Description
Although antiviral drugs have been successfully developed for some viral diseases, there remains a clear, unmet medical need to develop novel antiviral agents for the control and management of many viruses that currently have no or limited treatment options as well as a need to overcome the limitations associated with the existing antiviral drugs, such as adverse effects and emergence of drug-resistant mutations. The second edition of Antiviral Methods and Protocols features: All chapters are new and written by experts in the field, reflecting the major recent technical advances in antiviral research and discovery. This edition focuses on many important human viruses, such as human immunodeficiency virus type 1 (HIV-1), hepatitis viruses (hepatitis B and C viruses), herpes viruses, human respiratory syncytial virus (RSV), and influenza virus, while also featuring some important emerging viruses, such as dengue virus, West Nile virus, and chikungunya virus. As a volume in the highly successful Methods in Molecular Biology series, 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. Comprehensive and cutting-edge, Antiviral Methods and Protocols, Second Edition will serve as an excellent laboratory reference for pharmaceutical and academic biologists, medicinal chemists, and pharmacologists as well as for virologists in the field of antiviral research and drug discovery. Part I: Human Immunodeficiency Virus Type 1 (HIV-1) 1. A Fluorescence-Based High Throughput Screening Assay to Identify HIV-1 Inhibitors Peggy Geluykens, Koen Van Acker, Johan Vingerhoets, Christel Van den Eynde, Marnix Van Loock, and Gry Dams 2. A Homogeneous Time-Resolved Fluorescence Assay to Identify Inhibitors of HIV-1 Fusion Liesbet Smeulders, Lieve Bunkens, Inge Vereycken, Koen Van Acker, Pascale Holemans, Emmanuel Gustin, Marnix Van Loock, and Gry Dams 3. Identification of HIV-1 Reverse Transcriptase Inhibitors Using a Scintillation Proximity Assay Bertrand Van Schoubroeck, Marnix Van Loock, Tania Ivens, Pascale Dehertogh, Dirk Jochmans, and Gry Dams 4. Biochemical Screening Assays to Identify HIV-1 Integrase Inhibitors Marleen Clynhens, Alexandra Smets, Inge Vereycken, Marnix Van Loock, Reginald Clayton, Geert Meersseman, and Olivia Goethals 5. HIV-1 Genotyping of the Protease-Reverse Transcriptase and Integrase Genes to Detect Mutations that Confer Anti-Retroviral Resistance Peter Van den Eede, Liesbeth Van Wesenbeeck, Yvan Verlinden, Maxim Feyaerts, Veerle Smits, Ann Verheyen, Leen Vanhooren, Alain Deloof, Jorge Villacian, and Theresa Pattery Part II: Hepatitis Viruses 6. In Vitro Kinetic Profiling of Hepatitis C Virus NS3 Protease Inhibitors by Progress Curve Analysis Rumin Zhang and William T. Windsor 7. A Novel Hepatitis C Virus NS5B Polymerase Assay of De Novo Initiated RNA Synthesis Directed from a Heteropolymeric RNA Template Eric Ferrari and Hsueh-Cheng Huang 8. Selecting and Characterizing Drug-Resistant Hepatitis C Virus Replicon Inge Vliegen, Leen Delang, and Johan Neyts 9. A Cellular Replicon-Based Phenotyping Assay to Determine Susceptibility of Hepatitis C Virus Clinical Isolates to NS3/4A Protease Inhibitors Leen Vijgen, Jannick Verbeeck, Barbara Van Kerckhove, Jan Martin Berke, Diana Koletzki, Gregory Fanning, and Oliver Lenz 10. Expression and Purification of Hepatitis C Virus Protease from Clinical Samples Liesbet van der Helm 11. Surface Plasmon Resonance as a Tool to Select Potent Drug Candidates for Hepatitis C Virus NS5B Polymerase Erna Cleiren, Benoit Devogelaere, and Katleen Fierens 12. Amplification and Sequencing of the Hepatitis C Virus NS3/4A Protease and the NS5B Polymerase Regions for Genotypic Resistance Detection of Clinical Isolates of