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
4. Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput SequencingArmelle 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, 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
