Main 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.

Contents:

Standard Influenza protocols and surveillance

1. Influenza Virus isolation, preparation and titration

2. Vaccine selection and preparation

3. Isolation of clinical strains, sequencing, and reverse genetics

4. Diagnosis

5. Temporal-spatial analysis and real time surveillance of virus outbreaks (i.e. Ebola)

6. How the general population, internet, SNS helps predict epidemics (Overview)

Systems approach to discover Influenza virus-host interactions

7. Integrated Omics and Systems Virology (Overview)

8. Computational Biology of Infectious Diseases and study of virus evolution

9. Haploid Screening for host factors in virus infection

10. Proteomics, and affinity-MS virus interactome

11. Influenza Virus Replicon system in Yeast

12. Virus Receptor Hunting using Ligand Based Receptor Capture

13. Fully-automated screen using FDA-approved drug libraries

Dissecting cell biology of Influenza infection

14. Cell Biology of influenza virus-host interactions (Overview)

15. Influenza virus entry assays in tissue culture cells

16. DC-SIGN mediated virus uptake analysis

17. In vitro assay to detect virus disassembly during endocytic transit

18. Endosome fractionation and detection of viral and cellular antigens

19. Virus-liposome fusion assays using cryo EM

20. Visualizing influenza capsid uncoating in the cytoplasm of cells using combined cryo EM, SEM, and aqueous AFM

21. Quantitative PCR based analysis of Influenza virus endocytic escape

22. Virus uncoating detection using beta lactamase fused VLPs

23. Purification of viral polymerase using MultiBac system for structural biology

24. Influenza polymerase transcription analysis - vRNA vs cRNA

25. Image Analysis: From Single Cell analysis to High throughput imaging (Overview)

26. Single molecule FISH of incoming and egressing influenza vRNPs

27. Live imaging of replication and egress using a GFP influenza virus

28. Virus fluorescent labeling for imaging and super-resolution microscopy

29. Cryo EM of influenza virus progeny during budding

30. Assessing virus growth in cells depleted of host factors with siRNA or CRISPR/Cas9

Influenza animal models, physiological systems, and immunology

31. Animal models: mice, ferrets, pigs, monkeys and CRISPR animals (Overview)

32. IAV in vivo imaging, virus titration and immune response analysis

33. MxA and interferon (Overview)

34. Clinical bacteria and viral co-infection studies

35. 3D ex vivo culture system to study virus infection and entry