While the situation has improved, hundreds of thousands of chickens and ducks had to be euthanized after the outbreak last fall, and it caused egg and poultry prices to soar.
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Animal rights activists have targeted Sonoma County's chicken and duck farms for years. In a previous I-Team report, we had undercover video from an activist who got a job at Reichardt duck farm in 2014.
She said, "The things I saw were absolutely horrifying. They still haunt me to this day."
MORE: Traces of H5N1 bird flu virus found in some milk, pasteurized dairy: FDA
Now, a report from the California Department of Food and Agriculture says it's "plausible" that activists spread avian flu during security breaches inside the duck barns on Oct. 24 and Nov. 14 of last year.
Bill Mattos of the California Poultry Federation tells us that the avian flu outbreak was devastating for the poultry industry in Sonoma County -- more than 250,000 chicken and ducks were killed.
"When you have a depopulation of a ranch because of bird flu, the ranch is disinfected and cleaned," Mattos said. "And then it's got to stay empty for a while for it to make sure it doesn't have any more diseases. So that farmer is out a few months of actually work income."
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The activists from Direction Action Everywhere posted video from the farms last fall, saying, "We have gone back to Sunrise and Reichardt and we have documented more criminal animal cruelty and we have saved several more lives, including Elsie and River."
Now, they say poultry producers and state regulators are blaming them for shortcomings in the industry. Almira Tanner is the lead organizer for Direct Action Everywhere.
MORE: How NorCal's avian flu outbreak will impact you after more than 1 million birds euthanized
She told us, "They're trying to deflect blame onto the whistleblowers so that people don't look at the reality of the situation, which is that factory farming is a recipe for disaster when it comes to public health."
The state report also raises concerns about biosecurity -- different farms sharing personnel and equipment, and it says the avian flu most probably came from wild birds and that the wind can spread it across different farms.
Tanner said, "One of the things that I think is important to note is that these animals in these facilities are so sick. We've documented extensive diseases that they have that makes them incredibly vulnerable to any sort of pathogen."
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Mattos countered, "The trespassing in an animal, a place that does business and tries to raise animals, really hurts the industry, but it also hurts the consumer."
Several of the activists have been prosecuted for trespassing. They say they'll continue to do whatever it takes to share their perspective.
Take a look at more stories by the ABC7 News I-Team.