Fish Diseases

USGS fish disease research is focused on developing advanced tools for rapid disease detection and control.  USGS scientists are improving our understanding of the factors controlling the epidemiology of aquatic animal diseases and the impact of disease on wild fish populations.  Our scientists are also investigating the effects of warming waters, drought, and invasive species on fish disease dynamics.

Cooperative Research

Infectious Hematopoietic Necrosis virus research — Western Fisheries Research Center

Bacterial Kidney Disease Research and Its Relation to the Great Lakes Fisheries — Western Fisheries Research Center

DNA Vaccine against North American Spring Viremia of Carp Virus (SVCV) — USGS Technology Transfer

Fish Health Branch — Leetown Science Center

Fish Disease Databases & Tools

Molecular Epidemiology of Aquatic Pathogens: IHNV and VHSV Databases

The MEAP-IHNV database and  MEAP-VHSV database contain thousands of records of background information and genetic sequencing data for individual isolates of the fish viruses, Infectious hematopoietic necrosis virus (IHNV) and Viral hemorrhagic septicemia virus (VHSV).

AquaPathogenX: A Template Database for Tracking Field Isolates of Aquatic Pathogens

The AquaPathogen X database is a template for recording information on individual isolates of aquatic pathogens. The database is available for download from the USGS Western Fisheries Research Center website (

  • USGS Fact Sheet 2012-3015: AquaPathogen X: A Template Database for Tracking Field Isolates of Aquatic Pathogens
    This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp)...
  • Journal of Fish Diseases: Development of an aquatic pathogen database (AquaPathogen X) and its utilization in tracking emerging fish virus pathogens in North America
    The cataloguing of isolates from different aquatic pathogens simultaneously is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and elucidation of key risk factors associated with pathogen incursions into new water systems. An application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak, was also developed...



Fish Parasite Ecology Software Tool (Fish PEST) is a web tool aimed to model the distribution of parasites on fish hosts. Fish PEST integrates parasitological data with ecological, biogeographic and phylogenetic information of fish hosts.

  • Trends in Parasitology: FishPEST: an innovative software suite for fish parasitologists
    Fish Parasite Ecology Software Tool (FishPEST) integrates fish parasite information from scientific literature, internet databases and museum collections with phylogenetic, biogeographical and ecological host data coming from Fishbase. FishPEST is a dynamic web-based system using the open source scripting language Python and the Python-based web framework Django...


  • Publications

  • Science to Support Aquatic Animal Health

    Healthy aquatic ecosystems are home to a diversity of plants, invertebrates, fish and wildlife. Aquatic animal populations face unprecedented threats to their health and survival from climate change, water shortages, habitat alteration, invasive species and environmental contaminants. These environmental stressors can directly impact the prevalence and severity of disease in...

    USGS Fact Sheet 2016-3091, 2 p.

  • Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the USA

    The white sucker Catostomus commersonii is a freshwater teleost often utilized as a resident sentinel. Here, we sequenced the full genome of a hepatitis B-like virus that infects white suckers from the Great Lakes Region of the USA. Dideoxysequencing confirmed the white sucker hepatitis B virus (WSHBV) has a circular genome (3542 bp) with the prototypical codon organization of hepadnaviruses. Electron microscopy demonstrated that complete virions of approximately 40 nm were present in the plasma of infected fish. 

    Journal of Virology, v. 89, November 2015

  • The parasite Ichthyophonus sp. in Pacific herring from the coastal NE Pacific

    The protistan parasite Ichthyophonus occurred in populations of Pacific herring Clupea pallasii Valenciennes throughout coastal areas of the NE Pacific, ranging from Puget Sound, WA north to the Gulf of Alaska, AK. Infection prevalence in local Pacific herring stocks varied seasonally and annually, and a general pattern of increasing prevalence with host size and/or age persisted throughout the NE Pacific. An exception to this zoographic pattern occurred among a group of juvenile, age 1+ year Pacific herring from Cordova Harbor, AK in June 2010, which demonstrated an unusually high infection prevalence of 35%. Reasons for this anomaly were hypothesized to involve anthropogenic influences that resulted in locally elevated infection pressures.

    Journal of Fish Diseases, March 2015

  • Infectious diseases affect marine fisheries and aquaculture economics

    Seafood is a growing part of the economy, but its economic value is diminished by marine diseases. Infectious diseases are common in the ocean, and here we tabulate 67 examples that can reduce commercial species' growth and survivorship or decrease seafood quality. These impacts seem most problematic in the stressful and crowded conditions of aquaculture, which increasingly dominates seafood production as wild fishery production plateaus.

    Annual Review of Marine Science, v. 7, January 2015