Metagenomic Approaches for Detecting Viral Diversity in Water Environments
Publication: Journal of Environmental Engineering
Volume 145, Issue 8
Abstract
Methods for detecting and monitoring known and emerging viral pathogens in the environment are imperative for understanding risk and establishing regulatory standards in environmental and public health sectors. Next-generation sequencing (NGS) has uncovered the diversity of entire microbial populations, enabled discovery of novel organisms, and allowed pathogen surveillance. Metagenomics, the sequencing and analysis of all genetic material in a sample, is a detection method that circumvents the need for cell culturing and prior understanding of microbial assemblies, which are necessary in traditional detection methods. Advancements in NGS technologies have led to subsequent advancements in data analysis methodologies and practices to increase specificity, and accuracy of metagenomic studies. This paper highlights applications of metagenomics in viral pathogen detection, discusses suggested best practices for detecting the diversity of viruses in environmental systems (specifically water environments), and addresses the limitations of virus detection using NGS methods. Information presented in this paper will assist researchers in selecting an appropriate metagenomics approach for obtaining a comprehensive view of viruses in water systems.
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Journal of Environmental Engineering
Volume 145 • Issue 8 • August 2019
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©2019 American Society of Civil Engineers.
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Received: Jul 14, 2018
Accepted: Dec 7, 2018
Published online: May 22, 2019
Published in print: Aug 1, 2019
Discussion open until: Oct 22, 2019
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