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; Taylor D. Wadley; Bualan Kaewnapan; Niracha Athipanyasilp; Andrew Skidmore; Donghoon Chung; Chutikarn Chaimayo; Michael Whitt; Wannee Kantakamalakul; Ruengpung Sutthent; Navin Horthongkham; David W. Ussery; Colleen B. Jonsson; Intawat Nookaew

doi:10.3389/fmicb.2019.00260

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
, Taylor D. Wadley
, Bualan Kaewnapan
, Niracha Athipanyasilp
, Andrew Skidmore
, Donghoon Chung
, Chutikarn Chaimayo
, Michael Whitt
, Wannee Kantakamalakul
, Ruengpung Sutthent
, Navin Horthongkham
, David W. Ussery
, Colleen B. Jonsson
, Intawat Nookaew

Department of Microbiology

University of Arkansas for Medical Sciences
University of Tennessee Health Science Center
University of São Paulo
Siriraj Hospital
University of Louisville School of Medicine

Research output: Contribution to journal › Article › peer-review

59 Citations (Scopus)

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.

Original language	English
Article number	260
Journal	Frontiers in Microbiology
Volume	10
Issue number	FEB
DOIs	https://doi.org/10.3389/fmicb.2019.00260
Publication status	Published - 2019

Keywords

Genome
MinION
Nanopore sequencing
Native RNA
Rapid detection
Single-stranded RNA
Subgenomic mRNA
Virus

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10.3389/fmicb.2019.00260

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Wongsurawat, T., Jenjaroenpun, P., Taylor, M. K., Lee, J., Tolardo, A. L., Parvathareddy, J., Kandel, S., Wadley, T. D., Kaewnapan, B., Athipanyasilp, N., Skidmore, A., Chung, D., Chaimayo, C., Whitt, M., Kantakamalakul, W., Sutthent, R., Horthongkham, N., Ussery, D. W., Jonsson, C. B., & Nookaew, I. (2019). Rapid sequencing of multiple RNA viruses in their native form. Frontiers in Microbiology, 10(FEB), Article 260. https://doi.org/10.3389/fmicb.2019.00260

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title = "Rapid sequencing of multiple RNA viruses in their native form",

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.",

keywords = "Genome, MinION, Nanopore sequencing, Native RNA, Rapid detection, Single-stranded RNA, Subgenomic mRNA, Virus",

author = "Thidathip Wongsurawat and Piroon Jenjaroenpun and Taylor, \{Mariah K.\} and Jasper Lee and Tolardo, \{Aline Lavado\} and Jyothi Parvathareddy and Sangam Kandel and Wadley, \{Taylor D.\} and Bualan Kaewnapan and Niracha Athipanyasilp and Andrew Skidmore and Donghoon Chung and Chutikarn Chaimayo and Michael Whitt and Wannee Kantakamalakul and Ruengpung Sutthent and Navin Horthongkham and Ussery, \{David W.\} and Jonsson, \{Colleen B.\} and Intawat Nookaew",

year = "2019",

doi = "10.3389/fmicb.2019.00260",

language = "English",

volume = "10",

journal = "Frontiers in Microbiology",

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Wongsurawat, T , Jenjaroenpun, P, Taylor, MK, Lee, J, Tolardo, AL, Parvathareddy, J, Kandel, S, Wadley, TD, Kaewnapan, B, Athipanyasilp, N, Skidmore, A, Chung, D, Chaimayo, C, Whitt, M, Kantakamalakul, W, Sutthent, R, Horthongkham, N, Ussery, DW, Jonsson, CB & Nookaew, I 2019, 'Rapid sequencing of multiple RNA viruses in their native form', Frontiers in Microbiology, vol. 10, no. FEB, 260. https://doi.org/10.3389/fmicb.2019.00260

TY - JOUR

T1 - Rapid sequencing of multiple RNA viruses in their native form

AU - Wongsurawat, Thidathip

AU - Jenjaroenpun, Piroon

AU - Taylor, Mariah K.

AU - Lee, Jasper

AU - Tolardo, Aline Lavado

AU - Parvathareddy, Jyothi

AU - Kandel, Sangam

AU - Wadley, Taylor D.

AU - Kaewnapan, Bualan

AU - Athipanyasilp, Niracha

AU - Skidmore, Andrew

AU - Chung, Donghoon

AU - Chaimayo, Chutikarn

AU - Whitt, Michael

AU - Kantakamalakul, Wannee

AU - Sutthent, Ruengpung

AU - Horthongkham, Navin

AU - Ussery, David W.

AU - Jonsson, Colleen B.

AU - Nookaew, Intawat

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Genome

KW - MinION

KW - Nanopore sequencing

KW - Native RNA

KW - Rapid detection

KW - Single-stranded RNA

KW - Subgenomic mRNA

KW - Virus

UR - https://www.scopus.com/pages/publications/85064222600

U2 - 10.3389/fmicb.2019.00260

DO - 10.3389/fmicb.2019.00260

M3 - Article

AN - SCOPUS:85064222600

SN - 1664-302X

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

IS - FEB

M1 - 260

ER -

Rapid sequencing of multiple RNA viruses in their native form

Abstract

Keywords

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