Subtypes 1a and 1b Diana Koletzki, Theresa Pattery, Bart Fevery, Leen Vanhooren, and Lieven J. Stuyver 13. A Southern Blot Assay for Detection of Hepatitis B Virus Covalently Closed Circular DNA from Cell Cultures Dawei Cai, Hui Nie, Ran Yan, Ju-Tao Guo, Timothy M. Block, and Haitao Guo 14. In Vitro Phenotyping of Recombinant Hepatitis B Virus Containing the Polymerase/Reverse Transcriptase Gene from Clinical Isolates Yang Liu and Kathryn M. Kitrinos Part III: Flaviviruses 15. Cell-Based Antiviral Assays for Screening and Profiling Inhibitors Against Dengue Virus Edwin Yunhao Gong, Marleen Clynhens, Tania Ivens, Pedro Lory, Kenny Simmen, and Guenter Kraus 16. A Duplex Real-Time RT-PCR Assay for Profiling Inhibitors of Four Dengue Serotypes Edwin Yunhao Gong, Alexandra Smets, Nick Verheyen, Marleen Clynhens, Emmanuel Gustin, Pedro Lory, and Guenter Kraus 17. High Throughput Screening Using Dengue Virus Reporter Genomes Wolfgang Fischl and Ralf Bartenschlager 18. Fluorimetric and HPLC-Based Dengue Virus Protease Assays Using a FRET Substrate Christoph Nitsche and Christian D. Klein 19. Expression and Purification of Dengue Virus NS5 Polymerase and Development of a High Throughput Enzymatic Assay for Screening Inhibitors of Dengue Polymerase Edwin Yunhao Gong, Hannah Kenens, Tania Ivens, Koen Dockx, Katrien Vermeiren, Genevive Vandercruyssen, Benoit Devogelaere, Pedro Lory, and Guenter Kraus 20. Detection and Quantification of Flavivirus NS5 Methyl-transferase Activities Siew Pheng Lim, Christophe Bodenreider , and Pei-Yong Shi 21. Testing Antiviral Compounds in a Dengue Mouse Model Wouter Schul, Andy Yip, and Pei-Yong Shi 22. Construction of Self-Replicating Subgenomic West Nile Virus Replicons for Screening Antiviral Compounds Sofia L. Alcaraz-Estrada, Erin Donohue Reichert, and Radhakrishnan Padmanabhan Part IV: Herpes Viruses 23. Methods for Screening and Profiling Inhibitors of Herpes Simplex Viruses Edwin Yunhao Gong 24. In Vivo Evaluation of Antiviral Efficacy Against Genital Herpes Using Mouse and Guinea Pig Models Frances Valencia, Ronald L. Veselenak, and Nigel Bourne 25. A Fluorescence-Based High Throughput Screening Assay for Identifying Human Cytomegalovirus Inhibitors Christel Van den Eynde, Ellen Van Damme, Tania Ivens, and Edwin Yunhao Gong Part V: Respiratory Viruses 26. A Fluorescence-Based High Throughput Antiviral Compound Screening Assay Against Respiratory Syncytial Virus Leen Kwanten, Ben De Clerck, and Dirk Roymans 27. Screening and Evaluation of Anti-Respiratory Syncytial Virus Compounds in Cultured Cells Anna Lundin, Tomas Bergstrm, and Edward Trybala 28. Evaluation of Antiviral Efficacy Against Human Respiratory Syncytial Virus Using Cotton Rat and Mouse Models Joke Van den Berg, Leen Kwanten, and Dirk Roymans 29. In Vivo Evaluation of Antiviral Compounds on Respiratory Syncytial Virus Using a Juvenile Vervet Monkey (Chlorocebus pygerythrus) Infection Model Lieselot Houspie, Hans Stevens, Maina Ngotho, Els Keyaerts, Gabriela Ispas, Ren Verloes, Marc Van Ranst, and Piet Maes 30. Methods to Determine Mechanism of Action of Anti-Influenza Inhibitors Angela Luttick, Stephanie Hamilton, and Simon P. Tucker 31. Methods for Evaluation of Antiviral Efficacy Against Influenza Virus Infections in Animal Models Donald F. Smee and Dale L. Barnard Part VI: Alphaviruses 32. Development of a High Throughput Antiviral Assay for Screening Inhibitors of Chikungunya Virus and Generation of Drug-Resistant Mutations in Cultured Cells Edwin Yunhao Gong, Jean-Franois Bonfanti, Tania Ivens, Marijke Van der Auwera, Barbara Van Kerckhove, and Guenter Kraus 33. A Mouse Model of Chikungunya Virus with Utility in Antiviral Studies Ashley Dagley and Justin G. Julander
