Using surveillance data for early warning modelling of highly pathogenic avian influenza in Europe reveals a seasonal shift in transmission, 2016-2022

Abstract

Avian influenza in wild birds and poultry flocks constitutes a problem for animal welfare, food security and public health. In recent years there have been increasing numbers of outbreaks in Europe, with many poultry flocks culled after being infected with highly pathogenic avian influenza (HPAI). Continuous monitoring is crucial to enable timely implementation of control to prevent HPAI spread from wild birds to poultry and between poultry flocks within a country. We here utilize readily available public surveillance data and time-series models to predict HPAI detections within European countries and show a seasonal shift that happened during 2021-2022. The output is models capable of monitoring the weekly risk of HPAI outbreaks, to support decision making.

Figure 1

An overview of the different model comparisons and different baseline models used for selecting the final multivariate highly pathogenic avian influenza virus time-series models for the HPAI1621 and HPAI2122 data. Within-country/between-country effects denote that covariates/offsets/seasonality/power law was only included in the within-country/between-country effects of the epidemic component. All models included country area relative to all the country areas as offset in the endemic component.

Figure 2

Number of reported highly pathogenic avian influenza (H5 subtype) detections between 2016 and 2022 summed over 37 European countries (including Faroe Islands) shown (A) geographically as numbers per 10,000 km², and (B) over time. The dataset contained a total of 15,549 detections of varying sizes in both wild and domestic birds. The map in A) was created using the package tmap in R 4.1.2.

Figure 3

Country-wise model fit, and the relative contribution of model components based on the final multivariate time-series models for the HPAI1621 data. Dots show the actual counts of reported highly pathogenic avian influenza (H5 subtype) detections in domestic and wild birds. Only countries with > 200 detections are depicted. The last panel shows the overall model fit aggregated over all the 37 countries. Note that the scales on the Y-axes are different for some of the graphs, and zero/missing detections have been omitted. Although actual counts from week 47–52 in 2021 are depicted, they were not part of the training set in the model, and thus are not part of the model fit.

Figure 4

Country-wise model fit, and the relative contribution of model components based on the final multivariate time-series models for the HPAI2122 data. Dots show the actual counts of reported highly pathogenic avian influenza (H5 subtype) detections in domestic and wild birds. Only countries with > 200 detections are depicted. The last panel shows the overall model fit aggregated over all the 37 countries. Note that the scales on the Y-axes are different for some of the graphs, and zero/missing detections have been omitted. Although actual counts from week 44–49 in 2022 are depicted, they were not part of the training set in the model, and thus are not part of the model fit.

Figure 5

Simulation-based long-term forecast for (A) the HPAI1621 final model starting from the last week in 2019 (left-hand dot), and (B) the HPAI2122 final model starting from week 39 in 2021. The plots show weekly number of predicted and observed highly pathogenic avian influenza (H5 subtype) detections aggregated over all countries. The fan charts represent the 1% and 99% quantiles of the simulations (N = 500) each week; their mean is displayed as a white line. Actual reported number of detections are depicted with open circles. Data from week 47 to week 52 in 2021 for the HPAI1621 model and week 44–49 in 2022 in the HPAI2122 model were not used to train the models.