV-DNA by sequence-encoded Quantitative Invader assay in a single tube without using calibration curves.
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Affiliation(s)
- Nan Sheng
- School of Life Science and Technology
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Bingjie Zou
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Huan Tong
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Yan Lu
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Sixi Xing
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- Ministry of Education
- School of Pharmacy
- China Pharmaceutical University
- Nanjing 210009
| | - Qinxin Song
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Guohua Zhou
- School of Life Science and Technology
- China Pharmaceutical University
- Nanjing 210009
- China
- Department of Pharmacology
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4
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Miyasaka A, Yoshida Y, Yoshida T, Murakami A, Abe K, Ohuchi K, Kawakami T, Watanabe D, Hoshino T, Sawara K, Takikawa Y. The Real-world Efficacy and Safety of Ombitasvir/Paritaprevir/Ritonavir for Hepatitis C Genotype 1. Intern Med 2018; 57:2807-2812. [PMID: 29780135 PMCID: PMC6207834 DOI: 10.2169/internalmedicine.0810-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Objective There are few reports on the outcomes of 12-week paritaprevir, ombitasvir, and ritonavir (PTV/OBV/r) treatment in real-world clinical settings. We aimed to evaluate the efficacy and safety of 12-week treatment with ritonavir-boosted paritaprevir and ombitasvir in patients with hepatitis C virus (HCV) genotype 1 infection in a real-world setting. Methods Fifty-eight patients with chronic hepatitis or compensated hepatic cirrhosis and genotype-1 HCV infection were treated with PTV/OBV/r and followed for 24 weeks after the completion of treatment in 10 centers in northern Tohoku. The efficacy and safety of this 12-week treatment regimen was analyzed. Results Among the 58 treated patients, 18 (31%) had compensated liver cirrhosis, while 11 (19%) patients had experienced treatment failure with another treatment regimen. NS5A resistance-associated variants (RAVs) were detected at baseline in 3 patients (5.2%), including Y93H in two patients and L31M in two patients. One patient had NS5A RAVs at both positions 93 and 31. The overall sustained virological response (SVR) 24 rate was 96.6%. Three patients with NS5A RAVs also achieved an SVR24. The SVR24 rate was not significantly affected by age, sex, prior treatment, prior history of HCC, or liver stiffness. The mean alanine aminotransferase (ALT) levels decreased significantly during this treatment. Adverse events occurred in 15 patients (26%), 26% of which were grade 1 or 2. No severe adverse events occurred. Conclusion In this real-world study, 12-week PTV/OBV/r treatment was effective and safe for treating patients with HCV-1 infection who had chronic hepatitis or compensated hepatic cirrhosis.
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Affiliation(s)
- Akio Miyasaka
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Japan
| | - Yuichi Yoshida
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Japan
| | | | - Akihiko Murakami
- Department of Gastroenterology, Iwate Prefectural Miyako Hospital, Japan
| | | | | | | | - Daisuke Watanabe
- Department of Gastroenterology, Noshiro Yamamoto Medical Association Hospital, Japan
| | - Takao Hoshino
- Department of Gastroenterology, Akita Kosei Medical Center, Japan
| | - Kei Sawara
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Japan
- Department of Gastroenterology, Iwate Prefectural Kamaishi Hospital, Japan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University School of Medicine, Japan
- Department of Hepatology, San-ai Hospital, Japan
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5
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Sedeno-Monge V, Vallejo-Ruiz V, Sosa-Jurado F, Santos-Lopez G. Polymorphisms in the hepatitis C virus core and its association with development of hepatocellular carcinoma. J Biosci 2018; 42:509-521. [PMID: 29358564 DOI: 10.1007/s12038-017-9695-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Little is known about the mechanisms underlying hepatocellular carcinoma (HCC). Some studies have focused on the role of HCV viral proteins in hepatocyte transformation. In this work we have compiled and analysed current articles regarding the impact of polymorphisms in the HCV core gene and protein on the development of HCC. An exhaustive search for fulltext articles until November 2016 in PubMed database was performed using the MeSH keywords: 'hepatitis C', 'polymorphisms', 'core', 'hepatocellular cancer' and 'hepatocarcinogenesis'. Nineteen full-text articles published between 2000 and 2016 were considered. Different articles associate not only the HCC development with polymorphisms at residues 70 and 91 in the core protein, but more with mortality and treatment response. Also, different polymorphisms were found in core and other viral proteins related to HCC development. Eleven articles reported that HCC development is significantly associated with Gln/His70, four associated it with Leu91 and two more associated it with both markers together. Additional studies are necessary, including those in different types of populations worldwide, to validate the possibility of the usability and influence in chronically HCV-infected patients as well as to observe their interaction with other risk factors or prognosis and genetic markers of the host.
