Diann J Prosser Cody M Kent Jeffery D Sullivan Kelly A Patyk Mary-Jane McCool Mia Kim Torchetti Kristina Lantz Jennifer M Mullinax 20240312 raster digital data Reston, Virginia U.S. Geological Survey https://doi.org/10.5066/P91AP4XL Diann J Prosser Cody M Kent Jeffery D Sullivan Kelly A Patyk Mary-Jane McCool Mia Kim Torchetti Kristina Lantz Jennifer M Mullinax 2024 publication These data describe the creation, execution, and results of an effort to model the risk of avian influenza transmission across the wild waterfowl - domestic poultry interface at weekly intervals for the contiguous United States. Some of these data were collated as inputs for models to identify transmission risk for avian influenza viruses from wild waterfowl to domestic poultry. OTher data are the actual model outputs. Finally, the analysis code is included. Each zipped folder in this release also contains a single text file explaining the contents of the folder to facilitate ease of use. 2024 publication date Complete None planned contiguous United States -124.9805 -66.9727 49.3824 24.8466 None avian influenza poultry wild waterfowl USGS Metadata Identifier USGS:65775d6ad34e952b22746199 None contiguous United States None American Black Duck American Wigeon Blue-winged Teal Brant Goose Bufflehead Cackling Goose Canada Goose Canvasback Cinnamon Teal Common Eider Common Goldeneye Gadwall Greater Scaup Greater White-fronted Goose Green-winged Teal Hooded Merganser Lesser Scaup Long-tailed Duck Mallard Mottled Duck Mute Swan Northern Pintail Northern Shoveler Redhead Ring-necked Duck Ross's Goose Ruddy Duck Snow Goose Tundra Swan Wood Duck Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Anseriformes Family Anatidae Genus Anas Species Anas rubripes TSN: 175068 Species Anas crecca TSN: 175081 Species Anas platyrhynchos TSN: 175063 Species Anas fulvigula TSN: 175070 Species Anas acuta TSN: 175074 Genus Mareca Species Mareca americana Species Mareca strepera Subspecies Mareca strepera strepera Genus Spatula Species Spatula discors Species Spatula cyanoptera Subspecies Spatula cyanoptera cyanoptera Species Spatula clypeata Genus Branta Species Branta bernicla TSN: 175011 Species Branta hutchinsii TSN: 714068 Species Branta canadensis TSN: 174999 Genus Bucephala Species Bucephala albeola TSN: 175145 Species Bucephala clangula TSN: 175141 Genus Aythya Species Aythya valisineria TSN: 175129 Species Aythya marila TSN: 175130 Species Aythya affinis TSN: 175134 Species Aythya americana TSN: 175125 Species Aythya collaris TSN: 175128 Genus Somateria Species Somateria mollissima TSN: 175155 Genus Anser Species Anser albifrons TSN: 175020 Species Anser rossii Species Anser caerulescens TSN: 175029 Genus Lophodytes Species Lophodytes cucullatus TSN: 175183 Genus Clangula Species Clangula hyemalis TSN: 175147 Genus Cygnus Species Cygnus olor TSN: 174985 Species Cygnus columbianus TSN: 174987 Genus Oxyura Species Oxyura jamaicensis TSN: 175175 Genus Aix Species Aix sponsa TSN: 175122 None. Please see 'Distribution Info' for details. None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Diann J Prosser U.S. Geological Survey, Northeast Region Research Wildlife Biologist mailing address

