dsRNA-Seq: Identification of viral infection by purifying and sequencing dsRNA

Decker, Carolyn J.; Steiner, Halley R.; Hoon-Hanks, Laura L.; Morrison, James H.; Haist, Kelsey C.; Stabell, Alex C.; Poeschla, Eric M.; Morrison, Thomas E.; Stenglein, Mark D.; Sawyer, Sara L.; Parker, Roy

doi:10.1101/738377

Cited by 8 publications

(8 citation statements)

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“…Previous studies reported that the degree of concentrations for viral RNA sequences in dsRNA-seq data differed from that in virus species ( Urayama et al , 2016 ; Decker et al , 2019 ). We cannot rule out the possibility that some RNA viruses are easier to detect in total RNA-seq than in dsRNA-seq.…”

Section: Resultsmentioning

confidence: 91%

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

et al. 2020

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Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.

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Section: Resultsmentioning

confidence: 91%

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

et al. 2020

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“…Thus, quantifying pervasive transcription across genes or TEs is sometimes precisely what is being sought, and can be achieved by calculating the ratio between sense and antisense RNA at the features of interest in directional RNA-seq data 111 . More specific approaches have been developed such as dsRNA-seq 184 , which enriches dsRNA by digestion of single-stranded RNA and immunoprecipitation of dsRNA with a sequence-independent anti-dsRNA antibody, followed by sequencing. This approach was originally developed to identify viral dsRNAs.…”

Section: Te-chimeric Transcriptsmentioning

confidence: 99%

Measuring and interpreting transposable element expression

2020

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Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur, but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA-sequencing include transposon-derived transcripts, the majority of computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from gene-TE chimeric transcripts or pervasive transcription. Here, we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.

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“…Given that the sequencing method used to detect the reovirus sequences was designed to enrich for dsRNA and that this virus was undetectable by qRT-PCR it is difficult to fully grasp the viral load in these chameleons. This does, however highlight the utility of dsRNA-seq for the identification of viruses with dsRNA genomes [ 20 ]. The standard shotgun sequencing method we initially used that did not specifically enrich for dsRNA failed to detect the reovirus infection ( Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

“…The RNA-seq libraries were sequenced using a dual-indexed, single-end, 1 × 150 method on an Illumina NextSeq 500 instrument with either a NextSeq 500/550 Mid or High Output Kit v2 (150 cycles). An independent metagenomic sequencing run was also performed on the same RNA samples using a library preparation method with enrichment of double-stranded RNA [ 20 ]. This was run on the same platform using a dual-indexed, paired-end, 2 × 75 sequencing method.…”

Section: Methodsmentioning

confidence: 99%

Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease

Hoon-Hanks

Stöhr

Anderson

et al. 2020

Viruses

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Serpentoviruses are an emerging group of nidoviruses known to cause respiratory disease in snakes and have been associated with disease in other non-avian reptile species (lizards and turtles). This study describes multiple episodes of respiratory disease-associated mortalities in a collection of juvenile veiled chameleons (Chamaeleo calyptratus). Histopathologic lesions included rhinitis and interstitial pneumonia with epithelial proliferation and abundant mucus. Metagenomic sequencing detected coinfection with two novel serpentoviruses and a novel orthoreovirus. Veiled chameleon serpentoviruses are most closely related to serpentoviruses identified in snakes, lizards, and turtles (approximately 40–50% nucleotide and amino acid identity of ORF1b). Veiled chameleon orthoreovirus is most closely related to reptilian orthoreoviruses identified in snakes (approximately 80–90% nucleotide and amino acid identity of the RNA-dependent RNA polymerase). A high prevalence of serpentovirus infection (>80%) was found in clinically healthy subadult and adult veiled chameleons, suggesting the potential for chronic subclinical carriers. Juvenile veiled chameleons typically exhibited a more rapid progression compared to subadults and adults, indicating a possible age association with morbidity and mortality. This is the first description of a serpentovirus infection in any chameleon species. A causal relationship between serpentovirus infection and respiratory disease in chameleons is suspected. The significance of orthoreovirus coinfection remains unknown.

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dsRNA-Seq: Identification of viral infection by purifying and sequencing dsRNA

Cited by 8 publications

References 50 publications

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

Measuring and interpreting transposable element expression

Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease

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