FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance

Microbes and Environments
Syun-Ichi UrayamaTakuro Nunoura

Abstract

Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. We herein constructed an effective metagenomic method for RNA viruses by targeting long double-stranded (ds)RNA in cellular organisms, which is a hallmark of infection, or the replication of dsRNA and single-stranded (ss)RNA viruses, except for retroviruses. This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. Our approach will be a powerful tool for cataloging RNA viruses associated with organisms of interest.

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Citations

May 4, 2016·Archives of Virology·Satoshi KoyamaSyun-Ichi Urayama
Apr 4, 2017·Microbes and Environments·Takashi Narihiro, Yoichi Kamagata
Dec 28, 2016·Microbes and Environments·Ken Takai
Jul 6, 2018·Microbes and Environments·Hiroyuki Ogata
Jan 11, 2018·Astrobiology·Aaron J BerlinerKenneth M Stedman
Oct 16, 2018·Microbes and Environments·Syun-Ichi UrayamaNorio Miyamoto
Jun 20, 2020·Microbes and Environments·Yuto ChibaSyun-Ichi Urayama
Dec 23, 2019·Archives of Virology·Fumika FukasawaSatoshi Koyama
Aug 6, 2019·Frontiers in Cellular and Infection Microbiology·Tünde KartaliTamás Papp
Sep 27, 2018·Molecular Ecology Resources·Syun-Ichi UrayamaTakuro Nunoura
Mar 20, 2020·Journal of Virology·Jackie E MaharEdward C Holmes
Nov 17, 2020·Frontiers in Microbiology·Syun-Ichi UrayamaTakuro Nunoura
Jan 26, 2021·Archives of Virology·Tamaki Uehara-IchikiKaoru Hanada

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Methods Mentioned

BETA
RNA-seq
column chromatography
PCR
affinity purification
electrophoresis

Software Mentioned

MrBayes
BLASTN
Tablet viewer
EMIRGE
plus
Genetyx
MEGA5
ProtTest2
MEGAN
FLDS

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