Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic.

Better control of highly pathogenic avian influenza ( HPAI) outbreaks requires deeper understanding of within- flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within- flock transmission rate parameter ( ss). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model ( GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI- like mortality to improve the accuracy of estimates from the back- calculation approach. The estimated ss was 3.2 ( 95% confidence interval ( CI) 2.3- 4.3) per day with a basic reproduction number of 12.8 ( 95% CI 9.2- 17.2). Although flock- level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated ss was highly sensitive to the bird- level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back- calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.