(1) develop a novel environmental surveillance platform that will give poultry farmers advanced warning of highly pathogenic avian influenza (HPAI) in their area and will enable rapid environmental…

The Department of Agriculture Animal and Plant Health Inspection Service (APHIS) awarded a $803,771 Cooperative Agreement to the Trustees of Indiana University on April 1, 2026, under the Plant and Animal Disease, Pest Control, and Animal Care program (CFDA 10.025) to develop and validate an environmental surveillance platform for highly pathogenic avian influenza (HPAI) detection.

Indiana University will conduct field, laboratory, and desk-based activities across three environmental domains. In aquatic environments, the recipient will sample surface water; in terrestrial environments, it will sample coprophagous blow flies; and in the built environment, it will sample wastewater from treatment plants. Collected samples will be analyzed using digital PCR for specific influenza genes, mitochondrial DNA sequencing to identify infected wildlife species, and whole genome sequencing to understand HPAI transmission. Indiana University will validate source-tracking methods through partnerships with the Indiana Department of Natural Resources, sampling wild birds (alive and dead) and hunter-harvested ducks. Controlled feeding studies will assess how long influenza virus persists in flies under varying environmental conditions. The recipient will identify optimal sampling locations and frequencies, develop a public-facing real-time dashboard to alert commercial poultry farms in Indiana to HPAI circulation in wildlife, and identify wildlife species of greatest concern for transmission to poultry to enable species-targeted interventions.

Work is performed in Bloomington, Indiana, with a period of performance extending from April 1, 2026, through May 3, 2029.

(1) develop a novel environmental surveillance platform that will give poultry farmers advanced warning of highly pathogenic avian influenza (HPAI) in their area and will enable rapid environmental surveillance during the response to an outbreak; and (2) validate and implement a molecular method to pinpoint which wildlife species in a region are infected by HPAI. We will conduct field, lab, and desk-based activities to achieve our objectives. In the field, we will monitor aquatic environments by sampling surface water, terrestrial environments by sampling coprophagous blow flies, and the built environment by sampling wastewater from nearby treatment plants. We will analyze the samples we collect for molecular HPAI signals using digital PCR for specific influenza genes, mitochondrial DNA sequencing to identify which species are the source of the infection, and whole genome sequencing to understand HPAI transmission. We will validate our results on the source of infection by sampling wild birds (alive and dead) and hunter-harvested ducks in partnership with the indiana department of natural resources. To validate the new method of using flies as biomonitors, we will conduct controlled feeding studies to assess how long influenza virus persists in flies under different environmental conditions. This project will identify the best sampling locations and best sampling frequency for collecting data on HPAI circulation in wildlife. The project will develop a public-facing dashboard to share results in real time with commercial poultry farms in indiana. The dashboard will give the farms early warning that HPAI is circulating in wildlife. In addition, our source tracking methods will identify the species of greatest concern for HPAI transmission to poultry, enabling species-targeted interventions to prevent transmission. This project will provide actionable data to commercial poultry farms in indiana, to our colleagues at state agencies (i.e., indiana board of animal health, indiana department of natural resources), and to our collaborators in the poultry industry (i.e., indiana state poultry association). The environmental surveillance platform will be rapidly scalable so that other states with poultry industries suffering from HPAI can adopt the platform for longitudinal monitoring and outbreak response.