Poultry farms in Victoria, NSW and the ACT have been hit hard since late May, with chickens being culled to prevent further spread.
The CSIRO said last week that genetic sequencing has revealed three different strains of H7 — a highly pathogenic avian influenza — have hit farms at roughly the same time.
It is a grim first for Australia with spillover from Australia's wild birds blamed.
But just why so many different strains are occurring at the same time remains a mystery.
"These separate viruses are all closely related to Australian-lineage, low path H7 strains that we know are carried in local wild birds," said Dr Frank Wong, from the CSIRO's Australian Centre for Disease Preparedness.
He said Australia was not able to carry out continuous surveillance of viruses in wild birds and that made unravelling the mystery difficult.
"There could be many reasons. We don't really know. The wild bird dynamics at a particular point in time, climate, changes in perhaps weather patterns or just coincidence."
The centre's director, Dr Debbie Eagles, said she could not rule out more strains popping up.
But she hoped the current farm outbreaks would be contained via the strict biosecurity protocols that were now in place.
Meanwhile, Australia was also braced for the possible arrival of another very dangerous strain that has caused mass mortality of farmed poultry but also wildlife around the globe.
It is feared the H5 highly pathogenic strain could hit Australia as soon as spring as migratory birds arrive. Australia is the last continent still free of it.
It has caused devastation overseas, including in marine mammals such as elephant seals and sea, lions but it has also been found in commercial herds, including dairy cows and the milk they produce.
Dr Wong said there had been human cases of H5 in the United States but all were linked to people that had close contact with diseased animals.
"The virus is still not adapted to infection in humans," he said.
"All of the infections have been from close contact with infected birds or livestock. People involved in outbreak control are aware of this and take appropriate precautions.
"Also, these infections have been very mild ... most of the infections linked to the dairy herds have been like conjunctivitis or red eye."
Both experts said Australia's National Avian Influenza Wild Bird Surveillance Program had been critical in unravelling what was happening in Australia with the H7 strains, and would also be invaluable in detecting H5's arrival.
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