Frontiers in Microbiology (Feb 2019)
Rapid Sequencing of Multiple RNA Viruses in Their Native Form
- Thidathip Wongsurawat,
- Piroon Jenjaroenpun,
- Mariah K. Taylor,
- Jasper Lee,
- Aline Lavado Tolardo,
- Jyothi Parvathareddy,
- Sangam Kandel,
- Sangam Kandel,
- Taylor D. Wadley,
- Bualan Kaewnapan,
- Niracha Athipanyasilp,
- Andrew Skidmore,
- Donghoon Chung,
- Chutikarn Chaimayo,
- Michael Whitt,
- Wannee Kantakamalakul,
- Ruengpung Sutthent,
- Navin Horthongkham,
- David W. Ussery,
- David W. Ussery,
- Colleen B. Jonsson,
- Intawat Nookaew,
- Intawat Nookaew
Affiliations
- Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Mariah K. Taylor
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
- Jasper Lee
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
- Aline Lavado Tolardo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, United States
- Sangam Kandel
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Sangam Kandel
- Department of Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR, United States
- Taylor D. Wadley
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Bualan Kaewnapan
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Andrew Skidmore
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
- Donghoon Chung
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
- Chutikarn Chaimayo
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Michael Whitt
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
- Wannee Kantakamalakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Ruengpung Sutthent
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- David W. Ussery
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- David W. Ussery
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
- Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Intawat Nookaew
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- DOI
- https://doi.org/10.3389/fmicb.2019.00260
- Journal volume & issue
-
Vol. 10
Abstract
Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subgenomic mRNA/mRNA simultaneously, (iii) detect a complex transcriptomic architecture without the need for assembly, (iv) enable real-time detection. Using this protocol, positive-ssRNA, negative-ssRNA, with/without a poly(A)-tail, segmented/non-segmented genomes were mixed and sequenced in parallel. Mapping of the generated sequences on the reference genomes showed 100% length recovery with up to 97% identity. This work provides a proof of principle and the validity of this strategy, opening up a wide range of applications to study RNA viruses.
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