When geographic information meets molecular data.
N. J. Olesen, S. Kahns, S.P. Jonstrup, H.F. Skall
Annual Meeting of the National Reference Laboratories for Molluscs Diseases, Nantes 23-24 March 2010
2
Fish farms on digital maps• Easy tool for creating overview
– Where are the infected farms situated?• Epidemiological analysis of disease spread
– Picture of status every month• Risk-assesment
– Which farms are at the same stream?• Risk-management
– Creation of ”zones”
3
Fish farms on digital maps –How?• Digital maps are available in many different
forms• Requires a register on the fish farms which will
be linked to the map• It is possible to ad graphics even to simple
maps –manipulation of maps requires more expensive software
6Council Directive 2006/88/EC, require authorisation of all farms
Introduce an authorisation
System of aquaculture
production business
Establish a complete
overview of the
aquaculture industry in EU
• Name & address
• Registration number
• GIS position (optional or if possible)
• Production type
• Water supply details
• Information on health status
Electronically available EU-wide
(Article 59)
7Green: Cat.I
Red: Cat. II
Yellow: Cat III
These maps will be made available for and in all Member States
Map: Sten Mortensen
9
www.fishpathogens.eu
Aim and status
To provide a platform for storing and (if wanted) sharing of informationon different fish pathogens isolates.
This includes: Isolate information and characteristicsGeographical information of isolateAll information on available sequences
•VHSV database is public available.•IHNV database is established (publication accepted in JFD)and was opened last week
•SVCV database is established (data need to be added)•ISAV database layout is being discussed and under development•IPN, Perch RV etc in line.
10
Database design
Developed using Open Source software - low cost platform
Use of controlled vocabulary (restricted list of values) improves thequality of searches against database
Division of data into isolate and sequence reports allows different users adding isolate and sequence reports and makes it easy for several sequences to be added to a single isolate.
Data are reviewed by a pathogen expert before it is made publically available
The database can be easily created multiple times for different pathogens
14
Publication
FishPathogens.eu/vhsv: A user- friendly Viral Haemorrhagic Septicaemia Virus (VHSV) isolate and sequence database
Søren Peter Jonstrup, Tanya Gray, Søren Kahns, Helle Frank Skall, Mike Snow and Niels Jørgen Olesen
Journal of Fish Diseases 2009
21
VHSV Genotype Ia in Denmark mainly belongs to cluster Ia-1
>95
>95
>95
Ib
Recent Danish VHSV
Older Danish VHSV isolates
Recent Danish VHSV isolate
Austrian/germa VHSV isolatesOlder Danish VHSV isolates
22
2008, Karstofte å (Skjern å system)2008, Tangen2004, Holten å (Skjern å system)
3 Danish isolates in the European Cluster
Non-Danish genotype Ia-2
Non-Danish genotype Ia-2
24Thomas Wahli VHSHS--casescases in in SwitzerlandSwitzerland 22006006
Series 1Series 2
Location of series1+2
25
Background
• 2 series of VHS-outbreaks in spring 2006• Association within and between series?• Virus isolates to Aarhus for sequencing
VHSHS--casescases in in SwitzerlandSwitzerland
27
Conclusions
• Evidence for virus transfer via transport of infected fish• Evidence for virus infection via river water• Two separate events• Origin of virus in first affected farms from both series not
clear
VHSHS--casescases in in SwitzerlandSwitzerland
28
Spring 2005, mass mortality of freshwater drum occurred in Lake Ontario, Bay of Quinte
Lake OntarioFreshwater drum
Occurrence of a new subtype of North American VHSV in the Great Lakes Kyle Garver
29
0.1
WAph1993
95.225
93-390
04-040
04-29
02-235 93.372
99-01002-229
02-4105-14
NBmum2000
FR-L59X
DK-4p101
UK-H17 5 93IR-F13.02.97
SCOt1995
UK-860 94
GE-1.2DK-7974
DK-2835
FRArt1971
DK-F1
JA1996DEN1962
SE-SVA-14
NO-A
DK-1p52
Genotype I
Genotype II
Genotype III
Genotype IV
North American VHSV phylogenetic analysis
European
North American
30North American VHSV Tree
0.1
DK-1p52FR-L59X
DK-4p101UK-H17 5 93IR-F13.02.97
SCOt1995UK-860 94
GE-1.2DK-7974
FRArt1971DK-2835
DENac1962DK-F1NO-A163-68
SE-SVA-14JAKRf1996
NBmum00
BCherring93WAherring93
BCherring95WAcoho94
WAcoho91BCatlantic98
BCatlantic05OReulachon01BCatlantic04
BCatlantic99BCherring04
BCherring02BCpilchad02
AKherring93JAflounder99AKcod90WAcoho8893herring372MA herring
BCatlantic05herring0202pilchardCAsardine02BCpilchard02-229BCpilchard02-41
BCherring99CAsardine01
European types(genogroup I-III)
North American types(genogroup IV)
East Coast
West Coast
100
99
31
0.1
SCOt1995
WAcoho88AKcod90JAflounder99MAherr00AKherring93BCherring93BCatlantic98WAcoho91BCherring95WAherring93WAcoho94BCatlantc99OReulachon01BCatlantic02
CAsardine01BCherring99CAsardine02BCpilchard02
CAsardine02
NBmum2000Lake Ontario Drum
FR1971
JAKRf1996DENac1962
Genogroup IV (North American VHSV)
100
100
100
West CoastIVa
East CoastIVb
Freshwater Drum VHSV strain analysis
32Great Lakes VHSV
’05 Lake OntarioFreshwater drum
’06 Lake St. ClairFreshwater DrumSmallmouth BassBluegill
’03 Lake St. ClairMuskellunge
33Summary
•All requirements for molecular epidemiology are in hand for someFish pathogenic viruses:
•All farms and their disease status available on Web.•Pathogen databases providing large amount sequence data for alignement and tracing.•Giving new and more efficient approaches for disease control
34Summary
•Genotyping more simple for viruses than parasites,e.g. VHSV only 11.000 BP genome.•GIS information also on Molluscs farms 2006/88/EC provision•Geographic coordinates of pathogens easy to obtain.•Sequence data to agree upon.•WWW.Fishpathogens.eu could easyly be adapted tomollusc pathogens if interested.