In addition to the Aviagen case, samples were also taken from a backyard flock in Madison County and the TaCo-Bet Trade Day flea market in Scottsboro in Jackson County.
The birds involved are waterfowl, primarily ducks and geese.
Ag officials said operators at the second premises were closely monitoring and regularly testing poultry for signs of avian influenza.
Tennessee's Department of Agriculture is not identifying the farm where the chickens were destroyed, saying only that it is located in the state's Lincoln County, which is just west of Chattanooga and borders Alabama.
It is not the same as the China H7N9 virus that has impacted poultry and infected humans in Asia, nor is it related to the virus that caused the 2015 US outbreak. Alabama officials are working closely with the Tennessee and federal agriculture officials.
Officials stress that neither HPAI nor LPAI pose a risk to the food supply and none of the affected animals entered the food chain. While avian flu, at present, is not a threat to human health, it can devastate commercial poultry operations resulting in huge financial losses. The wild birds' feces is blamed for sickening chickens.
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Another highly pathogenic outbreak would likely represent a financial blow for poultry operators such as Tyson Foods Inc and Pilgrim's Pride Corp because it would kill more birds or require flocks to be culled.
Antibodies for bird flu were detected by Aviagen, but a spokeswoman for the company told Reuters that the flock reported "no evidence of clinical disease".
No significant mortality was found among the birds in the Lauderdale County commercial operation, Alabama's agriculture department said.
In 2015, an avian influenza outbreak triggered the destruction of millions of chickens and turkeys in the Midwest. Tony Frazier, state veterinarian.
All bird owners, whether commercial producers or backyard enthusiasts, should continue to practice good biosecurity, prevent contact between their birds and wild birds, and report sick birds or unusual bird deaths to State/Federal officials, either through their state veterinarian or through USDA's toll-free number at 1-866-536-7593.