University of Hong Kong scientists said they had discovered a mutation of the Streptococcus pyogenes bacteria that causes scarlet fever, making it more infectious and deadly.
The new strain of the disease was resistant to some of the antibiotics traditionally used to tackle it, causing an unusually widespread and aggressive outbreak in Hong Kong, they said.
A 15-year-old boy and a 7-year-old girl have died of scarlet fever in Hong Kong in the past three weeks, the first deaths in the city from the disease in 10 years.
More than 300 cases have been reported in 2011, three times as many as last year. Some schools have reported clusters of cases.
Dr Tse Hung-hing of the Hong Kong Medical Association said alternative antibiotics should now be used by doctors to tackle the disease.
Scarlet fever - named after the strawberry rash it leaves on victims' tongues - was a major childhood killer in the past but is now rarely fatal in developed countries thanks to antibiotic control.