Aquaculture is one of the fastest growing sectors of global food production, and as such, it is critical to safeguard food security through timely detection, prevention, and control of infectious diseases that threaten the industry. A bottleneck in rapidly detecting novel diseases exists, which results in delayed response measures and further agricultural losses. Metagenomic sequencing offers unbiased detection of unculturable, novel, and under-characterized agents previously undetected by traditional methods. Here we present a case in which metagenomic sequencing identified a novel virus producing cytopathic effect (CPE) in vitro during routine surveillance testing and known agents were not detected by validated assays. We discuss how this technology can be applied to clinical veterinary diagnostics in an outbreak scenario when the infectious agent is not determined by existing validated assays.
Tissue pools from clinically normal bass and minnow were submitted to WADDL for annual health screening by virus culture. CPE developed from all pools in the first and filtered second passage on EPC cells. Cells were harvested and submitted for Blue Book PCR testing for IHNV, VHSV, IPNV and SVCV. Additional PCR tests were ordered from a secondary lab, including Fathead Minnow nidovirus and picornavirus, golden shiner virus and white sucker virus. No known viruses were detected. Using metagenomic sequencing, a novel astrovirus was discovered which bears similarity to Dongbei arctic lamprey astrovirus. This astrovirus only present in cultures with CPE and was not detected in normal, uninoculated cell culture controls.
Thus far, a number of novel fish astroviruses have been discovered by metegenomic sequencing of apparently healthy fish. Based on the assembled genome, a novel astrovirus PCR assay was developed as a rule-out diagnostic test for future CPE results of unknown etiology. This pipeline of sequencing for pathogen discovery can also be applied directly to tissue for the detection of unculturable agents, reducing turnaround time significantly. The use of this technology in a clinical setting is still under development, but the potential application is broad. Improved metagenomics could significantly improve time to detection, intervention, and prevent further losses for many sectors of animal production and disease prevention.