Preface…
Table of Contents…
Contributing Authors…
1. Exploring the Archaeal Virosphere by Metagenomics
Yifan Zhou, Yongjie Wang, David Prangishvili, and Mart Krupovic
2. From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
Simone Rampelli, Silvia Turroni, and Marco Candela
3. Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses
Kira Moon and Jang-Choen Cho
4. Discovery and Identification of Viruses Infecting Oomycetes
Anna Poimala and Eeva J. Vainio
5. Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction using Improved Assemble Tools
Kota Kambara, Hanako Shimura, Kaien Fujino, and Chikara Masuta
6. Determination of the Mycovirome of a Necrotrophic Fungus
Ana Ruiz-Padilla, Julio L. Rodríguez-Romero, Davide Pacifico, and María A. Ayllón
7. From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species
Enrique A. Guevara-Rivera, Edgar A. Rodríguez-Negrete, Rosa Lozano-Durán, Eduardo R. Bejarano, Alan M. Torres-Calderón, Ángela P. Arce-Leal, Norma E. Leyva-López, and Jesús Méndez-Lozano
8. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters
Enric Cuevas-Ferrando, Gloria Sánchez, and Alba Pérez-Cataluña
9. Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples
Quentin Lamy-Besnier and Julian R. Garneau
10. Exploration and Retrieval of Virus-Related Molecular Data using ExTaxsI: The Monkeypox Use Case
Alberto Brusati, Giulia Agostinetto, Antonia Bruno, Maurizio Casiraghi, Dario Pescini, Anna Sandionigi, and Bachir Balech
11. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics
María Cebriá-Mendoza, Wladimiro Díaz, Rafael Sanjuán, and José M. Cuevas
12. Targeted Whole Genome Sequencing of the Capripoxvirus Genome from Clinical Tissue Samples and Lyophilized Vaccine Batches
Elisabeth Mathijs and Frank Vandenbussche
13. Viromes of Plants Determined by High-Throughput Sequencing of Virus Derived siRNAs
Nikoletta Jaska-Czotter, Zsuzanna Nagyne-Galbacs, Almash Jahan, Emese Demian, and Éva Várallyay
14. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids
Rachelle Bester and Hans J. Maree
15. Identification of DNA Viruses in Ancient DNA from Herbarium Samples
Gianluca Grasso, Silvia Rotunno, Régis Debruyne, Lucie Bittner, Laura Miozzi, Roland Marmesse, and Valeria Bianciotto
16. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses
Giulia Tarquini, Simone Maestri, Paolo Ermacora, and Marta Martini
17. Detection of Plant Viruses using Nanopore Sequencing Based Metagenomic Approach
Anja Pecman, Nataša Mehle and Denis Kutnjak
18. Application of Nanopore-Based Sequencing to Identify Virus Infections in Woody Plants
Serafina Serena Amoia, Michela Chiumenti, and Angelantonio Minafra
19. Distribution of Small RNAs Along Transposable Elements in Vitis vinifera during Somatic Embryogenesis
Silvia Rotunno, Paola Leonetti, Gyorgy Szittya, and Vitantonio Pantaleo
Subject Index List…