Main description:

This volume details the most updated concepts and experimental protocols developed by leading researchers in the field. Chapters guide readers through methods on bioinformatics tools, hepatitis c virus(HCV) cloning, culture, and purification, HCV life cycle, host immune responses, and small animal models. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Hepatitis C Virus Protocols aims to ensure successful results in the further study of this vital field.

Contents:

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 Fahnoe 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, Gines Avila, 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

Solene Denolly, Francois-Loic 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

Severin Coleon, Sonia Assil, and Marlene 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, Patrick Lau, and Steven KH Foung

28. Detection of Antibodies to HCV E1E2 by Lectin-Capture ELISA

Marian Major and Mansun Law

29. In vitro Neutralization Assay using Cultured Hepatitis C Virus

Jannick Prentoe and Jens Bukh

30. Standardized Method for the Study of Antibody Neutralization of HCV pseudoparticles (HCVpp)

Justin R. Bailey, Richard A. Urbanowicz, Jonathan K. Ball, Mansun Law, and Steven K. H. Foung

Part V: Small Animal Models

31. Detection of Antigen-specific CD8+ T Cells in the Livers of HCV Core Transgenic Mice

Dustin A. Cobb, Aditya P. Dandekar, and Young S. Hahn

32. Mice with Chimeric Human Livers and Their Applications

Donna N Douglas and Norman M Kneteman

33. Mouse Models for Studying HCV Vaccines and Therapeutic Antibodies

Jenna M. Gaska, Qiang Ding, and Alexander Ploss