Montana State wins $1.9 million to study how bird flu attacks chicken gut cells

From flock-level losses to single-cell biology

When highly pathogenic avian influenza (HPAI) hits a poultry operation, the response is blunt: cull the entire flock. There is no approved treatment, vaccination remains complicated by trade restrictions and uncertain efficacy, and the economic losses are staggering. But most research on H5N1 and related strains has examined the virus's impact at the level of the whole bird - tracking symptoms, mortality, and transmission patterns. A new $1.9 million USDA grant to Montana State University aims to go much deeper.

Emma Loveday, an assistant professor in MSU's Department of Microbiology and Cell Biology, will lead a team examining how avian influenza infection impacts individual cells in the chicken intestine. The grant is part of a national USDA initiative that intensified after the unexpected jump of HPAI into dairy cattle in 2024 - one of the first known instances of that type of cross-species transmission.

Why the gut, and why organoids?

Bird flu does not look like human flu. Infected chickens do not cough and sneeze. The virus transmits through breath, feathers, and fecal matter in environments where birds are in close contact. The intestine is a critical battleground for infection, but studying viral dynamics in a living gut is impractical and raises biosafety challenges.

The MSU team's approach sidesteps this by building organoids - miniature organ structures cultivated in the lab that mimic different regions of the avian gut. Loveday will work alongside Diane Bimczok, an expert in organoid models and director of MSU's Cellular Analysis Core, and Matt Taylor, whose research spans viral evolution and immune system responses. Ron June from MSU's Department of Mechanical and Industrial Engineering rounds out the team.

By infecting these organoids with HPAI strains and observing the cellular response in detail, the researchers hope to understand how the virus grows, spreads, and propagates at a scale that whole-animal studies cannot achieve. The organoids and resulting data will be shared with the broader scientific community.

The vaccination dilemma

Vaccination seems like an obvious solution, but the reality is complicated. Numerous HPAI vaccines are in development, yet their efficacy remains unclear. Even if a vaccine reduces disease severity, vaccinated birds may still carry and shed the virus, creating a silent reservoir. And there is a regulatory catch: many trading partners will not accept poultry products from vaccinated flocks, making vaccination a potential economic liability for producers.

This creates pressure to find alternatives - ways to prevent viral spread through better understanding of infection mechanisms rather than through vaccination alone. If researchers can identify the cellular pathways that H5N1 exploits in the gut, they may be able to develop targeted interventions that disrupt transmission without the regulatory complications of vaccination.

The scale of the threat

The urgency is real. Over the past four years, H5N1 has caused lethal disease in wildlife across North and South America. The virus has been identified in dairy cattle across 19 states (though not yet in Montana). More than 70 human cases have been recorded, though human infections remain rare.

For the poultry industry, the stakes are more immediate. A single outbreak on a large operation can require culling tens of thousands of birds, with losses measured in millions of dollars. The USDA's decision to fund cellular-level research reflects a recognition that managing HPAI requires understanding the virus at a finer resolution than flock-level surveillance can provide.

MSU's biosafety infrastructure

The project will draw on several of MSU's specialized facilities, including the Bioimaging and Analytical Core Labs in the Center for Biofilm Engineering, the Cellular Analysis Core, and the Jutila Research Laboratory - a BSL3 facility built to CDC specifications for work with dangerous pathogens. Each faculty member on the grant will also oversee graduate students, creating hands-on research training opportunities in facilities that are unique within Montana.

The three-year project represents a bet that understanding avian flu at the cellular level will yield practical strategies for an industry that currently has few options beyond culling when an outbreak occurs.