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