Farm-level reproduction number during an epidemic of infectious salmon anemia virus in southern Chile in 2007-2009

An epidemic of infectious salmon anemia virus (ISAV) has greatly impacted salmon production in Chile with devastating social and economic consequences. The epidemic is analyzed here and is likely the largest ISAV outbreak reported affecting one of the most productive regions for salmon farming activities in the world. After re-emerging in 2007, ISAV rapidly expanded the following two years, both in magnitude and geographic range, affecting about 65% and 50% of salmon farms located at the 10th and 11th regions of Chile, respectively. A useful metric for the control of infectious diseases that quantifies the progression of an epidemic is the reproduction number at the farm level (R_f), which describes the mean number of secondary cases generated by an infectious farm. The parameter in this study was estimated for individual farms (R_fi), specific phases (R_tf), and for the entire epidemic (R_f) by using several analytical approaches based on the characterization of the epidemic curves for the two regions. For the initial spread and the epidemic growth phase, initial and intrinsic growth rates were used to estimate R_tf. In addition, two approaches (epidemic final size and nearest neighbor analyses) were used to obtain an individual (R_fi) and overall estimate of R_f for the complete epidemic. In general, two distinct regional patterns of spread were identified. In the 10th region, after an explosive initial spread of ISAV in which R_tf reached 12.0-16.9, a smaller epidemic growth of 1.6≤R_tf≥2.5 and a final burnout with R_tf<1 were observed. For the 11th region, R_tf only reached 2.4 during the initial spread phase, ranged from 1.6≤R_tf≥4.4 during the epidemic growth phases and ended when R_tf was <1.0. The epidemic was characterized by clustering of ISAV 'superspreaders' farms i.e., farms with statistically significantly (P<0.047) higher R_fi values. Distances between pairs of infected farms were statistically significantly (P=0.003) shorter in the 10th compared to the 11th region. Overall, R_f ranged from 1.6 to 2.5 and 1.3 to 1.7 in the 10th and 11th regions, respectively. Our findings suggest that control efforts were able to protect 38-60% and 23-41% of the farms in the 10th and 11th regions, respectively, and may have resulted in the epidemic not spreading further. In addition, control strategies in highly populated areas using a control zone of at least 10km radius may be more effective than the 5km zone recommended by the World Animal Health Organization.