The province's veterinary office says it has ruled out infected feed or the movement of pigs to and from the farm.
The Manitoba government says samples from 60 locations linked to the farm have not tested positive for the virus, known as porcine epidemic diarrhea.
But officials say they have found a second sample of the virus at an unidentified facility that handles large numbers of pigs in the province.
The highly contagious virus has been confirmed on 43 farms in Ontario and on one farm in each of Manitoba, Quebec and Prince Edward Island.
The virus, which originated in China and has killed millions of piglets in the United States, is unique to pigs and is no threat to people.
Last month, the Canadian Food Inspection Agency said it hadn't been able to confirm a link between the virus and feed pellets containing hog blood plasma.