Estimating adequate contact rates and time of Highly Pathogenic Avian Influenza virus introduction into individual United States commercial poultry flocks during the 2022/24 epizootic

Ssematimba, A.; Malladi, S.; Bonney, P. J.; St. Charles, K. M.; Hutchinson, H. C.; Schoenbaum, M.; Marusak, R.; Culhane, M. R.; Cardona, C. J.

doi:10.1101/2024.09.08.611909

bioRxiv · 10.1101/2024.09.08.611909

Estimating adequate contact rates and time of Highly Pathogenic Avian Influenza virus introduction into individual United States commercial poultry flocks during the 2022/24 epizootic

Ssematimba, A.·Malladi, S.·Bonney, P. J.·St. Charles, K. M.·Hutchinson, H. C.·Schoenbaum, M.·Marusak, R.·Culhane, M. R.·Cardona, C. J.

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Abstract

Following confirmation of the first case of the ongoing U.S. HPAI H5N1 epizootic in commercial poultry on February 8, 2022, the virus has continued to devastate the U.S. poultry sector and the pathogen has since managed to cross over to livestock and a few human cases have also been reported. Efficient outbreak management benefits greatly from timely detection and proper identification of the pathways of virus introduction and spread. In this study, using changes in mortality rates as a proxy for HPAI incidence in a layer, broiler and turkey flock, mathematical modeling techniques, specifically the Approximate Bayesian Computation algorithm in conjunction with a stochastic within-flock HPAI transmission model, were used to estimate the time window of pathogen introduction into the flock (TOI) and adequate contact rate (ACR) based on the daily mortality and diagnostic test results. The estimated TOI was then used together with the day when the first positive sample was collected to calculate the most likely time to first positive sample (MTFPS) which reflects the time to HPAI detection in the flock. The estimated joint (i.e., all species combined) median of the MTFPS for different flocks was six days, the joint median most likely ACR was 6.8 newly infected birds per infectious bird per day, the joint median R0was 13 and the joint median number of test days per flock was two. These results were also grouped by species and by epidemic phase and discussed accordingly. We conclude that findings from this and related studies are beneficial for the different stakeholders in outbreak management and combining TOI analysis with complementary approaches such as phylogenetic analyses is critically important for improved understanding of disease transmission pathways. The estimated parameters can also inform models used for surveillance design, risk analysis, and emergency preparedness.

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Ssematimba, A., Malladi, S., Bonney, P. J., St. Charles, K. M., Hutchinson, H. C., Schoenbaum, M., Marusak, R., Culhane, M. R., Cardona, C. J.. 2024-09-09. Estimating adequate contact rates and time of Highly Pathogenic Avian Influenza virus introduction into individual United States commercial poultry flocks during the 2022/24 epizootic. https://doi.org/10.1101/2024.09.08.611909

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