FishPathogens.eu/vhsv: a user‐friendly viral haemorrhagic septicaemia virus isolate and sequence database

Abstract

A database has been created, http://www.FishPathogens.eu, with the aim of providing a single repository for collating important information on significant pathogens of aquaculture, relevant to their control and management. This database will be developed, maintained and managed as part of the European Community Reference Laboratory for Fish Diseases function. This concept has been initially developed for viral haemorrhagic septicaemia virus and will be extended in future to include information on other significant aquaculture pathogens. Information included for each isolate comprises sequence, geographical origin, host origin and useful key literature. Various search mechanisms make it easy to find specific groups of isolates. Search results can be presented in several different ways including table‐based, map‐based and graph‐based outputs. When retrieving sequences, the user is given freedom to obtain data from any selected part of the genome of interest. The output of the sequence search can be readily retrieved as a FASTA file ready to be imported into a sequence alignment tool of choice, facilitating further molecular epidemiological study.

The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

“…Due to the economic impact of IHNV, VHSV, and SVCV, routine surveillance for these viruses is conducted in cultured host populations, and molecular epidemiology is a valuable tool for fish health management (Breyta et al, 2016; Emmenegger et al, 2011; Jonstrup et al, 2009). Local, regional, and global phylogenies have revealed sources of disease outbreaks, virus transmission routes, virus emergence events and host jumps (e.g.…”

Development of an aquatic pathogen database (AquaPathogen X) and its utilization in tracking emerging fish virus pathogens in North America

“…Two other fish pathogen web‐accessible databases that store epidemiological information on individual fish virus isolates have been developed by Danish fish health researchers. The first database, http://www.fishpathogens.eu/vhsv/index.php, focuses on European isolates of viral haemorrhagic septicaemia virus (VHSV), another OIE‐listed aquatic rhabdovirus historically found in European trout aquaculture (Jonstrup, Gray, Kahns, Skall, Snow & Olesen 2009). Because of the introduction and spread of IHNV in Europe since 1987 (Baudin‐Laurencin 1987; Bovo, Giorgetti, Jørgensen & Olesen 1987), this same group developed a second database of IHNV isolates (Jonstrup, Schuetze, Kurath, Gray, Jensen Bang & Olesen 2010; http://www.fishpathogens.eu/ihnv).…”

An isolate and sequence database of infectious haematopoietic necrosis virus (IHNV)

“…This ensures that the database will be continuously updated in the future and that the number of added isolates and sequences will grow continuously. This concept has so far worked very well for VHSV (Jonstrup et al 2009) and we believe that the same can be achieved for IHNV.…”

“…Registering as a user will also add a ‘my page’ to the website from where the user can add reports as well as browse and edit personal reports. Registered users of the VHSV database (Jonstrup et al. 2009) will automatically be registered users of the IHNV database.…”

“…Fishpathogens.eu is a database developed and maintained by the European Community Reference Laboratory for Fish Diseases. The database was launched in June 2009 focusing on viral haemorrhagic septicaemia virus (VHSV) (Jonstrup, Gray, Kahns, Skall, Snow & Olesen 2009). VHSV, like IHNV, is also a member of the genus Novirhabdovirus (Skall, Olesen & Mellergaard 2005).…”