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About 63% of North Island commercial poultry farms and 79% of South Island farms have been tested for a poultry virus found at Mainland Poultry in Otago - and no other sites have tested positive.
Biosecurity New Zealand was working with the poultry industry on a delimiting survey to test every commercial poultry farm in the country.
In September, it announced it was managing a possible case of Infectious Bursal Disease Virus type 1 (IBDV-1) at the Mainland Poultry egg farm in Waikouaiti.
The virus - not found in New Zealand for 20 years - posed no risk to human health or the health of other animals.
Yesterday, Ministry for Primary Industries IBDV response manager David Yard said testing confirmed the virus in layer hens at the egg farm, while another Mainland property at Hillgrove, near Moeraki, also tested positive.
The survey was expected to be completed in December to confirm the disease was contained to those two locations.
Biosecurity New Zealand was working closely with Mainland and the two affected sites to manage any possibility of spread.
The two sites were under Notices of Direction which controlled the movement of risk goods, such as live poultry, rearing shed manure and equipment.
There were no animal welfare concerns; birds on the farm were not showing any clinical signs of the disease or exhibiting production losses, Mr Yard said.
The remaining Mainland properties had tested negative and were ''continuing with business as usual''.
MPI had stopped certifying poultry products as IBDV-1 free for countries that required that certification and it was working with affected markets to re-establish trade ''as quickly as possible''.
It had been looking at how the virus might have entered New Zealand but, at this stage, there was no definitive answer.
''As with most animal disease incursions, we are looking at pathways such as imported veterinary medicines, travelling farm workers and other imported goods,'' he said.