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Affiliation(s)
- Virginia Sedeno-Monge
- Departamento de Ciencias de la Salud, Universidad Popular Autonoma del Estado de Puebla, Puebla, Mexico
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6
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Safety and effectiveness of daclatasvir and asunaprevir dual therapy in patients with genotype 1 chronic hepatitis C: results from postmarketing surveillance in Japan. Hepatol Int 2018; 12:244-253. [DOI: 10.1007/s12072-018-9872-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022]
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7
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Hayashi K, Ishigami M, Ishizu Y, Kuzuya T, Honda T, Kawashima H, Ishikawa T, Tachi Y, Hattori M, Katano Y, Goto H, Hirooka Y. Comparison of direct sequencing and Invader assay for Y93H mutation and response to interferon-free therapy in hepatitis C virus genotype 1b. J Gastroenterol Hepatol 2018; 33:249-255. [PMID: 28440885 DOI: 10.1111/jgh.13809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM Virologic failure of interferon-free therapy has been associated with Y93H mutation in the non-structure 5A region in hepatitis C virus (HCV) genotype 1b, and screening is recommended. A simple assay based on Q-Invader technology was developed for Y93H mutant screening to reduce cost and effort. The present study sought to compare two methods of detection of Y93H mutation and to evaluate the effect of Y93H mutation on response to interferon-free therapy. METHODS Y93H mutation was examined in 258 patients with HCV genotype 1b using both direct sequencing analysis and the polymerase chain reaction (PCR)-Invader assay. Daclatasvir and asunaprevir or ledipasvir and sofosbuvir therapy was administered to 205 patients whose sustained virological responses (SVR) were checked. RESULTS Hepatitis C virus was detected in 232 of 258 patients by direct sequencing and in 236 of 258 patients by the PCR-Invader assay. Forty of 231 cases were defined as Y93 mutation by direct sequencing, and 46 of 236 cases were defined as Y93 mutation by the PCR-Invader assay. SVR of patients who were Y93H by direct sequencing, Y93H by the PCR-Invader assay, and Y93H by both methods was 62.5%, 82.4%, and 50%, respectively. CONCLUSIONS The sensitivity of the PCR-Invader assay was similar to that of direct sequencing analysis; however, the PCR-Invader assay had a better ability to detect minor strains. Combination of the two assays would improve prediction of the response to daclatasvir and asunaprevir, but Y93H mutation had little effect on SVR in ledipasvir and sofosbuvir therapy.
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Affiliation(s)
- Kazuhiko Hayashi
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoji Ishizu
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teiji Kuzuya
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kawashima
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Ishikawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiko Tachi
- Department of Gastroenterology, Komaki City Hospital, Komaki, Japan
| | - Masashi Hattori
- Department of Gastroenterology, Yamashita Hospital, Ichinomiya, Japan
| | - Yoshiaki Katano
- Department of Internal Medicine, Banbuntane Hotokukai Hospital, Fujita Health University, Nagoya, Japan
| | - Hidemi Goto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Ishigami M, Hayashi K, Honda T, Kuzuya T, Ishizu Y, Ishikawa T, Nakano I, Urano F, Kumada T, Yoshioka K, Hirooka Y, Goto H. Daclatasvir and asunaprevir treatment in patients infected by genotype 1b of hepatitis C virus with no or subtle resistant associated substitutions (RAS) in NS5A-Y93. J Med Virol 2017; 90:736-744. [PMID: 29111616 DOI: 10.1002/jmv.24978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
In this study, we investigated the real-world data of the first approved interferon-free regimen in Japan, daclatasvir and asunaprevir (DCV+ASV), in chronic hepatitis C patients infected HCV genotype 1b with no or subtle amount of baseline resistant associated substitutions (RAS). Among 924 patients registered in our multicenter study, 750 patients who were proven not to be infected with NS5A-Y93H RAS by direct sequencing and to have no or subtle amount (less than 20%) of NS5A-Y93H RAS by probe assays (Cycleave or PCR invader assay) were included in this study. We investigated the anti-viral effect and factors associated with SVR12. In statistical analysis, P < 0.05 was considered as significant. The SVR12 rate in this population was 92.1% (562/618). Factors associated with SVR12 were male (odds ratio: 2.128; 95%CI: 1.134-4.000, P = 0.019); lower serum γGTP (odds ratio: 1.007; 95%CI: 1.002-1.012, P = 0.006); lower HCV-RNA (odds ratio: 1.848; 95%CI: 1.087-3.145, P = 0.023), and RVR (odds ratio: 6.250; 95%CI: 2.445-15.873, P < 0.001). No patients with γGTP ≧ 80 IU/L without RVR showed SVR12 (0/4, 0%) and one patients with γGTP ≧ 20-< 80 IU/L and HCV-RNA ≧ 6.5 logIU/mL without RVR (5/10, 50%) and two female patients with RVR but γGTP ≧ 80 IU/L and HCV-RNA ≧ 6.5 logIU/mL (7/13, 53.8%) showed a low SVR12 rate. In the present study, we showed a good viral response with DCV-ASV treatment and identified four predictive factors associated with SVR12. These four markers could be a good predictive markers for the viral effect of this treatment regimen in patients with no or subtle amount of RAS in NS5A-Y93.
