WASHINGTON — The head of the government’s fight against the Zika virus said that “we are now essentially out of money” and warned that the country is “about to see a bunch of kids born with microcephaly” in the coming months.

Friday’s warning from Centers for Disease Control and Prevention Director Thomas Frieden came as lawmakers start to sort out a stopgap government funding bill that is being targeted to also carry long-delayed money to battle Zika.

Zika is spreading more widely in the U.S. and can not only cause microcephaly — in which babies are born with grave brain defects — but other problems that the country will face for decades. And 671 pregnant women in the states and Washington, D.C., have the virus, leading to the birth of 17 babies with microcephaly so far.

Frieden said funding delays have slowed long-term studies of the disease and production of new tests for it. “We haven’t been able to get a running start” on a long-term battle against Zika, he said.

Frieden added that “we don’t like to see” the use of pesticides such as Friday morning’s spraying of naled, in Miami Beach. But, he said, new technologies for the application of such toxic chemicals are safe for humans. The two localized mosquito-borne outbreaks in Miami are “quite difficult to control,” Frieden said, adding that the type of mosquitoes that spread Zika “are the cockroach of mosquitoes.”

President Barack Obama in February requested $1.9 billion to fight Zika, but Republicans controlling Congress acted slowly on the request. A Capitol Hill fight this summer stalled the Zika aid. Republicans attached restrictions on any of the money going to affiliates of Planned Parenthood in Puerto Rico. Democrats objected and blocked the $1.1 billion measure.

In the interim, the administration has shifted about $650 million from other accounts to battle Zika, most of it unused money approved two years ago to fight Ebola. That money is almost gone.

Now, negotiations are underway to break the impasse over Zika and add it to the only piece of legislation that has to pass Congress before the election: A stopgap funding bill to avert a government shutdown on Oct. 1.

Democrats and the White House have greater leverage now since their approval is needed for the stopgap spending bill, and Republicans are signaling they’ll likely lift the restrictions on delivering contraception, treatment and care through Planned Parenthood, an organization that many Republicans loathe since it is a major provider of abortion.

A bipartisan consensus is emerging to fund the government through mid-December, though some House tea party conservatives are opposed and want a longer duration for the measure to avert a lame duck session of Congress.

Since the summertime impasse, Zika has spread even more widely, and frustration is mounting from lawmakers representing affected areas. Almost 3,000 people in the continental U.S. have been found to have Zika, and the total is far higher since most people don’t display symptoms. The figures including Puerto Rico and the other territories are much worse.

“Look if we don’t, then fire all of us,” said Florida GOP Rep. David Jolly, whose state is bearing the brunt of the disease in the continental U.S. “If we can’t get Zika funding by the end of September then we’re nothing but a bunch of idiots up here.”

“I think we’ll look at this delay in time and say, ‘How could they have waited so long?’ This was so urgent. It was the very definition of an emergency,” Frieden said. “Not only is this unanticipated, it’s unprecedented. It’s potentially catastrophic, and it’s certainly that for the kind of brain damage we’re seeing.”

Frieden noted that it is extremely unusual to have a new cause for a severe birth defect and that the health care system will be grappling with the effects of Zika for years. While microcephaly is the most immediate result of the outbreak, Frieden noted that infants are having problems swallowing and with their vision and hearing.

“We don’t know what congenital Zika syndrome will look like,” Frieden said. “We will likely be dealing with this for decades to come.”