Virus-Host Interactions Methods and Protocols

This detailed volume spotlights methods to investigate a variety of virus-host interactions in humans, other mammals, fish, or insects. It explores viruses such as white spot syndrome virus (WSSV), honeybee viruses, Nipah virus, EBV, SVCV, HSV-1, HIV-1, A H1N1, and SARS-CoV-2, as well as applications of techniques such as qPCR, serum antibody responses, 4C analysis, cell membrane fusion, biosensors, computational modelling, quantitative proteomics, and other genetic tools to decipher those viral infections and interactions. Written for 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

1. Genetic Tools for Studying the Roles of Sphingolipids in Viral Infections

            Gaelen Guzman, Cameron Creek, Scotland Farley, and Fikadu G. Tafesse

 

2. Detection of Serum Antibody Responses in Nipah Virus-Infected Pigs

            Kerstin Fischer, Bradley Pickering, and Sandra Diederich

 

3. Computational Integration of HSV-1 Multi-Omics Data

            Caroline C. Friedel

 

4. A Cell Membrane Fusion Assay for the Fish Pathogen Spring Viremia of Carp Virus (SVCV)

            Ainhoa Gómez, David Talavera, and Luis Perez

 

5. Viral Quantification in Bee Samples Using Synthetic DNA Sequences with Real Time PCR (qPCR)

            Nuria Morfin, Jose O. Macías-Macías, and Ernesto Guzman-Novoa

 

6. Inhibition of White Spot Syndrome Virus (WSSV) in Pacific White Shrimp (Litopenaeus vannamei) Using Polyamine-Modi?ed Carbon Quantum Dots

            Hung-Yun Lin, John Han-You Lin, Han-Jia Lin, and Li-Li Chen

 

7. Computational Modeling of IN-CTD/TAR Complex to Elucidate Additional Strategies to Inhibit HIV-1 Replication

            Liming Qiu, Savita Bhutoria, Ganjam V. Kalpana, and Xiaoqin Zou

 

8. Protein-Protein and Protein-RNA Interaction Assays to Determine Similarity of INI1/SMARCB1 and TAR RNA in Binding to HIV-1 Integrase

            Ganjam V. Kalpana

 

9. 4C Analysis of EBV-Host DNA Interactome

            Kyoung-Dong Kim and Paul M. Lieberman

 

10. Detection Methods for H1N1 Virus

            Ravina, Subodh, Krishna Kant Sharma, and Hari Mohan

 

11. Detection of SARS-CoV-2 in Human Breast Milk

            Rüdiger Groß, Carina Conzelmann, Jan Münch, and Janis A. Müller

 

12. The Rhizopus Holobiont: A Model to Decipher Fungal-Bacterial-Viral Symbioses

            Astrid N. Espino-Vázquez, Gonzalo Córdova-López, J. Francisco Cabrera-Rangel, J. Valeria Mendoza-Servín, and Laila P. Partida-Martínez

 

13. Combining Metabolic Pulse Labeling and Quantitative Proteomics to Monitor Protein Synthesis upon Viral Infection

            Boris Bogdanow, Niki Katsimani, Fan Liu, and Matthias Selbach

 

14. Three-Dimensional Human Brain Organoids to Model HIV-1 Neuropathogenesis

            Roberta S. dos Reis, Shilpa Sant, and Velpandi Ayyavoo

 

15. Characterization of SARS-CoV-2 Glycoprotein Using a Quantitative Cell-Cell Fusion System

            Xiuyuan Ou and Zhaohui Qian

 

16. A Lentiviral Pseudotype System to Characterize SARS-CoV-2 Glycoprotein

            Dan Mi, Jiaxin Hu, and Zhaohui Qian