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.
Highlights
Pathogenic avian influenza (HPAI) virus epizootics often lead to enormous economic losses and, for some of the virus strains with a zoonotic potential, the risk of infecting humans is of an even greater concern
Experimental inoculation studies can provide data regarding the timing of infection and/or the onset and duration of shedding which are beneficial for estimating disease state durations, disease mortality rates, as well as transmission rate parameters
Using mortality data collected from flocks in the field during epidemics provides an option to infer the possible timing of infection for individual birds and estimate the rate of disease transmission for commercial poultry production systems
Summary
Pathogenic avian influenza (HPAI) virus epizootics often lead to enormous economic losses and, for some of the virus strains with a zoonotic potential, the risk of infecting humans is of an even greater concern. The first HPAI H5N2 virus-infected commercial turkey farm in Minnesota was detected in early March 2015 [1, 2]. A total of 160 commercial turkey operations (104 of which were in Minnesota) were affected, leading to the destruction of 7.4 million turkeys. For the other affected poultry operation types, 43 million table-egg layers and pullets were culled [1]. The impact on the US economy was estimated to be close to US$3.3 billion, of which US$1.6 billion was in direct losses in euthanised animals and the rest was due to restocking costs and lost future production among others [1, 3]
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