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Affiliation(s)
- Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Kazuhiko Hayashi
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Teiji Kuzuya
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Yoji Ishizu
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Tetsuya Ishikawa
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Isao Nakano
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Fumihiro Urano
- Department of Gastroenterology, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Takashi Kumada
- Department of Gastroenterology, Ogaki Municipal Hospital, Ogaki, Gifu, Japan
| | - Kentaro Yoshioka
- Division of Liver and Biliary Diseases, Department of Internal Medicine, Fujita Health University, Toyoake, Aichi, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
| | - Hidemi Goto
- Department of Gastroenterology and Hepatology, Nagoya University School of Medicine, Nagoya, Aichi, Japan
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9
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Fujii H, Umemura A, Nishikawa T, Yamaguchi K, Moriguchi M, Nakamura H, Yasui K, Minami M, Tanaka S, Ishikawa H, Kimura H, Takami S, Nagao Y, Shima T, Itoh Y. Real-world efficacy of daclatasvir and asunaprevir with respect to resistance-associated substitutions. World J Hepatol 2017; 9:1064-1072. [PMID: 28951778 PMCID: PMC5596313 DOI: 10.4254/wjh.v9.i25.1064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/17/2017] [Accepted: 07/17/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate daclatasvir (DCV) and asunaprevir (ASV) efficacy in hepatitis C (HCV) patients, with respect to resistance-associated substitutions (RASs).
METHODS A total of 392 HCV-infected patients from multiple centers were included in this study. We evaluated their clinical courses and sustained virologic responses (SVR) according to pretreatment factors (gender, age, history of interferon-based regimens, platelet counts, level of viremia, pretreatment NA5A:L31, and Y93 substitutions). We also analyzed the pretreatment and post-treatment major RASs of NS3:D168, NS5A:L31 and Y93 substitutions using a direct-sequencing method in 17 patients who were unable to achieve SVR at 12 wk after treatment completion (SVR12).
RESULTS The overall SVR12 rate was 88.3%. Thirty-one patients discontinued treatment before 24 wk because of adverse events, 23 of whom achieved SVR12. There were no significant differences in SVR12 rates with respect to gender, age, history of interferon-based regimens, and platelet counts. The SVR12 rate in patients with viral loads of ≥ 6.0 log IU/mL was significantly lower than those with viral loads of < 6.0 log IU/mL (P < 0.001). The SVR12 rate in patients with Y93 substitution-positive was significantly lower than those with Y93 substitution-negative (P < 0.001). The L31 substitution-positive group showed a lower SVR12 rate than the L31 substitution-negative group, but the difference was not statistically significant. Seventeen patients who did not achieve SVR12 and had available pretreatment and post-treatment sera had additional RASs in NS3:D168, NS5:L31, and Y93 substitution at treatment failure.
CONCLUSION Combination of DCV and ASV is associated with a high SVR rate. Baseline RASs should be thoroughly assessed to avoid additional RASs after treatment failure.
