Comparative Viral Metagenomics of Environmental Samples from Korea

Abstract

The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts.

The Global Dispersion of Pathogenic Microorganisms by Dust Storms and Its Relevance to Agriculture

“…Fluorescence in situ hybridization may allow phylogenetic identification of bacteria (Amann et al, 1996;Korzeniewska and Harnisz, 2012). Electron microscopy has been used to enumerate smaller particles such as viruses and allows their classification based on their morphology (Hanssen et al, 2010;Kim et al, 2013;Whon et al, 2012;Yamaguchi et al, 2012).…”

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

“…For example, use of NGS technologies has played a key role in the identification of Israeli acute paralysis virus associated with colony collapse disorder in honeybees (16) and of a polyomavirus in human Merkel cell carcinoma (30). Rapid development in NGS technologies has dramatically reduced the cost and time for pathogen identification by metagenomics approaches, leading to a recent explosion in metagenomics studies on viruses and viroids in plants (46,61,84). After a short introduction of the main NGS platforms currently available, this article reviews recent applications of the homology-dependent and homology-independent metagenomics approaches to the identification and detection of viruses and viroids in plants.…”

Peer Review #1 of "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils (v0.1)"

“…Both allow qualitative observations of viral sequences but preclude quantitative ecological inferences. Specifically, MDA causes dramatic shifts in relative abundances of DNA templates, which impact subsequent estimates of viral populations diversity, and, most dramatically, over-amplify ssDNA viruses (Binga, Lasken, and Neufeld, 2008;Yilmaz, Allgaier, and Hugenholtz 2010;Kim, Whon, and Bae 2013;Marine et al 2014). RP-SISPA is biased towards the most abundant viruses or largest genomes, and leads to uneven coverage along the amplified genomes (Karlsson, Belák, and Granberg 2013).More recently, quantitative amplification methods have emerged that use transposon-mediated tagmentation (Nextera, for dsDNA;Trubl et al 2018;Segobola et al 2018) or acoustic shearing to fragment and a custom adaptase (Accel-NGS 1S Plus, for dsDNA and ssDNA; Roux et al 2016;Rosario et al 2018) to ligate adapters to DNA templates, before PCR amplification is used to obtain enough material for sequencing.…”