The H5N8 strain of bird flu has been identified in Germiston on a commercial egg-laying farm, which is home to about 400 000 birds.
Not all the birds are in egg production.
Kevin Lovell, CEO of the SA Poultry Association, said the virus was confirmed on Friday last week.
Depopulating the chickens started last weekend and the area is under quarantine.
This strain of bird flu has now been identified on four farms, with the other three being in Mpumulanga.
Despite three of the four farms having good bio-security, of which the Germiston site is one, the virus made it onto the farms, Lovell said.
He said between 95 to 98 per cent of the chickens should be euthanased by the end of next week.
Lovell said the four outbreaks will in the end result in the culling of about 900 000 chickens.
He said there are roughly 145 million live commercial chickens in South Africa at any given time.
Bomikazi Molapo of the Department of Agriculture, Forestry and Fisheries, said she could not reveal the location of the farm, but confirmed it was in Germiston.
How it is spread:
Lovell said the virus is believed to have been spread by wild water birds.
The H5N8 strain can be spread by humans, droppings, feathers or contaminated water, to name a few.
The virus is not harmful to humans.
Meanwhile, Lovell said role players, which among others includes, the Department of Agriculture, Forestry and Fisheries and the SA Poultry Association, are sampling faeces from dams to identify water sources which could be home to the virus.
Other articles you may be interested in:
Disaster looms for chicken farmers
Avian flu: What you need to know
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