Part I: Review of Hepatitis C Virus and Bioinformatic Tools 1. Overview of Direct Acting Antiviral Drugs and Drug Resistance of Hepatitis C Virus Darrick K. Li and Raymond T. Chung 2. Similarities and Differences between HCV Pseudoparticle (HCVpp) and Cell Culture HCV (HCVcc) in the Study of HCV Laura Riva and Jean Dubuisson 3. Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR) Yun Zhang, Christian Zmasek, Guangyu Sun, Christopher N. Larsen, and Richard H. Scheuermann Part II: Methods for Virus Cloning, Culture, and Purification 4. Establishment of Replication-competent HCV Strain with Minimum Modifications Takanobu Kato, Asako Murayama, and Takaji Wakita 5. Full-length Open Reading Frame Amplification of Hepatitis C Virus Ulrik Fahnøe and Jens Bukh 6. InFusion Cloning for the Generation of Biologically Relevant HCV Chimeric Molecular Clones Barnabas King, Richard Urbanowicz, Alexander W. Tarr, Jonathan K. Ball, and C. Patrick McClure 7. Production and Purification of Cell Culture Hepatitis C Virus Cynthia de la Fuente and Maria Teresa Catanese 8. Embryonic or Induced Pluripotent Stem Cell-derived Hepatocellular Systems for HCV Culture Xianfang Wu and Viet Loan Dao Thi Part III: Methods for the Study of HCV Life Cycle 9. Molecular Identification of Transmitted/Founder Hepatitis C Viruses and their Progeny by Single Genome Sequencing Hui Li, Muhammad N. Zahid, Shuyi Wang, and George M. Shaw 10. A Cell Culture Model for Persistent HCV Infection Victoria Castro, Ginés Ávila, Lidia Mingorance, and Pablo Gastaminza 11. Expression Cloning of Host Factors Required for the HCV Replication Cycle Sandra Ciesek and Thomas von Hahn 12. Application of Deep Mutational Scanning in Hepatitis C Virus Nicholas C. Wu and Hangfei Qi 13. Studying the Hepatitis C Virus-induced Epigenetic Signature after Cure with Direct-acting Antivirals Shira Perez and Meital Gal-Tanamy 14. Measuring Hepatitis C Virus Envelopment by using a Proteinase K Protection Assay Allison E. Roder and Stacy M. Horner 15. Membrane Fusion Assays for Studying Entry Hepatitis C Virus into Cells Solène Denolly, François-Loïc Cosset, and Natalia Freitas 16. Functional Characterization of Apolipoproteins in the HCV Life Cycle Luhua Qiao and Guangxiang (George) Luo 17. Investigating Hepatitis C Virus Infection Using Super-resolution Microscopy Pedro Matos Pereira, Caron Jacobs, and Joe Grove 18. Live Cell Imaging of Hepatitis C Virus Trafficking in Hepatocytes Yasmine Baktash and Glenn Randall 19. Cloning and Analysis of Authentic Patient-derived HCV E1/E2 Glycoproteins Richard A. Urbanowicz, Jonathan K. Ball, and Alexander W. Tarr 20. Simultaneous Quantification of Hepatitis C virus Envelope Glycoproteins E1 and E2 by Dual-color Fluorescence Immunoblot Analysis Fang Chen, Erick Giang, Radhika Gopal, and Mansun Law 21. Overcoming Challenges of Hepatitis C Virus Envelope Glycoprotein Production in Mammalian Cells Samantha A. Yost, Jillian Whidby, Abdul G. Khan, Yuanyuan Wang, and Joseph Marcotrigiano Part IV: Methods for Studying Immune Responses 22. Monitoring of Interferon Response Triggered by Cells Infected by Hepatitis C Virus or Other Viruses upon Cell-cell Contact Séverin Coléon, Sonia Assil, and Marlène Dreux 23. Complement Regulation and Immune Evasion by Hepatitis C Virus Young-Chan Kwon and Ranjit Ray 24. Direct ex vivo Functional Analysis of HCV-specific T Cells Su-Hyung Park and Eui-Cheol Shin 25. Simultaneous Analysis of HCV-specific CD4 + and CD8 + T Cells by Multi-color Flow Cytometry David Wolski and Georg M Lauer 26. Probing the Antigenicity of HCV Envelope Glycoproteins by Phage Display Antibody Technology Erick Giang, Fernando Aleman, and Mansun Law 27. Isolation of HCV Neutralizing Antibodies by Yeast Display Zhenyong Keck, Yong Wang, Patri sakriti opis