The CDC had spent as of Friday $194 million of the $222 million it was given to fight the virus, said agency director Dr. Thomas Frieden, The New York Times reported.
While harmless to most people, the mosquito-spread Zika virus can cause serious birth defects in newborns.
Congress broke for its summer recess without approving additional funding. With Zika circulating in Florida, Frieden said the need for new funding was urgent.
The CDC has sent about $35 million to Florida -- which has several dozen cases of locally transmitted Zika infections -- and much of that has been spent, Frieden said. But, he added, if another cluster of Zika cases occurs in Florida, or if there is an outbreak in a second state, the agency would not be able to send emergency funds, according to The Times.
"The cupboard is bare, there's no way to provide that," he said at a briefing with reporters in Washington, D.C.
Senate Republicans have scheduled a vote on $1.1 billion in Zika funding for next Tuesday, when Congress comes back into session, according to a spokesman for Senate majority leader Mitch McConnell, Republican of Kentucky.
But Democrats oppose that package because it would exclude Planned Parenthood from the list of providers that would get new funding for contraception to combat the spread of Zika, which also can be transmitted sexually.
Public health experts say the funding issue is critical because the Gulf Coast, where the Aedes mosquito that transmits Zika mostly lives, is only halfway through peak mosquito season. There's a high risk that Zika could start circulating in New Orleans or Houston, the newspaper reported.
The vast majority of Zika cases has been reported in South and Central America and the Caribbean. Brazil has been hit especially hard.
On Tuesday, a new report suggested that close to 6 percent of babies with the Zika-caused birth defect microcephaly may also experience hearing loss. Microcephaly is the most common and devastating birth defect seen so far with Zika. It causes babies to be born with abnormally small heads and brains. Vision problems and malformed joints have also been documented.
The hearing-loss findings were published Aug. 30 in the CDC's Morbidity and Mortality Weekly Report.
Hearing loss isn't the only worrisome news to surface recently about Zika's effect on infants: A case study suggested the virus can live and cause damage in newborns for at least two months after birth.
That report, published online Aug. 24 in the New England Journal of Medicine, involved a baby boy born in January to a woman in Sao Paulo, Brazil.
The mother developed symptoms of Zika illness -- rash, fever, headache, swollen joints -- in week 26 of her pregnancy. The doctors suspect she got the infection through sexual contact with the baby's father, who had traveled recently to a Zika-endemic region.
The baby appeared normal and healthy at birth, with a typical head circumference, according to a team led by Danielle Oliveira of the University of Sao Paulo.
However, closer investigation of the newborn by MRI brain scans revealed troubling neurological abnormalities, the report authors said.
Brazil has reported thousands of cases of microcephaly so far.
However, the danger of mosquito-borne Zika infection for pregnant American women became more imminent this month, with two neighborhoods in the Miami area reporting cases of locally acquired infection. The CDC is now advising that pregnant women avoid traveling to these areas of Miami to reduce their risk of contracting Zika.
The CDC also is advising pregnant women not to travel to an area where active Zika transmission is ongoing, and to use insect repellent and wear long pants and long-sleeved shirts if they are in those areas. Partners of pregnant women are advised to use a condom to guard against sexual transmission during pregnancy.
The U.S. Centers for Disease Control and Prevention provides more information on mosquito-borne diseases.
This Q & A will tell you what you need to know about Zika.
To see the CDC list of sites where Zika virus is active and may pose a threat to pregnant women, click here.
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