Occurrence of Avian Influenza Virus in Groundwater—Study Provides Baseline Data and Informs Future Studies

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This pilot study provided baseline data on avian influenza virus (AIV) occurrence in groundwater underlying poultry farms and documented the challenges for conducting a pathogen transport study during a disease outbreak.


The highly pathogenic AIV (HPAIV) H5N2 outbreak during 2014–15 was the largest animal health emergency in U.S. history and led to the loss of 50 million birds and significant economic loss (an estimated 3.3 billion dollars) to the poultry and associated industries. HPAIV outbreaks in commercial poultry in the United States have historically been rare events, with only three outbreaks documented prior to 2014–15 (1924, 1983, and 2004).

Scientists at the U.S. Geological Survey (USGS), U.S. Department of Agriculture (USDA)–Agricultural Research Service, USDA–Animal and Plant Health Inspection Service, and the Wisconsin Department of Agriculture-Trade and Consumer Protection worked together on a pilot study to determine the occurrence of AIV in groundwater underlying poultry farms affected by HPAIV outbreaks They also sampled wastewater lagoons of outbreak-affected facilities because these storage structures could be a source for AIV to groundwater.

Scientists sampled a total of 20 wells, 6 lagoons, and 1 pond at or near 15 outbreak-affected operations (chicken layer, chicken pullet, turkey meat, and backyard) in Iowa and Wisconsin for the study conducted in 2015. All samples were analyzed for the influenza A matrix gene, the H5 subtype, and the poultry parvovirus.

This study provided the first baseline data on AIV occurrence in groundwater and documented the methods and challenges of conducting such a study during an ongoing animal health event. Results indicated that AIV was present in groundwater underlying poultry operations. Three wells and one lagoon were positive for the influenza A matrix gene. One well was positive for the H5 subtype that matched the outbreak virus gene although confirmatory cell culture and embryonating egg culture for live viruses results were negative. In addition, seven wells were positive for the poultry parvovirus, which provided supporting evidence for virus transport pathways between avian fecal wastes and groundwater.

This study is part of a long-term goal of the USGS Environmental Health Program to provide methodologies and information to aid in the understanding of the sources of microbial and chemical contaminants in the environment. Results of this pilot study provide information to guide future studies addressing AIV and other pathogen transport to groundwater. The scope of this study was limited to an evaluation of the occurrence of AIV in groundwater. Potential next steps include an evaluation of the risks that AIV in groundwater presents to poultry, other animals, and humans.

This study was supported by the USGS Environmental Health Program (Toxic Substances Hydrology and Contaminant Biology). Laboratory analyses were provided by the USGS–USDA Laboratory for Infectious Disease and the Environment and the USGS National Wildlife Health Center.

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