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Affiliation(s)
- Hideki Fujii
- Department of Gastroenterology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto 6050981, Japan
| | | | | | | | | | - Hideki Nakamura
- Department of Gastroenterology and Hepatology, North Medical Center, Kyoto Prefectural University of Medicine, Kyoto 6292261, Japan
| | | | - Masahito Minami
- Department of Internal Medicine, Aiseikai Yamashina Hospital, Kyoto 6078086, Japan
| | - Saiyu Tanaka
- Center for Digestive and Liver Diseases, Nara City Hospital, Nara 6308305, Japan
| | - Hiroki Ishikawa
- Department of Gastroenterology and Hepatology, Omihachiman Community Medical Center, Shiga 5230082, Japan
| | - Hiroyuki Kimura
- Department of Gastroenterology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto 6050981, Japan
| | - Shiro Takami
- Department of Gastroenterology, Otsu Municipal Hospital, Otsu 5200804, Japan
| | - Yasuyuki Nagao
- Department of Gastroenterology, Matsushita Memorial Hospital, Moriguchi 5708540, Japan
| | - Toshihide Shima
- Center of Gastroenterology and Hepatology, Saiseikai Suita Hospital, Suita 5640013, Japan
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Yoshida K, Hai H, Tamori A, Teranishi Y, Kozuka R, Motoyama H, Kawamura E, Hagihara A, Uchida-Kobayashi S, Morikawa H, Enomoto M, Murakami Y, Kawada N. Long-Term Follow-Up of Resistance-Associated Substitutions in Hepatitis C Virus in Patients in Which Direct Acting Antiviral-Based Therapy Failed. Int J Mol Sci 2017; 18:ijms18050962. [PMID: 28467359 PMCID: PMC5454875 DOI: 10.3390/ijms18050962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022] Open
Abstract
We evaluated the transition of dominant resistance-associated substitutions (RASs) in hepatitis C virus during long-term follow-up after the failure of DAAs (direct acting antivirals)-based therapy. RASs in non-structure (NS)3/4A, NS5A, NS5B, and deletions in NS5A from 20 patients who failed simeprevir/pegylated-interferon/ribavirin (SMV/PEG-IFN/RBV) and 25 patients who failed daclatasvir/asunaprevir (DCV/ASV) treatment were examined by direct sequencing. With respect to SMV/PEG-IFN/RBV treatment, RAS was detected at D168 in NS3/4A but not detected in NS5A and NS5B at treatment failure in 16 of 20 patients. During the median follow-up period of 64 weeks, the RAS at D168 became less dominant in 9 of 16 patients. Among 25 DCV/ASV failures, RASs at D168, L31, and Y93 were found in 57.1%, 72.2%, and 76.9%, respectively. NS5A deletions were detected in 3 of 10 patients treated previously with SMV/PEG-IFN/RBV. The number of RASs in the breakthrough patients exceeded that in relapsers (mean 3.9 vs. 2.7, p < 0.05). RAS at D168 in NS3/4A became less dominant in 6 of 15 patients within 80 weeks. Y93H emerged at the time of relapse, then decreased gradually by 99% at 130 weeks post-treatment. Emerged RASs were associated with the clinical course of treatment and could not be detected during longer follow-up.
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Affiliation(s)
- Kanako Yoshida
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Hoang Hai
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Akihiro Tamori
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Yuga Teranishi
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Ritsuzo Kozuka
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Hiroyuki Motoyama
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Etsushi Kawamura
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Atsushi Hagihara
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Sawako Uchida-Kobayashi
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Hiroyasu Morikawa
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Masaru Enomoto
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Yoshiki Murakami
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
| | - Norifumi Kawada
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
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11
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Ikeda H, Watanabe T, Okuse C, Matsumoto N, Ishii T, Yamada N, Shigefuku R, Hattori N, Matsunaga K, Nakano H, Hiraishi T, Kobayashi M, Yasuda K, Yamamoto H, Yasuda H, Kurosaki M, Izumi N, Yotsuyanagi H, Suzuki M, Itoh F. Impact of resistance-associated variant dominancy on treatment in patients with HCV genotype 1b receiving daclatasvir/asunaprevir. J Med Virol 2016; 89:99-105. [PMID: 27329864 DOI: 10.1002/jmv.24608] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 12/13/2022]
Abstract
