Global risk mapping of highly pathogenic avian influenza H5N1 and H5Nx in the light of epidemic episodes occurring from 2020 onward

Reviewer #1 (Public review):

Summary:

The authors aim to predict ecological suitability for the transmission of highly pathogenic avian influenza (HPAI) using ecological niche models. This class of models identify correlations between the locations of species or disease detections and the environment. These correlations are then used to predict habitat suitability (in this work, ecological suitability for disease transmission) in locations where surveillance of the species or disease has not been conducted. The authors fit separate models for HPAI detections in wild birds and farmed birds, for two strains of HPAI (H5N1 and H5Nx) and for two time periods, pre- and post-2020. The authors also validate models fitted to disease occurrence data from pre-2020 using post-2020 occurrence data.

Strengths:

The authors follow the established methods of Dhingra et al., 2016 to provide an updated spatial assessment of HPAI transmission suitability for two time periods, pre- and post-2020. They explore further methods of model cross-validation and consider the diversity of the bird species that HPAI has been detected in.

Weaknesses:

The precise ecological niche that the authors are modelling here is ambiguous: if we treat the transmission of HPAI in the wild bird population and in poultry populations as separate transmission cycles, linked by spillover events, then these transmission cycles are likely to have fundamentally different ecological niches. While an "index case" in farmed poultry is relevant to the wildlife transmission cycle, further within-farm and farm-to-farm transmission is likely to be contingent on anthropogenic factors, rather than the environment. Similarly, we would expect "index cases" in outbreaks of HPAI in mammals to be relevant to transmission risk in wild birds - this data is not included in this manuscript. Such "index cases" in farmed poultry occur under separate ecological conditions to subsequent transmission in farmed poultry, so should be separated if possible. Some careful editing of the language used in the manuscript may elucidate some of my questions related to model conceptualisation.

The authors' handling of sampling bias in disease detection data in poultry is possibly inappropriate: one would expect the true spatial distribution of disease surveillance in poultry to be more closely correlated with poultry farming density, in contrast to human population density. This shortcoming in the modelling workflow possibly dilutes a key finding of the Results, that the transmission risk of HPAI in poultry is greatest in areas where poultry farming density is high.

Reviewer #2 (Public review):

Summary:

This study aimed to determine which spatial factors (conceived broadly as environmental, agronomic and socio-economic) explain greater avian influenza case numbers reported since 2020 (2020--2022) by comparing similar models built with data from the period 2015--2020. The authors have chosen an environmental niche modelling approach, where detected infections are modelled as a function of spatial covariates extracted at the location of each case. These covariates are available over the entire world so that the predictions can be projected back to space in the form of a continuous map.

Strengths:

The authors use boosted regression trees as the main analytical tool, which always feature among the best-performing models for environmental niche models (also known as habitat suitability models). They run replicate sets of the analysis for each of their model targets (wild/domestic x pathogen variant), which can help produce stable predictions. The authors take steps to ameliorate some forms of expected bias in the detection of cases, such as geographic variation in surveillance efforts, and in general more detections near areas of higher human population density.

Weaknesses:

The study is not altogether coherent with respect to time. Data sets for the response (N5H1 or N5Hx case data in domestic or wild birds ) are divided into two periods; 2015--2020, and 2020--2022. Each set is modelled using a common suite of covariates that are not time-varying. That suggests that causation is inferred by virtue of cases being in different geographic areas in those two time periods. Furthermore, important predictors such as chicken density appear to be informed (in the areas of high risk) from census data from before 2010. The possibility for increased surveillance effort *through time* is overlooked, as is the possibility that previously high-burden locations may implement practice changes to reduce vulnerability.