Viral Metagenomics: Methods and Protocols

✍ Scribed by Vitantonio Pantaleo,Michela Chiumenti (eds.)

• Publisher: Humana Press
• Year: 2018
• Tongue: English
• Leaves: 217
• Series: Methods in Molecular Biology 1746
• Edition: 1
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

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

✦ Subjects

Plant Sciences