Viral Metagenomics, 1st ed. 2018
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1746

This volume explores the use of viral metagenomics to diagnose known viruses for plant and food production, human and animal health, and identifying viral vectors like insects. The chapters in this book cover topics, such as sRNAs isolation from tissues of grapevines and woody plants, high-resolution screening of arthropod and plant viral communities, identifying new pathogens in fish, detecting viruses in mycorrhizal fungi and their orchid host, and insect virus discovery through metagenomic and cell culture-based approaches. 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 comprehensive, Viral Metagenomics: Methods and Protocols is a valuable resource for researchers and specialists who are interested in learning more about this evolving field.

Preface…

Table of Contents…

Contributing Authors…

1. Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics

Juris A. Grasis

2. SmallRNAs Isolation from Tissues of Grapevine and Woody Plants

Annalisa Giampetruzzi, Michela Chiumenti, Angelantonio Minafra, and Pasquale Saldarelli

3. Double Stranded RNA-Enriched Preparations to Identify Viroids by Next Generation Sequencing

Beatriz Navarro and Francesco Di Serio

Armelle Marais, Chantal Faure, Bernard Bergey, and Thierry Candresse

5. Work-Up of Human Blood Samples for Deep Sequencing of HIV-1 Genomes

Marion Cornelissen, Astrid Gall, Antoinette van der Kuyl, Chris Wymant, François Blanquart, Christophe Fraser, and Ben Berkhout

6. Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples

Ion Gutiérrez-Aguirre, Denis Kutnjak, Nejc Rački, Matevž Rupar, and Maja Ravnikar  

7. Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities

Sarah François, Denis Filloux, Emmanuel Fernandez, Mylène Ogliastro, and Philippe Roumagnac

8. Different Approaches to Discover Mycovirus Associated to Marine Organisms

Luca Nerva, Giovanna C. Varese, and Massimo Turina

9. Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections

Nikoletta Czotter, János Molnár, Réka Pesti, Emese Demián, Dániel Baráth, Tünde Varga, and Éva Várallyay

10. The Use of High Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen

Kris De Jonghe, Annelies Haegeman, Yoika Foucart, and Martine Maes

11. High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next Generation Sequencing

Arnfinn Lodden Økland, Are Nylund, Ali May, Adalberto Costessi, and Walter Pirovano

12. Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and their Host Orchid

Hanako Shimura, Chikara Masuta, and Yasunori Koda

13. DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method

Bachir Balech, Alfonso Monaco, Michele Perniola, Monica Santamaria, Giacinto Donvito, Saverio Vicario, Giorgio Maggi, and Graziano Pesole

14. From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

Simone Rampelli and Silvia Turroni

15. Shannon Entropy to Evaluate Substitution Rate Variation among Viral Nucleotide Positions in Datasets of Viral siRNAs

Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Walter Pirovano, and Vitantonio Pantaleo

16. Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches

Finny S. Varghese and Ronald P. van Rij

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts