Scottish Marine and Freshwater Science Volume 4 Number 3: Epidemiology and Control of an Outbreak of Viral Haemorrhagic Septicaemia in Wrasse Around Shetland Commencing 2012

Footnotes

¹ Parenti, P. and Randall, J.E. 2000. An annotated checklist of the species of labroid fish families Labridae and Scaridae. Ichthyological Bulletin of the J.L.B. Smith Institute of Ichthyology, 68, 1-97.

² Torrissen, O., Jones, S., Asche, F., Guttormsen, A., Skilbrei, O.T., Nilsen, F., Horsberg, T.E. and Jackson, D. 2013. Salmon lice - impact on wild salmonids and salmon aquaculture. Journal of Fish Diseases, 36, 171-194.

³ Treasurer, J.W. 2012. Diseases of north European wrasse (Labridae) and possible interactions with cohabited farmed salmon, Salmo salar L. Journal of Fish Diseases 35, 555-562.

⁴ The American English spelling of this virus, and others, is defined by the International Committee on Taxonomy of Viruses.

⁵ van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S.M., Maniloff, J., Mayo, M.A., McGeoch, D.J., Pringle, C.R. and Wickner, R.B. 2000. Virus Taxonomy. San Diego, Academic Press.

⁶ Skall, H.F., Olesen, N.J. and Mellergaard, S. 2005. Viral haemorrhagic septicaemia virus in marine fish and its implications for fish farming - a review. Journal of Fish Diseases, 28, 509-529.

⁷ Council Directive ( EC) 2006/88/ EC on animal health requirements for aquaculture animals and products thereof, and on the prevention and control of certain diseases in aquatic animals [2006]. Official Journal of the European Union, L328, 14-56.

⁸ The Aquatic Animal Health (Scotland) Regulations 2009 (S.S.I. 2009/85).

⁹ Snow, M., Cunningham, C.O., Melvin, W.T. and Kurath, G. 1999. Analysis of the nucleoprotein gene identifies distinct lineages of viral haemorrhagic septicaemia virus within the European marine environment. Virus Research, 63, 35-44.

¹⁰ World Organisation for Animal Health 2012. On-line update of Manual of Diagnostic Tests for Aquatic Animals; sixth edition. Paris, OIE. Available at http://www.oie.int/international-standard-setting/aquatic-manual/access-online/ (accessed 31 May 2013).

¹¹ Commission Implementing Directive ( EU) 2012/31/ EU amending Annex IV of Council Directive 2006/88/ EC as regards the list of fish species susceptible to Viral haemorrhagic septicaemia and the deletion of the entry for Epizootic ulcerative syndrome [2012]. Official Journal of the European Union, L297, 26-28.

¹² Council Directive ( EEC) 82/894/ EEC on the notification of animal diseases within the Community [1982]. Official Journal of the European Communities, L378, 58-62.

¹³ Commission Regulation ( EC) No 1251/2008 of 12 December 2008 implementing Council Directive 2006/88/ EC as regards conditions and certification requirements for the placing on the market and the import into the Community of aquaculture animals and products thereof and laying down a list of vector species [2008]. Official Journal of the European Union, L337, 41-75.

¹⁴ Kulldorff, M. 1997. A spatial scan statistic. Communications in Statistics - Theory and Methods, 26, 1481-1496.

¹⁵ Kulldorff. M. and Information Management Services 2011. SaTScan™ v9.1.1; software for the spatial and space-time scan statistics. www.satscan.org (accessed 31 May 2013).

¹⁶ Gravell, M. and Malsberger, R.G. 1965. A permanent cell line from the fathead minnow ( Pimephales promelas). Annals of the New York Academy of Sciences, 126, 555-565.

¹⁷ Lorenzen, N., Olesen, N.J. and Jørgensen, P.E.V. 1988. Production and characterisation of monoclonal antibodies to four Egtved virus structural proteins. Diseases of Aquatic Organisms, 4, 35-42.

¹⁸ This involves fitting a beta-binomial distribution to the number of VHS positive wrasse and the number of wrasse tested on VHS positive farms around Shetland. This distribution is used to estimate the probability of each farm out-with Shetland testing VHS positive given the number of wrasse tested on those farms and assuming that the farms are hypothetically infected. The mean of these probabilities is the chance of detecting an individual farm out-with Shetland as VHS positive. Confidence intervals are obtained by subjecting the probabilities of detection to a bootstrap corrected for bias and acceleration.

¹⁹ Matejusova, I., McKay, P., McBeath, A.J.A., Collet, B. and Snow, M. 2008. Development of a sensitive and controlled real-time RT-PCR assay for viral haemorrhagic septicaemia virus ( VHSV) in marine salmonid aquaculture. Diseases of Aquatic Organisms, 80, 137-144.

²⁰ Bland, F., Snow, M., Garver, K.A. and Matejusova, I. 2013. Genotype-specific Taqman assays for the detection and rapid characterisation of European strains of viral haemorrhagic septicaemia virus. Journal of Virological Methods, 187, 209-214.

²¹ Snow, M., Bain, N., Black, J., Taupin, V., Cunningham, C.O., King, J.A., Skall, H.F. and Raynard R.S. 2004. Genetic population structure of marine viral haemorrhagic septicaemia virus ( VHSV). Diseases of Aquatic Organisms, 61, 11-21.

²² Sequencher® version 4.9 sequence analysis software, Gene Codes Corporation, Ann Arbor, MI USA www.genecodes.com (accessed 31 May 2013).

²³ www.ebi.ac.uk/services/dna-rna (accessed 31 May 2013).

²⁴ The isolates comprised isolate DK-Hededam (Accession No. Z93412 for both N- and G- genes) as a representative of genotype I, isolate DK-1p53 (AJ130921 & AY546577 for N- and G- genes respectively) as a representative of genotype II, isolate UK-H17/2/95 (AJ130924 & AY546629 for N- and G-gene respectively) as a representative of genotype III and isolate US-Makah (X59241 & U28747 for N- and G-gene respectively) as a representative of genotype IV.

²⁵ Einer-Jensen, K., Ahrens, P. and Lorenzen, N. 2005. Parallel phylogenetic analysis using the N, G, or Nv gene from a fixed group of VHSV isolates reveal the same overall genetic typing. Diseases of Aquatic Organisms, 67, 39-45.

²⁶ Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J.D. and Higgins, D.G. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(539), 1-6.

²⁷ R Core Development Team 2011 & 2012. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, www.R-project.org (accessed 31 May 2013).

²⁸ Canty, C. and Ripley, B. 2012. boot: bootstrap R (S-Plus) functions. R package version 1.3-7.

²⁹ Venables, W. N. and Ripley, B. D. 2002. Modern Applied Statistics with S. Fourth edn. New York, Springer.

³⁰ Yee, T.W. 2010. The VGAM package for categorical data analysis. Journal of Statistical Software, 32(10), 1-34.

³¹ Salama, N.K.G. and Murray, A.G. 2011. Farm size as a factor in hydrodynamic transmission of pathogens in aquaculture fish production. Aquaculture Environment Interactions, 2, 61 - 74.

³² Gadoids in farm pens were sampled on two occasions (February and May 2013). One of 55 poor cod was VHS positive from the first sampling and one of three poor cod on the second sampling. Confidence limits were estimated by analysing the grouped data with a generalised linear model comprising an intercept only assuming a binomial error distribution and corrected for over-dispersion. The wide CI are a consequence of the over-dispersion between samplings.

³³ Evaluated by comparing the magnitude of the variance of the number of VHS positive pools for each combination of species and tow with the expected variance estimated from multiple random assignments of VHS positive status to pools.

³⁴ Swofford, D. L. 2003. PAUP*; Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland, Massachusetts, Sinauer Associates.

³⁵ Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.

³⁶ Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.

³⁷ Smail, D.A. 2000. Isolation and identification of viral haemorrhagic septicaemia ( VHS) viruses from cod Gadus morhua with the ulcus syndrome and haddock Melanogrammus aeglefinus having skin haemorrhages in the North Sea. Diseases of Aquatic Organisms, 41, 231-235.

³⁸ Fitch, W. M. 1971. Toward defining the course of evolution: minimum change for a specified tree topology. Systematic Zoology, 20, 406-416.

³⁹ The analysis comprised 1000 bootstrap replications of maximum parsimony branch-and-bound searches for the shortest unrooted tree using unweighted and unordered nucleic acid sequence differences of the N- and G-genes incorporated into the same analysis. Genotype III isolate UK-H17/2/95 was included for comparative purposes. While analyses utilising more sophisticated models are possible, the small number of substitutions available for analysis and uncertainty regarding the appropriate outgroup(s) suggests that this simple approach is the most suitable. The results of this analysis were confirmed using neighbor-joining.

⁴⁰ The detailed protocol of this virus isolation with ELISA confirmation test is not necessarily the same as that described in section 5.2 but was in accordance with OIE recommendations current at the time of testing.

⁴¹ Zepeda-Sein, C. 1998. Méthode d'évaluation des risques zoosanitaires lors des échanges internationaux. In Séminaire sur la Sécurité Zoosanitaire des Échanges dans les Caraibes, 9-11 Décembre 1997, Port of Spain,(Trinidad and Tobago), 2-17, Paris, OIE. It has not been possible to obtain the original source and the version used is that given and translated in Dufour, B., Boisseleau, D., Chartier, C., Durand, B., Ganiere, J., Guillotin, J., Lancelot, R., Moutou, F., Saegerman, C., Thebault, A and Toma, B. 2008. A Qualitative Risk Assessment Method in Animal Health. Maisons-Alfort, Agence Francaise de Securite Sanitaire des Aliments.

⁴² Commission Decision of 31 October 2008 implementing Council Directive 2006/88/ EC as regards surveillance and eradication programmes and disease-free status of Member States, zones and compartments. Official Journal of the European Union, L63, 15-39.

⁴³ Commission Decision of 22 March 2010 amending Annex I to Decision 2009/177/ EC as regards surveillance programmes for Ireland and Hungary and the disease-free status of Ireland for certain aquatic animal diseases. Official Journal of the European Union, L75, 28-32.

⁴⁴ Smail, D.A. 1995. Isolation and identification of viral haemorrhagic septicaemia ( VHS) virus from North Sea cod ( Gadus morhua L.). International Council for the Exploration of the Sea, Mariculture Committee, CM 1995/F:15.

⁴⁵ King, J.A., Snow, M., Smail, D.A. and Raynard, R.S. 2001. Distribution of viral haemorrhagic septicaemia virus in wild fish species of the North Sea, North East Atlantic Ocean and Irish Sea. Diseases of Aquatic Organisms, 47, 81-86.

⁴⁶ Salama, N.K.G. and Murray A.G. 2013. A comparison of modelling approaches to assess the transmission of pathogens between Scottish fish farms: the role of hydrodynamics and site biomass. Preventive Veterinary Medicine, 108, 285-293.

⁴⁷ Gregory, A., Munro, L.A., Snow, M., Urquhart, K.L., Murray, A.G. and Raynard R.S. 2008. An experimental investigation on aspects of Infectious salmon anaemia virus ( ISAV) infection dynamics in seawater Atlantic salmon, Salmo salar L. Journal of Fish Diseases, 32, 481-489.

⁴⁸ Traxler, G.S., Roome, J.R. and Kent, M.L. 1993. Transmission of Infectious hematopoietic necrosis virus in seawater. Diseases of Aquatic Organisms, 16, 111-114.

⁴⁹ Kim, R.K. and Faisal, M. 2012. Shedding of Viral haemorrhagic septicaemia virus (genotype IVb) by experimentally infected Muskellunge ( Esoc masquinongy). The Journal of Microbiology, 50, 278-284.

⁵⁰ Kocan, R., Bradley, M., Elder, N., Meyers, T., Batts, W. and Winton, J. 1997. North American strain of Viral haemorrhagic septicaemia virus is highly pathogenic for laboratory-reared Pacific herring. Journal of Aquatic Animal Health, 9, 279-290.

⁵¹ Kocan, R.M., Hershberger, P.K. and Elder, N.E. 2001. Survival of the North American strain of Viral haemorrhagic septicemia virus ( VHSV) in filtered seawater and seawater containing ovarian fluid, crude oil, and serum-enriched culture medium. Diseases of Aquatic Organisms, 44, 75-78.

⁵² Hawley, L.M. and Garver, K.A. 2008. Stability of Viral haemorrhagic septicaemia virus ( VHSV) in freshwater and seawater at various temperatures. Diseases of Aquatic Organisms, 82, 171-178.

⁵³ Turrell, W.R. 1990. Simulation of advection and diffusion of released treatments in Scottish sea lochs. Scottish Fisheries Working Paper No. 16/90.

⁵⁴ Hughes, S.L, Beaton, J. and Slesser, G. 2006. Current meter measurements east of Shetland October 2004-October 2005: monitoring oceanic exchanges with the North Sea - data report. Fisheries Research Service Internal Report No. 10/06.

⁵⁵ Scottish Executive 2000. Final report of the joint government/industry working group on infectious salmon anaemia ( ISA). Edinburgh, Scottish Executive.

⁵⁶ Murray A.G., Munro L.A., Wallace I.S., Berx B., Pendrey D., Fraser D. and Raynard R.S. 2010. Epidemiological investigation into the re-emergence and control of an outbreak of infectious salmon anaemia in the Shetland Islands, Scotland. Diseases of Aquatic Organisms, 91, 189-200.