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By Maggie Fox

Another government agency fighting Zika has run out of cash to do it, as Congress fights over whether and how to come up with more.

The National Institute of Allergy and Infectious Diseases has spent all the money it has for work on Zika, says the agency’s director, Dr. Anthony Fauci. That includes money for further work on a Zika vaccine.

“I have no more money left for Fiscal Year 2016 that ends on Sept. 30,” Fauci told NBC News.

Related: Full Zika Virus Coverage From NBC

The NIAID, part of the National Institutes of Health, had already been using cash borrowed from other projects.

“I have no more money left for Fiscal Year 2016 that ends on Sept. 30."

The Biomedical Advanced Research and Development Authority (BARDA), which plans for public health emergencies, is also almost out of money, the Health and Human Services Department says.

Centers for Disease Control and Prevention director Dr. Thomas Frieden has already said his agency has run through all its borrowed Zika money.

There is no word from Congress on a potential bill to keep work against Zika going, even as the number of affected Americans keeps going up. Nearly 3,000 travel-related cases have been reported to the CDC. And CDC said Thursday that nearly 16,000 people in U.S. territories — mostly Puerto Rico — had been infected.

Images obtained in the case of a 34-year-old woman with confirmed Zika virus infection, initially seen for a rash at 8 weeks of gestation. Fetal head cir?cumference was in the normal range at 12 and 16 weeks (5.8 cm and 11.9 cm, respectively) but then decreased to the 10th percentile at 22 weeks and was below the 3rd percentile in subsequent imaging examinations. (a-h) US images were obtained at 30 weeks. Head circumference on the axial image (a) measured 24 cm (?2.3 percentile, corresponding to a gestational age of 26 weeks 3 days). Note the open sylvian fissures and relatively smooth cortex, which are abnormal findings at this gestational age. Oblique axial image (b) shows cerebellar calcifications (seen as the echogenic outer contour of the cerebellar hemispheres) and inferior vermian hypoplasia with associated enlarged cisterna magna. A sagittal transvaginal image (c) shows calcifications in the basal ganglia (arrowheads) and more bulky calcifi?cation at the gray matter-white matter junction. Another sagittal transvaginal image (d) shows a relatively small corpus callosum (arrows). A coronal image (e) shows cortical and subcortical white matter calcifications in a linear pattern. The gyral pattern is abnormal, which is suggestive of polymicrogyria. A sagittal Color Doppler image (f) shows a stretched appearance of vessels coursing into the posterior fossa. An oblique axial grayscale transvaginal image in the posterior fossa (g) shows heterogeneous material in the confluence of sinuses due to blood clot (arrow). A three-dimensional US image of the face (h) shows a sloping forehead, compatible with frontal lobe hypoplasia. (i) Axial and (j) sagittal fetal MR images obtained at 29 weeks show atrophic frontal lobes, wide sylvian fissures, enlarged posterior fossa, abnormal gyral pattern, prominent cerebrospinal fluid spaces, and inferior vermian hypoplasia. On i, note the diffuse hypointense and undersulcated cortex, which is suggestive of mineralization and polymicrogyria. The hypoplastic corpus callosum can be seen on the sagittal view (j), as well as the inferior vermian hypoplasia, en?larged cisterna magna, and heterogeneous signal intensity in the confluence of sinuses. There is a subjectively thin spinal cord. (k) Postnatal axial MR image obtained at 81 days shows small frontal lobes and cortical thickening. The choroid plexi are enlarged. (l) Photograph of the neonate after birth.RSNA

These include 671 pregnant women in the 50 states and Washington, D.C. and another 1,080 in the territories. The CDC says 17 babies have been born with Zika-related birth defects and five have miscarried or been aborted because of severe defects.

Related: Zika Doubled Birth Defects in Brazil

And as CDC, NIH and other agencies take money from other disease programs to fight the more time-sensitive Zika battle, they may be shooting themselves in the foot, says Stephen Morrison, director of the Global Health Policy Center at the Center for Strategic and International Studies.

“The perverse effect of Congress starving the administration is the administration has no choice but to scramble and cannibalize itself to meet these urgent requirements,” Morrison told NBC news.

“And so they wind up sacrificing other very worthy things in orders to try and be responsible. But then the skeptics on the Hill can turn around and say, ‘We told you so — you don’t need any money’.”

“It reinforces the incentives for dysfunctionality,” he added. “It’s kid of sad because it just means that good deeds are punished.”

Some members of Congress say the money may need to be included in a continuing resolution — a stopgap bill that would keep the government running for three months over the volatile election period.

The money’s needed for work to develop a Zika vaccine; better tests to help doctors tell if someone's infected or has been infected with Zika and a better understanding of the birth defects Zika causes. Scientists also want to understand how often Zika causes a paralyzing condition called Guillain-Barré syndrome and families of babies born with Zika-connected birth defects will also need help.

The federal government is also working to find better ways to control the mosquitoes that spread Zika. The CDC helps local authorities prepare for and fight Zika, including supplying tests and mosquito repellent.

“The perverse effect of Congress starving the administration is the administration has no choice but to scramble and cannibalize itself to meet these urgent requirements."

Fauci says the money crunch is threatening vaccine research. Most experts say a vaccine is the only long-term solution to Zika, which will not go away so long as the mosquitoes that spread it exist.

“If the likely continuing resolution that will be passed for fiscal year 2017 (beginning Oct. 1) does not include additional money for Zika, then I will not be able to proceed with the Phase 2 vaccine trial that I am planning for early 2017 nor will I be able to initiate any new Zika activities,” Fauci said by e-mail.

“The (Health and Human Services) Secretary will then be faced with the very difficult choice of having to yet again move money from other areas to continue (or not) the Zika effort.”

Related: Zika Funding Fails Again in Congress

Zika virus infection has not only been shown to cause microcephaly — an abnormally small head caused by brain damage. It can also cause subtler damage that might not even show up for months or years after a baby is born, including hearing and vision problems. But it takes scientific studies — and money to pay for them — to find out how common a problem this is.

“That is what we are spending time on versus doing the research that will tell us exactly how many deaf children we can expect to have."

President Barack Obama asked for $1.9 billion in February for an emergency Zika response. Congress balked, with Republicans questioning the need for the money, and eventually forced the White House to shift $589 million that had been meant to fight Ebola and a few other projects to use against Zika instead.

A bill that would provide $1.1 billion has been on the table, but Democrats have blocked it because it specifically excludes Planned Parenthood clinics from getting any of the money. The Senate seemed ready Thursday to drop that requirement, but the House appears less flexible on the issue.