Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

Guoyan Zhao, Siddharth Krishnamurthy, Zhengqiu Cai, Vsevolod Popov, Amelia P. Travassos da Rosa, Hilda Guzman, Song Cao, Herbert W. Virgin, Robert B. Tesh, David Wang

Research output: Contribution to journalArticle

46 Citations (Scopus)

Abstract

Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.

Original languageEnglish (US)
Article numbere78470
JournalPLoS One
Volume8
Issue number10
DOIs
StatePublished - Oct 22 2013

Fingerprint

Viruses
data analysis
Phlebovirus
Orbivirus
Pipelines
viruses
Unclassified Viruses
Pathogens
unassigned viruses
Orthobunyavirus
Emerging Communicable Diseases
Arboviruses
arboviruses
Reoviridae
titanium
emerging diseases
pathogens
Titanium
Computational Biology
bioinformatics

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Zhao, G., Krishnamurthy, S., Cai, Z., Popov, V., Travassos da Rosa, A. P., Guzman, H., ... Wang, D. (2013). Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline. PLoS One, 8(10), [e78470]. https://doi.org/10.1371/journal.pone.0078470

Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline. / Zhao, Guoyan; Krishnamurthy, Siddharth; Cai, Zhengqiu; Popov, Vsevolod; Travassos da Rosa, Amelia P.; Guzman, Hilda; Cao, Song; Virgin, Herbert W.; Tesh, Robert B.; Wang, David.

In: PLoS One, Vol. 8, No. 10, e78470, 22.10.2013.

Research output: Contribution to journalArticle

Zhao, G, Krishnamurthy, S, Cai, Z, Popov, V, Travassos da Rosa, AP, Guzman, H, Cao, S, Virgin, HW, Tesh, RB & Wang, D 2013, 'Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline', PLoS One, vol. 8, no. 10, e78470. https://doi.org/10.1371/journal.pone.0078470
Zhao G, Krishnamurthy S, Cai Z, Popov V, Travassos da Rosa AP, Guzman H et al. Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline. PLoS One. 2013 Oct 22;8(10). e78470. https://doi.org/10.1371/journal.pone.0078470
Zhao, Guoyan ; Krishnamurthy, Siddharth ; Cai, Zhengqiu ; Popov, Vsevolod ; Travassos da Rosa, Amelia P. ; Guzman, Hilda ; Cao, Song ; Virgin, Herbert W. ; Tesh, Robert B. ; Wang, David. / Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline. In: PLoS One. 2013 ; Vol. 8, No. 10.
@article{1a577d3ec1f14357afcbc598b98aa053,
title = "Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline",
abstract = "Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.",
author = "Guoyan Zhao and Siddharth Krishnamurthy and Zhengqiu Cai and Vsevolod Popov and {Travassos da Rosa}, {Amelia P.} and Hilda Guzman and Song Cao and Virgin, {Herbert W.} and Tesh, {Robert B.} and David Wang",
year = "2013",
month = "10",
day = "22",
doi = "10.1371/journal.pone.0078470",
language = "English (US)",
volume = "8",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Identification of Novel Viruses Using VirusHunter -- an Automated Data Analysis Pipeline

AU - Zhao, Guoyan

AU - Krishnamurthy, Siddharth

AU - Cai, Zhengqiu

AU - Popov, Vsevolod

AU - Travassos da Rosa, Amelia P.

AU - Guzman, Hilda

AU - Cao, Song

AU - Virgin, Herbert W.

AU - Tesh, Robert B.

AU - Wang, David

PY - 2013/10/22

Y1 - 2013/10/22

N2 - Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.

AB - Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.

UR - http://www.scopus.com/inward/record.url?scp=84886003785&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84886003785&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0078470

DO - 10.1371/journal.pone.0078470

M3 - Article

VL - 8

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e78470

ER -