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.
N1 - Funding Information:
Work performed at the USGS National Wildlife Health Center was supported, in part, by funding from the Department of the Interior's Ecosystems Program. Work performed in the Genomics Center at USAMRIID was supported by 1881290 CB2851 ( TMTI0021_09_RD_T ) Genomics Center-High Speed Sequencing for Rapid Response and Countermeasure Development .
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
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U2 - 10.1016/j.jviromet.2014.05.018
DO - 10.1016/j.jviromet.2014.05.018
M3 - Article
C2 - 24880070
AN - SCOPUS:84902166512
SN - 0166-0934
VL - 206
SP - 42
EP - 45
JO - Journal of Virological Methods
JF - Journal of Virological Methods
ER -