12100 Beech Forest Road

Laurel MD 20708 US 301-497-5914 dprosser@usgs.gov This research was supported by the USDA Animal and Plant Health Inspection Service (Cooperative Agreement 6000001762), the U.S. Geological Survey Ecosystems Mission Area, and the National Science Foundation (NSF) “PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention” (no. 2200310). The use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA or U.S. Government determination or policy. Data were derived in excel as .csv files or in R as raster files. Any software suitable for opening these file types should be sufficient for use and manipulation. Full description of model validation results are provided in the associated manuscript. AUC for the full model was 0.84. All data were manually reviewed for consistency with input data. Data represents all available information from the reported inputs and is limited to data available in said inputs. NA NA Daniel Fink 2020 raster digital data https://science.ebird.org/en/status-and-trends Digital and/or Hardcopy 2020 publication date eBird Status and Trends Provided inputs for species specific abundance estimates at weekly intervals. Cody M. Kent Andrew M. Ramey Joshua T. Ackerman Justin Bahl Sarah N. Bevins Andrew S. Bowman Walter M. Boyce Carol J. Cardona Michael L. Casazza Troy D. Cline Susan E. De La Cruz Jeffrey S. Hall Nichola J. Hill Hon S. Ip Scott Krauss Jennifer M. Mullinax Jacqueline M. Nolting Magdalena Plancarte Rebecca L. Poulson Jonathan A. Runstadler Richard D. Slemons David E. Stallknecht Jeffery D. Sullivan John Y. Takekawa Richard J. Webby Robert G. Webster Diann J. Prosser 20220729 publication Scientific Reports vol. 12, issue 1 n/a Springer Science and Business Media LLC https://doi.org/10.1038/s41598-022-17396-5 Digital and/or Hardcopy 2022 publication date species prevalence Provided rasters detailing spatio-temporal estimates of species specific avian influenza prevalence rates for wild waterfowl. Kelly A. Patyk Mary J. McCool-Eye David D. South Christopher L. Burdett Susan A. Maroney Andrew Fox Grace Kuiper Sheryl Magzamen 20201210 publication Geospatial Health vol. 15, issue 2 n/a PAGEPress Publications https://doi.org/10.4081/gh.2020.913 Digital and/or Hardcopy 2020 publication date hybrid poultry model Provided data detailing the spatial distribution of poultry production across the landscape. Overview The risk of a spillover event can be modeled as the relative transmission risk (RR) between wild birds and domestic poultry operations using the following equations: RR=W×P Where W is the estimated number of infected waterfowl present at a given time and place and P is the number of poultry operations in that location weighted by their risk of a spillover event occurring. This equation can be further broken down to: RR=∑s (Was×Wps )×∑t (P × Prt ) where Was is the relative abundance of waterfowl of species s, Wps is the percentage of those waterfowl predicted to be positive with avian influenza virus, Pnt is the number of poultry operations of a given type t, and Prt is the relative risk associated with each operation type. Each of these component variables is described in detail in the next step 2024 Model components Predicted relative abundance models have become available via eBird Status & Trends (https://ebird.org/science/status-and-trends, and we used these waterfowl relative abundance models as one of our model inputs. In short, these models provide estimated relative abundance of each species based on the expected count of individuals detected by an expert birder on a 1 hour, 1 km transect at an optimal time of day. These predictions are estimated for all 52 weeks of the year at a spatial resolution of 2.96 km2. In total, we included estimates for 30 common waterfowl (Anatidae) species, which included all species for which we have prevalence estimates (below). Comparing relative abundance among multiple species can be problematic, as these methods do not account for species-specific differences in detection probability. However, this should be mitigated here as most waterfowl species are of roughly comparable size, visibility, and behavior. The estimated percentage of infected waterfowl (Wps) of each species at weekly intervals was developed in a previous model of avian influenza prevalence in wild waterfowl. In short, that model combined data from the National Wild Bird Surveillance Program and the Influenza Research Database for 30 species of waterfowl. The model was then used to generate spatiotemporal predictions of the proportion of birds that would test positive for avian influenza virus for 30 waterfowl species at weekly intervals for each county in the United States. The number and type of poultry operations (Pft) comes from the “hybrid poultry model” developed by the U.S. Department of Agriculture (USDA) . This model uses a baseline population from the Farm Location and Agricultural Production Simulator (FLAPS) that combines a poultry farm suitability surface with poultry farm numbers and types from the USDA, National Agricultural Statistics Service (NASS), Census of Agriculture (CoA), to stochastically place likely farm locations and assign them an operation type. Operation type included the commodity type (broiler, layer, pullet, or turkey), sector (breeding or production), and category (backyard or commercial). In 594 