Australia is aiming to eradicate bird flu. This is how scientists are tracking and tracing the outbreak

It's a nerve-wracking wait for answers.

The biosecurity agents have been and gone.

They took samples from a sick bird showing symptoms of a deadly avian disease.

Will my farm and business be forced shut?

Will my flock — thousands of chickens – be culled?

These are the thoughts racing through farmer Greg Palethorpe's mind.

"It makes you feel really poor," Mr Palethorpe told 7.30.

Greg's business – Farmer Brown's Free Range Eggs – is on the outskirts of Canberra, seven kilometres from a confirmed outbreak site, and within a tightly controlled quarantine zone.

"It's a trying time when you know there's potential for such a disease — that can cause such devastation to your hens and your business — potentially floating around."

The hen he found was lethargic, with red eyes and a swollen comb.

If it tests positive, the whole flock receives the same treatment.

"We'd have to cull all the hens on site, and then they'd either be buried or burnt here," he said.

Among the strict protocols on Greg's farm, there's a 'hot zone' and a 'cold zone' on his property, restricting the free movement of people, poultry, eggs, and machinery.

Tracking and tracing the outbreaks

The samples from Greg's farm are sent to Menangle, a semi-rural suburb on Sydney's city limit.

It's here on a sprawling 1,600-hectare property where scientists are tracking and tracing the outbreak in a busy biosecure virology lab.

"We've had a big upturn in the number of samples coming in for avian influenza testing," veterinary virologist Dr Andrew Read told 7.30.

"We've done over 1,400 tests, a lot of those are pools, with five birds per sample."

Dr Read is one of the chief scientists involved in surveillance for the state of New South Wales and the ACT, at the Elizabeth Macarthur Agricultural Institute.

"For chickens, [the virus] is really contagious," Dr Read said, explaining the importance of surveillance testing.

"They'll sneeze, make these little droplets, if they're the right size, then they'll continue floating in the wind.

"It can potentially spread on the wind up to a kilometre or so, if the conditions are right."

In his ice-white lab, specimen tubes are received twice a day.

They're triaged according to threat, with high-risk cases marked red.

"We are able to show birds are actively shedding the virus by the amount of virus [the samples] had in them," Dr Read said.

The procedure is likened to PCR testing used to track and trace COVID-19, and the science is so specific they're able to detect the exact genetics of each virus and predict their origins.

At this stage, in Australia, there's no sign of the H5N1 strain that's causing widespread deaths in birds and mammals overseas.

But further examination has revealed our country is in an unprecedented situation.

What makes this outbreak unprecedented?

The CSIRO's Australian Centre for Disease Preparedness (ACDP) has been conducting genetic sequencing on samples from all outbreak sites in NSW, ACT and Victoria.

Eleven farms have been infected, with more than 1.8 million poultry birds euthanised.

Testing has revealed three different strains appeared at roughly the same time between May and June. The ACDP confirmed to 7.30 this is an Australian first.

All belong to the 'H7' family of viruses, which has been responsible for every poultry outbreak in Australia's history.

"By comparing the viruses' genetic code, we can see the three strains causing the three outbreaks are not closely related but are more closely related to low pathogenic strains known to be carried by Australian wild birds," The ACDP's Dr Frank Wong told 7.30.

"This leads us to believe each outbreak is likely to have spilled over from wild birds, probably waterfowl and ducks, separately," he said.

Australia's Chief Veterinarian Dr Beth Cookson said many avian influenza viruses have the potential to infect other animals including humans.

"However, the majority of that occurs during very close contact with sick birds or their environments," she told 7.30.

"Currently the circulating strains are considered low-risk to other animals, including humans."

Still, the timing of the outbreaks remains somewhat of a mystery.

"What's surprising is they've all happened at the same time," Dr Andrew Read told 7.30, offering a theory.

"There may be increased interaction between wild birds and chickens these days … there's more free range.

Mutating death

There are two types of Avian Influenzas: low pathogenic (LPAI) and high pathogenic (HPAI).

The low pathogen version is carried and spread in wild duck populations.

"But once those chickens get infected, there's a mutation that happens, and turns into this high path avian influenza, which causes all the disease, causing chickens to die," Dr Read explained.

"It's a respiratory disease, but also a gastrointestinal disease."

The virus kills chickens by rapidly replicating itself, destroying the hosts' cells, causing a severe immune response, which leads to critical organ failure.

"They'll shed the virus by sneezing and coughing, but they shed a lot in their faeces as well," Dr Read said.

What's next?

After a short but agonising wait, farmer Greg got the results back for the sick chicken found on his Canberra farm.

"They were negative, so that means no bird flu, which was a great relief for me," he told 7.30.

"But every day we get on the farm, thinking, 'what are we going to see'?"

Scientists say there's no doubt another strain will pop up; they just can't say which one, where, or when.

Much like humans, birds' immunity changes over time, meaning different virus strains will appear and dominate in the coming years.

"For example, it seems H7 viruses are predominant this year, but next year it could be H3 or H10 viruses as the birds develop immunity," Dr Andrew Read said.

Dr Cookson said government departments, scientists, ecologists, and other experts are working together to understand future risks.

"Bird owners, no matter whether it's backyard poultry or bigger commercial poultry, can take this opportunity to make sure they've got good biosecurity in place," she said.

Funds have been set aside to investigate the potential of commercial avian influenza vaccines for farm hens, part of a $7 million package from the federal government that also includes millions for national surveillance initiatives.

Then there's the other looming threat – a potential outbreak of H5N1, the bird flu strain that's caused a global animal pandemic – including the death of thousands of penguins in Antarctica.

"The arrival of migratory birds from areas where H5 HPAI is present – particularly as spring approaches – means we face a constant risk that is outside of our control," Agriculture Minister Murray Watt said.

"We can't stop the natural migration patterns of wild birds that may be sick, but we can prepare ourselves if that does occur."

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