Sustained virological responses (SVR) by daclatasvir (DCV) and asunaprevir (ASV) therapy for genotype 1b hepatitis C virus (HCV) infected patients has been significantly affected by pre-existence of Y93 H resistance-associated variants (RAVs) in the non-structural protein 5A (NS5A) region. The aim of this study was to elucidate the dominancy of naturally occurring RAVs in viral quasispecies on treatment outcomes in patients with HCV. In total, 138 patients were prospectively selected from 152 patients treated with DCV and ASV, where evaluation of treatment outcomes at 12 weeks post-treatment was possible. Pre-treatment RAVs in the non-structural protein 3 and NS5A regions were detected by polymerase chain reaction (PCR)-Invader assays, and the ratio of Y93H RAVs in viral quasispecies was measured by quantitative PCR-Invader assay. Among 25 patients detected the Y93H RAV, the Y93H ratio was 1-25% in 5 patients, 26-75% in 7 patients, and ≥76% in 13 patients. Overall, SVR at 12 weeks after the completion of treatment (SVR12) was 91% (125/138), and those with Y93H ratios of <1%, 1-25%, 26-75%, and ≥76% were 99%, 100%, 71%, and 23%, respectively. Thus, the SVR12 decreased as the HCV Y93H ratio increased (P < 0.0001). The dominancy of pre-treatment RAVs of DCV and ASV affected its treatment outcomes, suggesting that evaluating the dominancy of HCV RAVs could be required for every other direct-acting antiviral agent treatments. J. Med. Virol. 89:99-105, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroki Ikeda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tsunamasa Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Chiaki Okuse
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan.,Division of Gastroenterology and Hepatology, Kawasaki Municipal Tama Hospital, Kawasaki, Japan
| | - Nobuyuki Matsumoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshiya Ishii
- Division of Gastroenterology, Yokohama City Seibu Hospital, Yokohama, Japan
| | - Norie Yamada
- Department of Internal Medicine, Center for Liver Diseases, Kiyokawa Hospital, Suginami, Japan
| | - Ryuta Shigefuku
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Nobuhiro Hattori
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kotaro Matsunaga
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroyasu Nakano
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tetsuya Hiraishi
- Division of Gastroenterology and Hepatology, Kawasaki Municipal Tama Hospital, Kawasaki, Japan
| | - Minoru Kobayashi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan.,Department of Internal Medicine, Center for Liver Diseases, Kiyokawa Hospital, Suginami, Japan
| | - Kiyomi Yasuda
- Department of Internal Medicine, Center for Liver Diseases, Kiyokawa Hospital, Suginami, Japan
| | - Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroshi Yasuda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masayuki Kurosaki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - Namiki Izumi
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Michihiro Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan. .,Division of Gastroenterology and Hepatology, Kawasaki Municipal Tama Hospital, Kawasaki, Japan.
| | - Fumio Itoh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
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12
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Kadjbaf D, Keshvari M, Alavian SM, Pouryasin A, Behnava B, Salimi S, Mehrnoush L, Karimi Elizee P, Sharafi H. The Prevalence of Hepatitis C Virus Core Amino Acid 70 Substitution and Genotypes of Polymorphisms Near the IFNL3 Gene in Iranian Patients With Chronic Hepatitis C. HEPATITIS MONTHLY 2016; 16:e37011. [PMID: 27630727 PMCID: PMC5010881 DOI: 10.5812/hepatmon.37011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/06/2016] [Accepted: 03/18/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Molecular studies have demonstrated that the hepatitis C virus (HCV) genotype and host genetics play predictive roles in the management of patients infected with HCV. OBJECTIVES This study aimed to investigate the HCV genotype, core amino acid (aa) 70 substitution, and polymorphisms near the IFNL3 gene (including rs12979860 and rs8099917) among Iranian patients with chronic hepatitis C (CHC). PATIENTS AND METHODS In this cross-sectional study, the molecular profiles of the HCV genotype, core aa 70 substitution, and rs12979860 and rs8099917 polymorphisms and plasma HCV RNA levels were determined in 429 CHC patients including 141 hemophilic, 84 thalassemic, and 204 non-hemophilic, non-thalassemic patients. RESULTS The hepatitis C virus subtype 1a was the most common subtype in the study population. Core aa substitution Arg70Gln was strongly associated with cirrhosis (OR = 2.49; 95% CI = 1.13 - 5.50; P = 0.020). Core aa 70 substitutions were more frequently observed in patients with the HCV subtype 1b than in patients with any other HCV subtypes (P < 0.001). Core aa 70 substitutions were also more common in patients with the rs12979860 TT genotype than in patients with non-TT genotypes (17.3% vs. 8.5%, P = 0.022) and also in rs8099917 non-TT genotypes than in the TT genotype (14.0% vs. 7.0%, P = 0.026). The HCV genotypes and rs8099917 polymorphisms were correlated in which HCV subtype 1b was in favor of rs8099917 GG and HCV subtype 3a favored rs8099917 TT (P = 0.021). Furthermore, the rs12979860 TT and rs8099917 GG genotypes showed significantly lower HCV RNA levels than the other genotypes (P < 0.001). CONCLUSIONS There is an as yet unexplained association between HCV and host parameters with unknown mechanisms in patients with chronic HCV infection. The assessments of core aa 70 substitution and polymorphisms near the IFNL3 gene could offer promising steps to improve the management of patients with HCV.
