Rapid Sequencing of Multiple RNA Viruses in Their Native Form
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, subge...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-02-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.00260/full |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
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 |
| spellingShingle |
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 Rapid Sequencing of Multiple RNA Viruses in Their Native Form Frontiers in Microbiology native RNA genome subgenomic mRNA single-stranded RNA virus nanopore sequencing |
| author_facet |
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 |
| author_sort |
Thidathip Wongsurawat |
| title |
Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
| title_short |
Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
| title_full |
Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
| title_fullStr |
Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
| title_full_unstemmed |
Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
| title_sort |
rapid sequencing of multiple rna viruses in their native form |
| publisher |
Frontiers Media S.A. |
| series |
Frontiers in Microbiology |
| issn |
1664-302X |
| publishDate |
2019-02-01 |
| description |
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. |
| topic |
native RNA genome subgenomic mRNA single-stranded RNA virus nanopore sequencing |
| url |
https://www.frontiersin.org/article/10.3389/fmicb.2019.00260/full |
| work_keys_str_mv |
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doaj-77bf6050d79c4e2caa6e6958a5ff13b12020-11-25T00:45:31ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-02-011010.3389/fmicb.2019.00260437443Rapid Sequencing of Multiple RNA Viruses in Their Native FormThidathip Wongsurawat0Piroon Jenjaroenpun1Mariah K. Taylor2Jasper Lee3Aline Lavado Tolardo4Jyothi Parvathareddy5Sangam Kandel6Sangam Kandel7Taylor D. Wadley8Bualan Kaewnapan9Niracha Athipanyasilp10Andrew Skidmore11Donghoon Chung12Chutikarn Chaimayo13Michael Whitt14Wannee Kantakamalakul15Ruengpung Sutthent16Navin Horthongkham17David W. Ussery18David W. Ussery19Colleen B. Jonsson20Intawat Nookaew21Intawat Nookaew22Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United StatesVirology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, BrazilRegional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Bioinformatics, University of Arkansas at Little Rock, Little Rock, AR, United StatesDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Microbiology and Immunology, University of Louisville, Louisville, KY, United StatesDepartment of Microbiology and Immunology, University of Louisville, Louisville, KY, United StatesDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United StatesDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesDepartment of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United StatesLong-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.https://www.frontiersin.org/article/10.3389/fmicb.2019.00260/fullnative RNAgenomesubgenomic mRNAsingle-stranded RNAvirusnanopore sequencing |