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

4

5

•Geographic spotting

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

8

Creation of a database on pathogens is a second important tool: www.fishpathogens.eu

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

11

Registering as user

88 registered users

12

Browsing

13

Map based search

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

15

When genotyping VHSV

Best resolution for typing: Full length G-gene sequence

16

VHSV Genotype I

17

VHSV Genotype I

Ie

IcId

Ib

18

VHSV Genotype Ia contains 2 clusters

Ie

IcId

Ib

Ia-1

Ia-2

19

VHSV in Denmark

VHSV Genotype I

Ie Ic

Ib

Id

Ia>95

>95

>95

20

VHSV Genotype Ia in Denmark mainly belongs to cluster Ia-1

>95

>95

>95

Ib

Ia-2

Ia-1

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

23

Karstofte å 2008-1

Holtum å 2004

Tangen 2008-2

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

26

Sequencing results series 2

Series 2

Series 1

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.