Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

Hon S. Ip, Michael R. Wiley, Renee Long, Gustavo Palacios, Valerie Shearn-Bochsler, Chris A. Whitehouse

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

Original languageEnglish (US)
Pages (from-to)42-45
Number of pages4
JournalJournal of Virological Methods
Volume206
DOIs
StatePublished - Sep 15 2014

Fingerprint

Mississippi
Viruses
DNA Sequence Analysis
Birds
Togaviridae
Technology
Arboviruses
Cyclonic Storms
High-Throughput Nucleotide Sequencing
Brain
Communicable Diseases
Cause of Death
Autopsy
Medicine
Genome
Costs and Cost Analysis
Population

Keywords

  • Conservation
  • Highlands J virus
  • Next-generation sequencing
  • Pathogen discovery
  • Rapid identification
  • Wildlife disease

ASJC Scopus subject areas

  • Virology

Cite this

Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing. / Ip, Hon S.; Wiley, Michael R.; Long, Renee; Palacios, Gustavo; Shearn-Bochsler, Valerie; Whitehouse, Chris A.

In: Journal of Virological Methods, Vol. 206, 15.09.2014, p. 42-45.

Research output: Contribution to journalArticle

Ip, Hon S. ; Wiley, Michael R. ; Long, Renee ; Palacios, Gustavo ; Shearn-Bochsler, Valerie ; Whitehouse, Chris A. / Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing. In: Journal of Virological Methods. 2014 ; Vol. 206. pp. 42-45.
@article{d9154dce4edc46bbb00630695417620f,
title = "Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing",
abstract = "Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.",
keywords = "Conservation, Highlands J virus, Next-generation sequencing, Pathogen discovery, Rapid identification, Wildlife disease",
author = "Ip, {Hon S.} and Wiley, {Michael R.} and Renee Long and Gustavo Palacios and Valerie Shearn-Bochsler and Whitehouse, {Chris A.}",
year = "2014",
month = "9",
day = "15",
doi = "10.1016/j.jviromet.2014.05.018",
language = "English (US)",
volume = "206",
pages = "42--45",
journal = "Journal of Virological Methods",
issn = "0166-0934",
publisher = "Elsevier",

}

TY - JOUR

T1 - Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

AU - Ip, Hon S.

AU - Wiley, Michael R.

AU - Long, Renee

AU - Palacios, Gustavo

AU - Shearn-Bochsler, Valerie

AU - Whitehouse, Chris A.

PY - 2014/9/15

Y1 - 2014/9/15

N2 - Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

AB - Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

KW - Conservation

KW - Highlands J virus

KW - Next-generation sequencing

KW - Pathogen discovery

KW - Rapid identification

KW - Wildlife disease

UR - http://www.scopus.com/inward/record.url?scp=84902166512&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84902166512&partnerID=8YFLogxK

U2 - 10.1016/j.jviromet.2014.05.018

DO - 10.1016/j.jviromet.2014.05.018

M3 - Article

C2 - 24880070

AN - SCOPUS:84902166512

VL - 206

SP - 42

EP - 45

JO - Journal of Virological Methods

JF - Journal of Virological Methods

SN - 0166-0934

ER -