U.S. counties with the greatest poultry production, the hybrid model incorporated remote sensing and artificial intelligence to detect buildings likely to be commercial poultry farms to improve the accuracy of the FLAPS predictions. Though there are likely some changes in poultry production numbers throughout the year (e.g., downtime between flock placement), these are static spatial data and have no temporal component. Finally, as there is known variation in the relative risk of different farm types, we developed a relative risk scaler for each poultry operation type. In short, this includes knowledge on risk by species and poultry type gained from several European studies (where data is available), as well as differences in risk between birds being housed indoors and outdoors. It has been well documented that different avian influenza virus strains vary with regard to differential risks, even within subtype. Of particular note are the H5 and H7 subtypes (defined by the hemagglutinin surface protein) which have the potential to mutate and become highly pathogenic after spilling over into domestic poultry. As such, we developed an additional pair of models focused on these two agriculturally important AIV subtypes. For these models, the overall risk was multiplied by the proportion of viruses expected for each subtype based on data from Kent et al. . This study presented the proportion of influenza positive birds expected to be infected with either the H5 or H7 subtype at the county level at monthly intervals for seven waterfowl species. As the taxonomic breadth of the available study was lower than that of our current efforts and because limited species differences were detected, for model input we averaged risks across all species. Additionally, the Kent et al. study provided predictions at monthly, instead of weekly intervals, so we interpolated these predictions to place them on the same weekly temporal scale as our models. In summary, four model sets were developed in this study: (a) primary models that are driven by LPAI endemically circulating waterfowl prevalence, (b) models targeted for H5 subtypes, (c) models targeted for H7 subtypes, and (d) the primary model set with environmental persistence components added to the equation. Each model set was conducted at two spatial scales: (a) ~2.96 km2 based on the waterfowl inputs (hereafter, 3 km2), and (b) county level which aligns with HPAI management and response. eBird Status and Trends species prevalence hybrid poultry model 2024 Raster Grid Cell 938 2023 1 Sinusoidal 0.0 0.0 0.0 coordinate pair 1 1 meters [WeekNumber]_[SpeciesName].tif A raster showing species specific prevalence estimates by week of year. Producer Defined Value Unique numeric value describing species specific prevalence rate. Species is identified in the file name. Week of year is identified in file name. File names are formated as Week_SpeciesName Producer Defined 0.019602785545714 0.12188678416332 American Black Duck_1.tif A raster showing species specific effective abundance estimates (prevalence multiplied by abundance). Producer Defined Value Unique numeric value describing effective waterfowl abundance, derived by multiplying species abundance from eBird Status and Trends by our prevalence estimates for each week of the year. Species is identified in the file name. Week of year is identified in file name. File names are formated as SpeciesName_Week Producer Defined 0.0 12.19846339137 _Week.1.tif Raster representing the relative risk of a transmission event from wild waterfowl to domestic poultry. Producer Defined Value Unique numeric values contained in each raster cell representing the relative risk of a transmission event from wild waterfowl to domestic poultry. Week of year is identified in the file name. Producer Defined 0.0 10528.078125 PoultryRisk.csv Comma Separated Value (CSV) file containing data. Producer Defined Species Type of poultry Producer Defined Chicken chicken Producer defined Turkey turkey Producer defined commodityType the specific use of poultry being grown Producer Defined broilers broilers Producer defined layers layers Producer defined layerpullets layerpullets Producer defined turkeys turkeys Producer defined Category value differentiating commercial and backyard farms Producer Defined Com commercial Producer defined BY backyard Producer defined Sector value differentiating the poultry sector type Producer Defined NA No Data Producer defined Production production farm Producer defined Breeding breeding farm Producer defined IndoorRR relative risk of poultry matrix given for birds kept indoors Producer Defined 0.2 7.7 OutdoorRR relative risk of poultry matrix given for birds kept outdoors Producer Defined 2.2 18.0 %Outdoor percent of birds kept outdoors Producer Defined 0.0 0.850756254 WeightedRisk relative weighted risk of farm type Producer Defined 0.217219656 16.46278941 U.S. Geological Survey GS ScienceBase mailing address

Denver Federal Center, Building 810, Mail Stop 302

Denver CO 80225 United States 1-888-275-8747 sciencebase@usgs.gov Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P91AP4XL None 20240312 Diann J Prosser U.S. Geological Survey, Northeast Region Research Wildlife Biologist mailing address

12100 Beech Forest Road

Laurel MD 20708 US 301-497-5914 dprosser@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999