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Affiliation(s)
- Danesh Kadjbaf
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, IR Iran
| | - Maryam Keshvari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Disease (MELD) Center, Tehran, IR Iran
| | - Ali Pouryasin
- Armin Pathobiology Laboratory, Tehran, IR Iran
- Department of Biology, Arsanjan Branch, Islamic Azad University, Arsanjan, IR Iran
| | - Bita Behnava
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Disease (MELD) Center, Tehran, IR Iran
| | - Shima Salimi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Disease (MELD) Center, Tehran, IR Iran
| | - Leila Mehrnoush
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Disease (MELD) Center, Tehran, IR Iran
| | | | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Disease (MELD) Center, Tehran, IR Iran
- Armin Pathobiology Laboratory, Tehran, IR Iran
- Corresponding Author: Heidar Sharafi, Middle East Liver Disease (MELD) Center, P. O. Box: 14155-3651, Tehran, IR Iran. Tel: +98-2188945186, Fax: +98-2188945188, E-mail:
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13
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Impact of Mutations at Amino Acid 70 in Hepatitis C Virus (HCV) Genotype 1b Core Region on Hepatocarcinogenesis following Eradication of HCV RNA. J Clin Microbiol 2015; 53:3039-41. [PMID: 26135874 DOI: 10.1128/jcm.01457-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/26/2015] [Indexed: 12/13/2022] Open
Abstract
The impact of the HCV genotype 1b core amino acid (aa) 70 mutant on the cumulative rate of hepatocellular carcinoma following eradication of HCV RNA by antiviral therapy was investigated with the Q-Invader assay. Multivariate analysis based on 649 patients indicated that a core aa70 Q-Invader mutant level ≥20% is a predictor of hepatocellular carcinoma.
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14
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Mukaide M, Sugiyama M, Korenaga M, Murata K, Kanto T, Masaki N, Mizokami M. High-throughput and sensitive next-generation droplet digital PCR assay for the quantitation of the hepatitis C virus mutation at core amino acid 70. J Virol Methods 2014; 207:169-77. [PMID: 25019167 DOI: 10.1016/j.jviromet.2014.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 01/08/2023]
Abstract
The next-generation droplet digital polymerase chain reaction (ddPCR) assay employs an emulsion-based endpoint to quantitate the amount of target DNA and is more robust than real-time PCR when analyzing sequence variations. However, no studies have applied this technique to quantitate mutations in polymorphic viral genomes. To develop this approach, a ddPCR-based assay was designed to quantitate with high-throughput and sensitivity mutations and their frequencies in codon 70 of the hepatitis C virus (HCV) gene that encodes the Core protein. The assay was linear from 2.5 to 10(5) copies per assay, and the limit of detection of mutants in the presence of a 20,000-fold excess of wild type was 0.005%. The results correlated well with those obtained using the COBAS(®) TaqMan(®) HCV Test, which is a real-time PCR assay for the quantitative detection of HCV RNA in human serum (n=87; range, 2.3-7.7log10IU/mL; Pearson's R(2)=0.9120; p<0.0001). The median frequencies of mutations by ddPCR were 0.262% (n=55; range, 0-37.951%) and 99.687% (n=32; range, 52.191-100%) for the wild-type and mutant sequences, respectively, by direct sequencing. The ddPCR assay should be useful for quantitating mutations in other polymorphic viral genomes.
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Affiliation(s)
- Motokazu Mukaide
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan; Research and development department, SRL, Inc., 5-6-50 Shin, Hino, Tokyo 191-0002, Japan
| | - Masaya Sugiyama
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Masaaki Korenaga
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan.
| | - Kazumoto Murata
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Tatsuya Kanto
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Naohiko Masaki
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
| | - Masashi Mizokami
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohonodi, Ichikawa, Chiba 272-8516 Japan
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15
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Tadokoro K, Suzuki F, Kobayashi M, Kawamura Y, Sezaki H, Hosaka T, Akuta N, Kobayashi M, Suzuki Y, Saitoh S, Arase Y, Ikeda K, Kumada H. Rapid and high sensitive detection of Y93H amino acid substitution in HCV NS5A region using the PCR-Invader assay. ACTA ACUST UNITED AC 2014. [DOI: 10.2957/kanzo.55.720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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