Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics -- SmallRNAs Isolation from Tissues of Grapevine and Woody Plants -- Double Stranded RNA-Enriched Preparations to Identify Viroids by Next Generation Sequencing -- Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing -- Work-Up of Human Blood Samples for Deep Sequencing of HIV-1 Genomes -- Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples -- Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities -- Different Approaches to Discover Mycovirus Associated to Marine Organisms -- Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections -- The Use of High Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen -- High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next Generation Sequencing -- Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and their Host Orchid -- DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method -- From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool -- Shannon Entropy to Evaluate Substitution Rate Variation among Viral Nucleotide Positions in Datasets of Viral siRNAs -- Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches.

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.