Publication

Applied shotgun metagenomics approach for the genetic characterization of dengue viruses

Lizarazo, E., Couto, N., Vincenti-Gonzalez, M., Raangs, E. C., Velasco, Z., Bethencourt, S., Jaenisch, T., Friedrich, A. W., Tami, A. & Rossen, J. W., Jun-2019, In : Journal of Biotechnology: X. 2, 10 p., 100009.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Lizarazo, E., Couto, N., Vincenti-Gonzalez, M., Raangs, E. C., Velasco, Z., Bethencourt, S., ... Rossen, J. W. (2019). Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. Journal of Biotechnology: X, 2, [100009]. https://doi.org/10.1016/j.btecx.2019.100009

Author

Lizarazo, Erley ; Couto, Natacha ; Vincenti-Gonzalez, Maria ; Raangs, Erwin C. ; Velasco, Zoraida ; Bethencourt, Sarah ; Jaenisch, Thomas ; Friedrich, Alexander W. ; Tami, Adriana ; Rossen, John W. / Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. In: Journal of Biotechnology: X. 2019 ; Vol. 2.

Harvard

Lizarazo, E, Couto, N, Vincenti-Gonzalez, M, Raangs, EC, Velasco, Z, Bethencourt, S, Jaenisch, T, Friedrich, AW, Tami, A & Rossen, JW 2019, 'Applied shotgun metagenomics approach for the genetic characterization of dengue viruses', Journal of Biotechnology: X, vol. 2, 100009. https://doi.org/10.1016/j.btecx.2019.100009

Standard

Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. / Lizarazo, Erley; Couto, Natacha; Vincenti-Gonzalez, Maria; Raangs, Erwin C.; Velasco, Zoraida; Bethencourt, Sarah; Jaenisch, Thomas; Friedrich, Alexander W.; Tami, Adriana; Rossen, John W.

In: Journal of Biotechnology: X, Vol. 2, 100009, 06.2019.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Lizarazo E, Couto N, Vincenti-Gonzalez M, Raangs EC, Velasco Z, Bethencourt S et al. Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. Journal of Biotechnology: X. 2019 Jun;2. 100009. https://doi.org/10.1016/j.btecx.2019.100009


BibTeX

@article{ab8c915b989840e7a56f778340eb7f9c,
title = "Applied shotgun metagenomics approach for the genetic characterization of dengue viruses",
abstract = "Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Additionally, presence of DENV quasispecies (intra-host variation) was revealed by detecting single nucleotide variants. Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1–4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext{\circledR} RNA to synthesize cDNA followed by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit. Libraries were sequenced using both the MiSeq and NextSeq. Bioinformatic analysis showed complete ORFs for all samples by all approaches, but longer contigs and higher sequencing depths were obtained with the TS kit. No differences were observed between MiSeq and NextSeq sequencing. Detection of multiple DENV serotypes in a single sample was feasible. Finally, results were obtained within three days with associated reagents costs between €130−170/sample. Therefore, shotgun metagenomics is suitable for identification and typing of DENV in a clinical setting.",
keywords = "Arboviruses, Dengue, Molecular epidemiology, Next-generation sequencing, Shotgun metagenomics",
author = "Erley Lizarazo and Natacha Couto and Maria Vincenti-Gonzalez and Raangs, {Erwin C.} and Zoraida Velasco and Sarah Bethencourt and Thomas Jaenisch and Friedrich, {Alexander W.} and Adriana Tami and Rossen, {John W.}",
year = "2019",
month = "6",
doi = "10.1016/j.btecx.2019.100009",
language = "English",
volume = "2",
journal = "Journal of Biotechnology: X",
issn = "2590-1559",

}

RIS

TY - JOUR

T1 - Applied shotgun metagenomics approach for the genetic characterization of dengue viruses

AU - Lizarazo, Erley

AU - Couto, Natacha

AU - Vincenti-Gonzalez, Maria

AU - Raangs, Erwin C.

AU - Velasco, Zoraida

AU - Bethencourt, Sarah

AU - Jaenisch, Thomas

AU - Friedrich, Alexander W.

AU - Tami, Adriana

AU - Rossen, John W.

PY - 2019/6

Y1 - 2019/6

N2 - Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Additionally, presence of DENV quasispecies (intra-host variation) was revealed by detecting single nucleotide variants. Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1–4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext® RNA to synthesize cDNA followed by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit. Libraries were sequenced using both the MiSeq and NextSeq. Bioinformatic analysis showed complete ORFs for all samples by all approaches, but longer contigs and higher sequencing depths were obtained with the TS kit. No differences were observed between MiSeq and NextSeq sequencing. Detection of multiple DENV serotypes in a single sample was feasible. Finally, results were obtained within three days with associated reagents costs between €130−170/sample. Therefore, shotgun metagenomics is suitable for identification and typing of DENV in a clinical setting.

AB - Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Additionally, presence of DENV quasispecies (intra-host variation) was revealed by detecting single nucleotide variants. Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1–4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext® RNA to synthesize cDNA followed by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit. Libraries were sequenced using both the MiSeq and NextSeq. Bioinformatic analysis showed complete ORFs for all samples by all approaches, but longer contigs and higher sequencing depths were obtained with the TS kit. No differences were observed between MiSeq and NextSeq sequencing. Detection of multiple DENV serotypes in a single sample was feasible. Finally, results were obtained within three days with associated reagents costs between €130−170/sample. Therefore, shotgun metagenomics is suitable for identification and typing of DENV in a clinical setting.

KW - Arboviruses

KW - Dengue

KW - Molecular epidemiology

KW - Next-generation sequencing

KW - Shotgun metagenomics

U2 - 10.1016/j.btecx.2019.100009

DO - 10.1016/j.btecx.2019.100009

M3 - Article

VL - 2

JO - Journal of Biotechnology: X

JF - Journal of Biotechnology: X

SN - 2590-1559

M1 - 100009

ER -

ID: 91284268