Analyses of the dynamics of drug-resistant hepatitis C virus clones focusing on the defective HCV clones

• Project/Area Number: 16K09358
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Gastroenterology
• Research Institution: Kyoto University
• Principal Investigator: Ohtsuru Shigeru 京都大学, 医学研究科, 准教授 (60437225)
• Co-Investigator(Kenkyū-buntansha): 上田 佳秀 京都大学, 医学研究科, 講師 (90378662) ; 小池 薫 京都大学, 医学研究科, 教授 (10267164) ; 竹田 治彦 千葉大学, 予防医学センター, 日本学術振興会特別研究員(PD) (40647525)
• Project Period (FY): 2016-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: C型肝炎ウイルス / 欠損型クローン / 薬剤耐性変異 / 肝臓学 / ディープシークエンス / 第3世代シークエンサー / 欠損型ウイルス / 薬剤耐性 / ディープシークエンサー解析

Outline of Final Research Achievements

The aim of this study is to unveil the dynamics of drug-resistant hepatitis C virus clones emerging after interferon-free therapies focusing on the defective HCV clones. We analyzed the dynamics of major drug-resistant nucleotide changes in the serum samples collected by the patients who received interferon-free therapies in Kyoto University Hospital and related hospitals using deep sequencing method. We detected 8 cases harboring defective HCV clones before treatment, some of which disappeared during the treatment period. We also focused on the third-generation sequencing platform, which can determine heterogeneous population of defective and non-defective HCV clones in the single-molecular resolution. Establishing this novel methodology, we demonstrated the dynamic changes of the quasispecies of HCV clones which possess long deletions on the viral genome, which would be shedding light on the pathogenesis of chronic HCV infection.

Academic Significance and Societal Importance of the Research Achievements

薬剤耐性変異の出現は完全なHCVの排除の障壁になっており、本研究では塩基置換だけではなく欠損型クローンという構造異常に着目した点に新規性があり、社会的な脅威である肝炎ウイルス撲滅にむけた病態解明に貢献したと考えられる。

Research Products

• [Journal Article] Single-molecular real-time deep sequencing reveals the dynamics of multidrug resistant haplotypes and structural variations in the hepatitis C virus genome. (2020)
  • Author(s): Yamashita T, Takeda H, Takai A, Arasawa S, Nakamura F, Mashimo Y, Hozan M, Ohtsuru S, Seno H,Ueda Y, Sekine A
  • Journal Title: Sci. Rep, Volume: 10 Issue: 1 Pages: 2651-2651
  • DOI: 10.1038/s41598-020-59397-2
  • NAID: 120006844879
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Exploring the hepatitis C virus genome using single molecule real-time sequencing. (2019)
  • Author(s): Takeda H, Yamashita T, Ueda Y, Sekine A
  • Journal Title: World J Gastroenterol Volume: 25 Issue: 32 Pages: 4661-4672
  • DOI: 10.3748/wjg.v25.i32.4661
  • Peer Reviewed / Open Access
• [Journal Article] The Oncogenic Potential of Regenerative Nodules in Cirrhotic Liver Confirmed By Total Transcriptome Analysis. (2018)
  • Author(s): Takeda H, Ohtsuru S, et al.
  • Journal Title: Hepatology Volume: 68
• [Journal Article] Third-generation sequencing unveils the evolution of multi-drug resistant hepatitis C virus clones during direct-acting antiviral therapy. (2017)
  • Author(s): H. Takeda, S. Ohtsuru, et al.
  • Journal Title: Hepatology Volume: 66, NUMBER1 (SUPPL)
• [Presentation] Single molecule real-time sequencing unveils the evolution of multi-drug resistant hepatitis C virus clones during direct-acting antiviral therapy. (2018)
  • Author(s): Takeda H, Ohtsuru S, et al.
  • Organizer: UEG Week (United European Gastroenterology)（国際学会）
• [Presentation] The Oncogenic Potential of Regenerative Nodules in Cirrhotic Liver Confirmed By Total Transcriptome Analysis. (2018)
  • Author(s): Takeda H, Ohtsuru S, et al.
  • Organizer: AASLD (American Association for the Study of Liver Diseases)（国際学会）
• [Presentation] Third-generation sequencing unveils the evolution of multi-drug resistant hepatitis C virus clones during direct-acting antiviral therapy. (2017)
  • Author(s): Haruhiko Takeda, Yoshihide Ueda, Tadashi Inuzuka, Shigeru Ohtsuru, Hiroshi Seno, Akihiro Sekine, Hiroyuki Marusawa
  • Organizer: AASLD (American Association for the Study of Liver Diseases)
  • Int'l Joint Research
• [Presentation] EMERGENCE OF MULTIDRUG-RESISTANT HEPATITIS C VIRUS DURING INTERFERON-FREE THERAPY WITH ASUNAPREVIR AND DACLATASVIR AFTER SIMEPREVIR-BASED TRIPLE THERAPY FOR RECURRENT HEPATITIS C AFTER LIVER TRANSPLANTATION (2016)
  • Author(s): Yoshihide Ueda, Haruhiko Takeda, Shigeru Ohtsuru, S. Uemoto, H. Marusawa
  • Organizer: United European Gastroenterology 2016
  • Place of Presentation: Vienna（Austria）
  • Year and Date: 2016-10-15
  • Int'l Joint Research