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.
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, WI, USA. Electronic address: hip@usgs.gov.
authors.forename: Hon S
authors.initials: HS
authors.lastname: Ip
authors.affiliation: Center for Genomic Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Wiley
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, WI, USA.
authors.forename: Renee
authors.initials: R
authors.lastname: Long
authors.affiliation: Center for Genomic Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Palacios
authors.affiliation: Center for Genomic Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
authors.forename: Valerie
authors.initials: V
authors.lastname: Shearn-Bochsler
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, WI, USA.
authors.forename: Chris A
authors.initials: CA
authors.lastname: Whitehouse
mesh_terms: D000524:Alphavirus / Q000302:isolation & purification*; D018354:Alphavirus Infections / Q000662:veterinary* / Q000821:virology; D000818:Animals; D001715:Bird Diseases / Q000821:virology*; D001717:Birds; D001921:Brain / Q000821:virology*; D016000:Cluster Analysis; D005260:Female; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Conservation; Highlands J virus; Next-generation sequencing; Pathogen discovery; Rapid identification; Wildlife disease