Transformation of shrimp farming from a small fisheries activity to a global industry over the past four decades has been made possible through the development of captive breeding programs that led to the availability of Specific Pathogen Free seed stock, availability of nutritionally optimal formulated feed, and implementation of new measures to improve biosecurity and farm management. Despite much progress achieved to enhance global production, maintaining a steady level of productivity has been difficult due to periodic and unpredictable disease pandemics. Often times diseases have spread beyond the point of origin across countries and even to different continents before the etiologic agent was discovered, and disease diagnostic tools and treatments were developed. To prevent the transboundary movement of diseases and economic losses that result due to disease pandemics, there is a need to identify the causal agent of a newly emerged disease rapidly and develop histopathology and molecular diagnostic tools.
We hypothesized conventional histopathology can be combined with genomics tools to expedite pathogen discovery. Having information on the genomic architecture of a novel pathogen will enable the development of molecular diagnostics to prevent its rapid spread. We demonstrated the feasibility of combining histopathology with next generation sequencing (NGS) to reconstruct the genome of a DNA virus, white spot syndrome virus (WSSV), and an RNA virus, Taura syndrome virus (TSV). Thin sections (5 μm) of paraffin embedded tissue samples were taken from a recent (2017 for WSSV) or old (15 year old for TSV) archived histology blocks at the Aquaculture Pathology Laboratory and examined for pathognomonic lesions of WSSV/TSV. Upon confirmation of viral infection, DNA (for WSSV)/ RNA (for TSV) were isolated and real-time PCR performed to confirm WSSV/ TSV infection before taking for NGS analysis. High quality sequence data were generated to reconstruct WSSV and TSV genomes. Phylogenetic analysis of TSV genome sequence reconstructed from the archived histology blocks formed clades with genome sequence of homologous isolates deposited to GenBank over decades. This validates the authenticity of TSV genome sequences generated from archived histology blocks.
This study confirms the feasibility of combining conventional histopathology and genomic tools to expedite pathogen discovery and in evolutionary studies. In addition, this demonstrated archived histology blocks could be a treasure trove for pathogen discovery and epidemiology. Conceptually from the time a new disease emerges, conducting the histopathology and NGS analyses to construct the unknown pathogen’s genome can be achieved in three months, and developing PCR-based molecular diagnostics can be attained in less than a month. The entire workflow presented here from genome reconstruction to developing molecular diagnostics will undoubtedly enable the industry to prevent the spread of a disease in near real time while shining a light on the epidemiology of diseases of shrimp aquaculture from the past.