Co-infection patterns of infectious salmon anaemia and sea lice in farmed Atlantic salmon, Salmo salar L., in southern Chile (2007–2009) P Valdes-Donoso 1 , F O Mardones 1 , M Jarpa 2 , M Ulloa 2 , T E Carpenter 1,3 and A M Perez 1,4 1 Center for Animal Disease Modeling and Surveillance (CADMS), UC Davis, Davis, CA, USA 2 National Fisheries Service, Valparaiso, Chile 3 EpiCentre, Massey University, Palmerston North, New Zealand 4 CONICET and Facultad de Ciencias Veterinarias UNR, Rosario, Argentina Abstract Infectious salmon anaemia virus (ISAV) caused a large epidemic in farmed Atlantic salmon in Chile in 2007–2009. Here, we assessed co-infection pat- terns of ISAV and sea lice (SL) based on surveil- lance data collected by the fish health authority. ISAV status and SL counts in all Atlantic salmon farms located in the 10th region of Chile were regis- tered monthly from July 2007 through December 2009. Each farm was categorized monthly accord- ing to its ISAV and SL status. A multinomial time- space scan test using a circular window was applied to identify disease clusters, and a multivariate regression model was fitted to quantify the associa- tion between disease-clustering and farm-manage- ment factors. Most of the identified clusters (9/13) were associated with high SL burdens. There were significant associations (P < 0.05) between man- agement factors and ISAV/SL status. Areas in which good management practices were associated with a reduced disease risk were identified. The findings of this study suggest that certain management prac- tices can effectively reduce the risk of SL and ISAV in the face of an epidemic and will be helpful towards creating an effective disease control pro- gramme in Chile. Keywords: Chile, infectious salmon anaemia, mul- tinomial logistic regression, multinomial scan test, salmon farming, sea lice. Introduction Salmon-farming activities in Chile have increased rapidly since the early 1980s, with a mean annual growth rate of 52% until 1998, making Chile one of the largest salmon producers in the world (Bjørndal 2002). Such development was facilitated by the appropriate climatic and geographic charac- teristics of certain regions of Chile, the use of modern husbandry methods and investments, the labour supply and low production costs, and the more liberalized economic policies (Barton 1997; Bjørndal 2002; Phyne & Mansilla 2003; Barton & Fløysand 2010). Fish growth and fattening phases occur in the 10th, 11th and 12th regions of Chile (Ibieta et al. 2011). Until the 2007 infec- tious salmon anaemia virus (ISAV) epidemic, the 10th region had the largest number of active sal- mon farms (375/533) and was the major salmon- producing region in the country (Halwart, Soto & Arthur 2007; Ibieta et al. 2011). The economic ‘boom’ of the industry resulted in an increased stocking density, reaching 1136 tons/farm, which was reflected by the number of fish per cage, the number of cages per farm and the number of farms in a given geographical area, all of which contributed to increasing the risk of exposure to sanitary hazards (Barton 1997; Smith et al. 2001; Asche et al. 2009; Barton & Fløysand 2010; Ibie- ta et al. 2011; Iizuka & Katz 2011). The emergence of infectious diseases in salmon in both seawater (SW) and freshwater (FW) stages has increased in Chile (Ibieta et al. 2011). At the beginning of the industry in the 1980s, sea lice Correspondence P Valdes-Donoso, 1044 Haring Hall. One Shields Avenue. Davis, CA 95616, USA (e-mail: pvaldesdonoso@ ucdavis.edu) 353 Ó 2013 Blackwell Publishing Ltd Journal of Fish Diseases 2013, 36, 353–360 doi:10.1111/jfd.12070