Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities

Methods Mol Biol. 2018:1746:77-95. doi: 10.1007/978-1-4939-7683-6_7.

Abstract

Viral metagenomic approaches have become essential for culture-independent and sequence-independent viral detection and characterization. This chapter describes an accurate and efficient approach to (1) concentrate viral particles from arthropods and plants, (2) remove contaminating non-encapsidated nucleic acids, (3) extract and amplify both viral DNA and RNA, and (4) analyze high-throughput sequencing (HTS) data by bioinformatics. Using this approach, up to 96 arthropod or plant samples can be multiplexed in a single HTS library.

Keywords: Arthropod; Diagnostic; High-throughput sequencing; Metagenomics; Plant; Random amplification; Virus discovery.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arthropods / virology*
  • Computational Biology
  • DNA, Viral / analysis*
  • DNA, Viral / genetics
  • DNA, Viral / isolation & purification
  • Genome, Viral*
  • High-Throughput Nucleotide Sequencing / methods*
  • Metagenomics*
  • Plants / virology*
  • Viruses / genetics*
  • Viruses / isolation & purification

Substances

  • DNA, Viral