USDA’s National Veterinary Services Laboratories (NVSL) has confirmed the full subtype for the highly pathogenic H7 avian influenza reported in Lincoln County, TN. The virus has been identified as North American wild bird lineage H7N9 HPAI based upon full genome sequence analysis of the samples at the NVSL. All eight gene segments of the virus are North American wild bird lineage. This is NOT the same as the China H7N9 virus that has impacted poultry and infected humans in Asia. While the subtype is the same as the China H7N9 lineage that emerged in 2013, this is a different virus and is genetically distinct from the China H7N9 lineage.

As additional background, avian influenza viruses are classified by a combination of two groups of proteins: hemagglutinin or “H” proteins, of which there are 16 (H1–H16), and neuraminidase or “N” proteins, of which there are 9 (N1–N9). Many different combinations of “H” and “N” proteins are possible. Each combination is considered a different subtype, and subtypes are further broken down into different strains. Genetically related strains within a subtype are referred to as lineage.

USDA continues to work with the Tennessee Department of Agriculture on the joint incident response. Birds on the affected premises have been depopulated, and burial is in progress.  An epidemiological investigation is underway to determine the source of the infection.

Federal and state partners continue to conduct surveillance and testing of poultry within an expanded 10-mile radius around the affected premises to ensure all commercial operations in the area are disease-free. In addition, strict movement controls are in place within an established control zone to prevent the disease from spreading. As of yesterday, all commercial premises within the surveillance area had been tested, and all of the tests from the surrounding facilities were negative for disease. Officials will continue to observe commercial and backyard poultry for signs of influenza, and all flocks in the surveillance zone will be tested again.

The rapid testing and response in this incident is the result of extensive planning with local, state, federal and industry partners to ensure the most efficient and effective coordination. Since the previous HPAI detections in 2015 and 2016, APHIS and its state and industry partners have learned valuable lessons to help implement stronger preparedness and response capabilities.

A second outbreak of bird flu has been identified in Middle Tennessee as the state veterinarian confirmed a flock of chickens at a commercial poultry breeding operation in Giles County tested positive for low pathogenic avian influenza.

However, the company that operates the breeding operation is a different business from the one associated with the recent detection of highly pathogenic avian influenza in nearby Lincoln County. At this time, officials do not believe one premises sickened the other.

On Monday, routine screening tests at the premises in Giles County, just west of Lincoln County, indicated the presence of avian influenza in the flock. State and federal laboratories confirmed the existence of H7N9 LPAI in tested samples.

"This is why we test and monitor for avian influenza," State Veterinarian Dr. Charles Hatcher said. "When routine testing showed a problem at this facility, the operators immediately took action and notified our lab. That fast response is critical to stopping the spread of this virus."

As a precaution, the affected flock was depopulated and buried. The premises is under quarantine. Domesticated poultry within a 6.2-mile radius of the site are also under quarantine and are being tested and monitored for illness, officials said.

To date, all additional samples have tested negative for avian influenza and no other flocks within the area have shown signs of illness, according to officials.

Kentucky's agriculture department yesterday announced that tests have confirmed low-pathogenic H7N9 avian flu at a commercial poultry farm, making it the third state to report the virus.
In related developments, Alabama officials announced that tests have likewise confirmed low-pathogenic H7N9 at two locations in different counties.
Expanded surveillance
Robert Stout, DVM, Kentucky's state veterinarian, said in a statement from the Kentucky Department of Agriculture (KDA) that the virus was first detected in routine preslaughter tests on a poultry flock from Christian County that were conducted by the Murray State University Breathitt Veterinary Center in Hopkinsville.
Christian County is located in western Kentucky near Tennessee's northern border. It is not adjacent to either of the two Tennessee counties that recently reported three H7N9 influenza outbreaks—one involving the low-pathogenic form and two the more worrisome highly pathogenic virus.
No clinical signs of illness were seen in the birds, and the location was placed under quarantine, with 22,000 hens destroyed as a precaution.
The US Department of Agriculture National Veterinary Services Laboratory (NVSL) confirmed the H7N9 finding.
State and federal partners are conducting surveillance in flocks within a 6-mile radius of the affected farm, and the company that owns the farm is doing additional testing at its other facilities in the area.
Kentucky's poultry and egg industry generated $1.2 billion in 2015, the KDA said.
Alabama reports 2 more low-path confirmations
Meanwhile, Alabama officials today announced that two flocks located 170 miles apart have tested positive for low-pathogenic H7N9. One is a commercial operation in Pickens County in the west central part of the state and the other is a backyard holding in Madison County in northern Alabama.
According to a press release from the Alabama Department of Agriculture and Industry (ADAI), the virus in the Pickens County flock was found during routine screening in tests conducted at the ADAI State Diagnostic Laboratory in Auburn, Ala. The birds have been placed under quarantine, and control measures are under way as a precaution.
The NVSL also confirmed the findings in the backyard flock from Madison County, and the ADAI said surveillance zones have been placed around the outbreak locations in Pickens and Madison counties.
Alabama has now reported three low-pathogenic H7N9 detections. On Mar 16 officials said the NVSL had confirmed the virus in guinea fowl from a flea market in Jackson County, which neighbors Madison County.
A suspected outbreak was also reported in a commercial flock in Lauderdale County, which prompted further testing. Dan Autrey, chief of staff for Alabama agriculture commissioner John McMillan, told CIDRAP News that follow-up tests turned up very little virus. He added that, based on serology tests, the findings are considered presumptive positive for low-pathogenic avian influenza.
Among the response steps, the state has banned poultry movement in some locations and has temporarily banned poultry exhibitions and assemblies.
Tony Frazier, DVM, Alabama's state veterinarian, said in the release, "The health of our poultry is critically important at this time. With confirmed cases of low pathogenic avian influenza in Alabama in both commercial and backyard flocks, the order reducing the assembly and commingling of poultry is the most effective way to practice strict biosecurity measures in our state."
The H7N9 viruses recently detected in the United States are related to North American wild bird lineages and have no connection to the H7N9 strain sickening people and poultry in China.