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Open AccessArticle

dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA

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Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
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Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA
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Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80302, USA
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(10), 943; https://doi.org/10.3390/v11100943
Received: 5 August 2019 / Revised: 6 October 2019 / Accepted: 7 October 2019 / Published: 14 October 2019
(This article belongs to the Section Animal Viruses)
RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that RNA viruses produce double-stranded RNA (dsRNA) while replicating. Purifying and sequencing dsRNA from the total RNA isolated from infected tissue allowed us to recover dsRNA virus sequences and replicated sequences from single-stranded RNA (ssRNA) viruses. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length or partial RNA viral genomes of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here, we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. In addition, a significant advantage of this method is the ability to identify replicated viral sequences of ssRNA viruses, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants. View Full-Text
Keywords: dsRNA; double-stranded RNA; emerging disease; emerging viruses; RNA virus; RNA-Seq dsRNA; double-stranded RNA; emerging disease; emerging viruses; RNA virus; RNA-Seq
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MDPI and ACS Style

Decker, C.J.; Steiner, H.R.; Hoon-Hanks, L.L.; Morrison, J.H.; Haist, K.C.; Stabell, A.C.; Poeschla, E.M.; Morrison, T.E.; Stenglein, M.D.; Sawyer, S.L.; Parker, R. dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA. Viruses 2019, 11, 943. https://doi.org/10.3390/v11100943

AMA Style

Decker CJ, Steiner HR, Hoon-Hanks LL, Morrison JH, Haist KC, Stabell AC, Poeschla EM, Morrison TE, Stenglein MD, Sawyer SL, Parker R. dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA. Viruses. 2019; 11(10):943. https://doi.org/10.3390/v11100943

Chicago/Turabian Style

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. 2019. "dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA" Viruses 11, no. 10: 943. https://doi.org/10.3390/v11100943

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