Raw data and code for figures and results presented in manuscript, 'Surveillance on California dairy farms reveals multiple possible sources of H5N1 influenza virus transmission'.

Transmission routes of highly pathogenic H5N1 between cows in a herd or to humans remain unclear due to limited data from affected dairy farms. We performed extensive air, farm wastewater, and milk sampling on 14 H5N1 positive dairy farms across two different California regions. Virus was detected in the air in milking parlors and from exhaled breath of cows. Infectious H5N1 virus was successfully detected in the air and in water streams on dairy farms. Longitudinal analysis of milk from the individual quarters of cows revealed a high prevalence of subclinical H5N1 positive cows and a heterogeneous distribution of infected quarters that maintained a consistent pattern over time. Our data highlight multiple potential modes of H5N1 transmission on dairy farms.