Viral Metagenomics: Methods and Protocols

Front Matter ....Pages i-xi
 Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics  (Juris A. Grasis)....Pages 1-25
 Small RNA Isolation from Tissues of Grapevine and Woody Plants  (Annalisa Giampetruzzi, Michela Chiumenti, Angelantonio Minafra, Pasquale Saldarelli)....Pages 27-36
 Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing  (Beatriz Navarro, Francesco Di Serio)....Pages 37-43
 Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing  (Armelle Marais, Chantal Faure, Bernard Bergey, Thierry Candresse)....Pages 45-53
 Workup 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 et al.)....Pages 55-61
 Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples  (Ion Gutiérrez-Aguirre, Denis Kutnjak, Nejc Rački, Matevž Rupar, Maja Ravnikar)....Pages 63-75
 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities  (Sarah François, Denis Filloux, Emmanuel Fernandez, Mylène Ogliastro, Philippe Roumagnac)....Pages 77-95
 Different Approaches to Discover Mycovirus Associated to Marine Organisms  (Luca Nerva, Giovanna C. Varese, Massimo Turina)....Pages 97-114
 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 et al.)....Pages 115-130
 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, Martine Maes)....Pages 131-149
 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, Walter Pirovano)....Pages 151-159
 Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid  (Hanako Shimura, Chikara Masuta, Yasunori Koda)....Pages 161-172
 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 et al.)....Pages 173-180
 From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool  (Simone Rampelli, Silvia Turroni)....Pages 181-185
 Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs  (Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Masoud Shams-bakhsh, Walter Pirovano, Vitantonio Pantaleo)....Pages 187-195
 Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches  (Finny S. Varghese, Ronald P. van Rij)....Pages 197-213
Back Matter ....Pages 215-217