Influenza Virus: Methods and Protocols

Description

This book provides researchers with widely used techniques for the study of virology, focusing on molecular biology and imaging to encourage mechanistic investigation of virus-host interactions. Chapters detail a broad range of methods from diagnosis, virus propagation, proteomics, haploid screening, lentiviral screening, virus entry, single molecule RNA imaging, correlative light and electron microscopy (CLEM), EM, light-sheet microscopy, biochemistry, viral transcription, physiological infection models, animal models, in vivo imaging, antigenic evolution, immunology to mathematical modelling. Reviews cover general influenza, clinical trials, both sides of the gain-of-function debate, and computational modelling. 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. Cutting-edge and thorough, Influenza Virus: Methods and Protocols aims to motivate experienced researchers and newcomers in the field and improve our overall understanding of influenza. Front Matter ....Pages i-xvi Understanding Influenza (Edward C. Hutchinson, Yohei Yamauchi)....Pages 1-21 Clinical Diagnosis of Influenza (Yoshinori Ito)....Pages 23-31 Influenza A Virus Genetic Tools: From Clinical Sample to Molecular Clone (Stéphanie Anchisi, Ana Rita Gonçalves, Béryl Mazel-Sanchez, Samuel Cordey, Mirco Schmolke)....Pages 33-58 Propagation and Titration of Influenza Viruses (Umut Karakus, Michel Crameri, Caroline Lanz, Emilio Yángüez)....Pages 59-88 Purification and Proteomics of Influenza Virions (Edward C. Hutchinson, Monika Stegmann)....Pages 89-120 Haploid Screening for the Identification of Host Factors in Virus Infection (Evelyn Fessler, Lucas T. Jae)....Pages 121-137 Phenotypic Lentivirus Screens to Identify Antiviral Single Domain Antibodies (Florian Ingo Schmidt)....Pages 139-158 Deciphering Virus Entry with Fluorescently Labeled Viral Particles (Anja B. Hoffmann, Magalie Mazelier, Psylvia Léger, Pierre-Yves Lozach)....Pages 159-183 Quantitative RT-PCR Analysis of Influenza Virus Endocytic Escape (Wen-Chi Su, Michael M. C. Lai)....Pages 185-194 Single-Molecule Sensitivity RNA FISH Analysis of Influenza Virus Genome Trafficking (Yi-ying Chou, Timothée Lionnet)....Pages 195-211 3D Electron Microscopy (EM) and Correlative Light Electron Microscopy (CLEM) Methods to Study Virus-Host Interactions (Inés Romero-Brey)....Pages 213-236 Correlative Light and Electron Microscopy of Influenza Virus Entry and Budding (Lorna Hodgson, Paul Verkade, Yohei Yamauchi)....Pages 237-260 Influenza Virus-Liposome Fusion Studies Using Fluorescence Dequenching and Cryo-electron Tomography (Long Gui, Kelly K. Lee)....Pages 261-279 Metal-Tagging Transmission Electron Microscopy and Immunogold Labeling on Tokuyasu Cryosections to Image Influenza A Virus Ribonucleoprotein Transport and Packaging (Martin Sachse, Isabel Fernández de Castro, Guillaume Fournier, Nadia Naffakh, Cristina Risco)....Pages 281-301 Live Imaging of Influenza Viral Ribonucleoproteins Using Light-Sheet Microscopy (Amar R. Bhagwat, Valerie Le Sage, Seema S. Lakdawala)....Pages 303-327 Purification of Unanchored Polyubiquitin Chains from Influenza Virions (Yasuyuki Miyake, Patrick Matthias, Yohei Yamauchi)....Pages 329-342 Assays to Measure the Activity of Influenza Virus Polymerase (Aartjan J. W. te Velthuis, Jason S. Long, Wendy S. Barclay)....Pages 343-374 In Vitro Models to Study Influenza Virus and Staphylococcus aureus Super-Infection on a Molecular Level (Christin Bruchhagen, Andre van Krüchten, Carolin Klemm, Stephan Ludwig, Christina Ehrhardt)....Pages 375-386 Infection of Cultured Mammalian Cells with Aerosolized Influenza Virus (Hannah M. Creager, Terrence M. Tumpey, Taronna R. Maines, Jessica A. Belser)....Pages 387-399 Animal Models in Influenza Research (Johanneke D. Hemmink, Catherine J. Whittaker, Holly A. Shelton)....Pages 401-430 Measuring Influenza Virus Infection Using Bioluminescent Reporter Viruses for In Vivo Imaging and In Vitro Replication Assays (Erik A. Karlsson, Victoria A. Meliopoulos, Vy Tran, Chandra Savage, Brandi Livingston, Stacey Schultz-Cherry et al.)....Pages 431-459 Selection of Antigenically Advanced Variants of Influenza Viruses (Gabriele Neumann, Shufang Fan, Yoshihiro Kawaoka)....Pages 461-486 Assessment of Influenza Virus Hemagglutinin Stalk-Specific Antibody Responses (Wen-Chun Liu, Raffael Nachbagauer, Florian Krammer, Randy A. Albrecht)....Pages 487-511 Analyses of Cellular Immune Responses in Ferrets Following Influenza Virus Infection (Anthony T. DiPiazza, Katherine A. Richards, Wen-Chun Liu, Randy A. Albrecht, Andrea J. Sant)....Pages 513-530 Parameter Estimation in Mathematical Models of Viral Infections Using R (Van Kinh Nguyen, Esteban A. Hernandez-Vargas)....Pages 531-549 Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza Viruses (Susanne Reimering, Alice C. McHardy)....Pages 551-565 Clinical Trials of Influenza Vaccines: Special Challenges (Adam Finn)....Pages 567-573 The Silver Lining in Gain-of-Function Experiments with Pathogens of Pandemic Potential (Michael J. Imperiale, Don Howard, Arturo Casadevall)....Pages 575-587 Why Do Exceptionally Dangerous Gain-of-Function Experiments in Influenza? (Marc Lipsitch)....Pages 589-608 How Computational Models Enable Mechanistic Insights into Virus Infection (Ivo F. Sbalzarini, Urs F. Greber)....Pages 609-631 Back Matter ....Pages 633-663