Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic
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Date
2019
Journal Title
Journal ISSN
Volume Title
Publisher
Epidemiology and Infection
Abstract
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 (β). 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 β 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 β 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.
Description
Keywords
Analysis of data, Avian flu, Mathematical modelling, Veterinary epidemiology
Citation
Ssematimba A, Malladi S, Hagenaars TJ, Bonney PJ, Weaver JT, Patyk KA, Spackman E, Halvorson DA, Cardona CJ (2019). Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic. Epidemiology and Infection 147, e179, 1–8. https://doi.org/ 10.1017/S0950268819000633