Viral Metagenomics: Methods and Protocols

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 Racki, Matevz 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 Malgorzata 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