The mutated strain shows changes in the hemagglutinin protein, which allows the virus to infect new hosts, the Adolfo Lutz Bacteriological Institute said.
The variant has been called A/Sao Paulo/1454/H1N1 by the institute, which compared it with samples of the A(H1N1) swine flu from California.
But it was unclear if the mutation makes the new strain more agressive than the current H1N1 virus, which has spread to at least 76 countries around the world, causing more than 160 deaths.
The 24-year-old Sao Paulo man who provided the sample has made a full recovery since being hospitalized with severe flu symptoms.
Pharmaceutical companies say they are gearing up to produce millions of doses of vaccines for the H1N1 strain. One company is promising delivery as early as July.
Photo: U.S. Centers for Disease Control and Prevention