Obama has already ordered 3,000 troops to help the effort in Africa.
"It's getting worse," said Obama. "It's spreading faster and exponentially.
The outbreak has claimed more than 1,000 lives in West Africa.
Mount Sinai Hospital said the man was in "stable condition" and "improving."
A widening outbreak threatens to overshadow a U.S.-Africa summit in Washington.
Health officials say there are 175 confirmed cases of Enterovirus D68 across the country.
Obama's video message stressed prevention as the outbreak worsens.
"I think we've got to let the science guide us," said Obama.
HHS chief Burwell met with African leaders as the death toll neared 900.
The "Level 3" warning comes as the death toll hits 729 in West Africa.