Current trends inRNAvirus detection through metatranscriptome sequencing data

Abstract

With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.

Serving the scientific community: FEBS Open Bio in 2024

“…Bacterial ribonucleases, together with other RNA regulators, are also involved in biofilm formation, as reviewed by Vânia Pobre and colleagues in the second article in the issue [4]. In the final article, So Nakagawa, Takashi Gojobori and colleagues introduce new developments in bioinformatics software and databases for the identification of RNA viruses and discuss viromes from various sources [5]. This issue also features an interview with Cecília, in which she discusses both her research and supporting women in science through her former position as Chair of the FEBS Working Group on Women in Science [6].…”

RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses

“…Following nucleic acid extraction, metatranscriptomic samples often proceed with ribosomal RNA (rRNA) removal and then complementary DNA (cDNA) generation by reverse transcription. Subsequently, random primers are used to enrich the resultant cDNA library, followed by adapter ligation and sequencing [54]. rRNA-reduced libraries are shown to produce more viral contigs than polyadenylation-selected libraries [55], proving their suitability for RNA phage samples.…”

NeoRdRp2 with improved seed data, annotations, and scoring

“…RNA viruses play pivotal roles in various environments and influence several ecosystems and organisms including humans, animals, and plants (1). Studies on RNA virus detection using metatranscriptome data have emerged as powerful tools for obtaining insights into both known and novel RNA viruses in samples (2). RNA-dependent RNA polymerase (RdRp) is a universal gene found in almost all RNA viruses except retroviruses and deltaviruses.…”

“…RNA-dependent RNA polymerase (RdRp) is a universal gene found in almost all RNA viruses except retroviruses and deltaviruses. RdRp sequences are commonly used to search for various RNA viruses from metatranscriptome data; however, because of the great diversity of RdRps, finding various RNA viruses based on homology-based searches using RdRp sequences is known to be difficult (2). To overcome this problem, we developed a bioinformatics pipeline to generate hidden Markov model (HMM) profiles from 12,502 RdRp domain sequences.…”