Skip to main content
SpringerLink
Log in

Viral Metagenomics

Methods and Protocols

  • Book
  • © 2024
  • Latest edition

Overview

Editors:
  1. Vitantonio Pantaleo

    1. Institute for Sustainable Plant Protection, National Research Council, Bari, Italy

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Laura Miozzi

    1. Institute for Sustainable Plant Protection, National Research Council, Torino, Italy

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2732)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

About this book

This second edition volume expands on the previous edition with discussions about the latest viral metagenomics aspects covering a range of different specimens such as soil, freshwater, wastewater, fecal samples, blood plasma, clinical tissues, fungi, and herbarium samples. Chapters also look at different viral groups including archaeal viruses, eukaryotic viruses, phages, mycoviruses, and circular DNA viruses. Techniques required for studying the three viral metagenomic steps of samples processing, library construction, and analysis of data are also discussed. 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 cutting-edge, Vital Metagenomics: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about this important and developing field.


Similar content being viewed by others

Keywords

Table of contents (19 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Exploring the Archaeal Virosphere by Metagenomics

    • Yifan Zhou, Yongjie Wang, David Prangishvili, Mart Krupovic
    Pages 1-22

  3. From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

    • Simone Rampelli, Silvia Turroni, Marco Candela
    Pages 23-28

  4. Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses

    • Kira Moon, Jang-Cheon Cho
    Pages 29-44

  5. Discovery and Identification of Viruses Infecting Oomycetes

    • Anna Poimala, Eeva Vainio
    Pages 45-65

  6. Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction Using Improved Assemble Tools

    • Kota Kambara, Hanako Shimura, Kaien Fujino, Chikara Masuta
    Pages 67-81

  7. Determination of the Mycovirome of a Necrotrophic Fungus

    • Ana Ruiz-Padilla, Julio L. Rodríguez-Romero, Davide Pacifico, Marco Chiapello, María A. Ayllón
    Pages 83-101

  8. 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 et al.
    Pages 103-117

  9. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters

    • Enric Cuevas-Ferrando, Gloria Sánchez, Alba Pérez-Cataluña
    Pages 119-131

  10. Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples

    • Quentin Lamy-Besnier, Julian R. Garneau
    Pages 133-144

  11. 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 et al.
    Pages 145-154

  12. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics

    • María Cebriá-Mendoza, Wladimiro Díaz, Rafael Sanjuán, José M. Cuevas
    Pages 155-164

  13. Targeted Whole Genome Sequencing of the Capripoxvirus Genome from Clinical Tissue Samples and Lyophilized Vaccine Batches

    • Elisabeth Mathijs, Frank Vandenbussche
    Pages 165-177

  14. Viromes of Plants Determined by High-Throughput Sequencing of Virus-Derived siRNAs

    • Nikoletta Jaksa-Czotter, Zsuzsanna Nagyné Galbács, Almash Jahan, Emese Demián, Éva Várallyay
    Pages 179-198

  15. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids

    • Rachelle Bester, Hans J. Maree
    Pages 199-219

  16. Identification of DNA Viruses in Ancient DNA from Herbarium Samples

    • Gianluca Grasso, Silvia Rotunno, Régis Debruyne, Lucie Bittner, Laura Miozzi, Roland Marmeisse et al.
    Pages 221-234

  17. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses

    • Giulia Tarquini, Simone Maestri, Paolo Ermacora, Marta Martini
    Pages 235-249

  18. Detection of Plant Viruses Using Nanopore Sequencing Based Metagenomic Approach

    • Anja Pecman, Nataša Mehle, Denis Kutnjak
    Pages 251-264

  19. Application of Nanopore-Based Sequencing to Identify Virus Infections in Woody Plants

    • Serafina Serena Amoia, Michela Chiumenti, Angelantonio Minafra
    Pages 265-278

  20. Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis

    • Silvia Rotunno, Paola Leonetti, György Szittya, Vitantonio Pantaleo
    Pages 279-286
Back to top

Editors and Affiliations

  • Institute for Sustainable Plant Protection, National Research Council, Bari, Italy

    Vitantonio Pantaleo

  • Institute for Sustainable Plant Protection, National Research Council, Torino, Italy

    Laura Miozzi

Bibliographic Information

  • Book Title: Viral Metagenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Vitantonio Pantaleo, Laura Miozzi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3515-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3514-8Published: 08 December 2023

  • Softcover ISBN: 978-1-0716-3517-9Due: 08 January 2024

  • eBook ISBN: 978-1-0716-3515-5Published: 07 December 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XII, 288

  • Number of Illustrations: 8 b/w illustrations, 30 illustrations in colour

  • Topics: Virology, Chemistry/Food Science, general, Biomaterials, Genetics and Genomics

Publish with us

Policies and ethics

Back to top

Search

Navigation