Data and code for "Strong and consistent effects of waterbird composition on HPAI H5 occurrences across Europe"

Study abstract:Since 2014, highly pathogenic avian influenza (HPAI) H5 viruses of clade 2.3.4.4 have been dominating the outbreaks across Europe, causing massive deaths among poultry and wild birds. However, the factors shaping these broad-scale outbreak patterns, especially those related to waterbird community composition, remain unclear. In particular, we do not know whether these risk factors differ from those of other H5 clades. Addressing this knowledge gap is important for predicting and preventing future HPAI outbreaks. Using extensive waterbird survey datasets from about 6,883 sites, we here explored the effect of waterbird community composition on HPAI H5Nx (clade 2.3.4.4) spatial patterns in 2016/17 and 2020/21 epidemics in Europe, and compared it with 2005/06 HPAI H5N1 (clade 2.2) epidemic. We showed that HPAI H5 occurrences in wild birds in the three epidemics were strongly associated with very similar waterbird community attributes, which suggested that, in nature, similar interspecific transmission processes operate between the HPAI H5 subtypes or clades. Importantly, community phylogenetic diversity consistently negatively affected H5 occurrence in all three epidemics, suggesting a dilution effect of phylogenetic diversity. In contrast, waterbird community variables showed much weaker associations with HPAI H5Nx occurrence in poultry. Our results demonstrate that models based on previous epidemics can predict future HPAI H5 patterns in wild birds, implying that it is important to include waterbird community factors in future HPAI studies to predict outbreaks and improve surveillance activities.File descriptions:"1 Analyzed Data.xlsx": The processed dataset for the regression analysis"FigData2 Single-variable Results.csv": The dataset used to generate the Figure 2."FigData3 variance partitioning.csv": The dataset used to generate the Figure 3."FigData4 Multi-variable results.csv": The dataset used to generate the Figure 4."1 Regression Analyses.R": The R code used for the regression analysis."Fig 2 Codes.R": The R code for generating Figure 2."Fig 3 Codes.R": The R code for generating Figure 3."Fig 4AC Codes.R": The R code for generating Figure 4."Distance_matrix_of_survey_locations.RData": The R data contains the locations of bird survey sites.