In February, the governor’s office and the health department announced ambitious battle plans. Millions of old tires where mosquitoes breed would be collected. Cemeteries would be drained of standing water.  Septic tanks and water meters would get screens, as would all schools attended by girls old enough to get pregnant. Teams would visit pregnant women’s houses to spray larvicide and screen windows.  Some of that was done, sometimes effectively. Humacao, a town on the southeast coast with pharmaceutical and electric plants that provide a steady tax base, moved faster than most municipalities, said José L. Báez, its chief of emergency management.  Workers collected 200,000 tires, packing them into two abandoned factories. At the local historic cemetery, teams filled empty urns with sand. Spray trucks worked steadily.  But it was never enough. Discarded tires kept popping up on roadsides. Mosquitoes bred in garbage cans. Teams could not legally enter abandoned properties or even fill depressions in privately owned graves. The town’s permethrin insecticides turned out to be ineffective, and daily rains washed away previous efforts.  No cutting-edge plans like releasing genetically modified mosquitoes are ready for deployment yet. The C.D.C. lab here has developed a bucket trap that drastically cuts mosquito populations, but millions of them would be needed to cover the island.  So, as a last resort, the C.D.C. on July 6 endorsed aerial spraying to eliminate mosquitoes with an insecticide called naled.  It was a gamble. Naled failed to stop a 1987 dengue outbreak here “and there is no guarantee it will work this time,” Dr. Petersen said. “But it’s the only thing that will alter the course of this epidemic.”  Modern spray nozzles and GPS-guided planes were more accurate, he argued, and superfine mists with small amounts of naled would drift into houses where mosquitoes hid in closets. Counties in Florida and Louisiana had recently knocked down populations of the yellow-fever mosquito by up to 99 percent with naled, he and others noted.  But naled is toxic to bees, birds and fish. The insecticide is not used in flea collars because it might be picked up by children stroking pets. It is banned in the European Union.  Puerto Rico rebelled. Protest marches drew hundreds wearing gas masks and carrying bee puppets. Top radio personalities, already angry over Congress imposing a control board to run the territory’s finances, accused federal officials of “colonialism” and reminded listeners that the military tested Agent Orange on Puerto Rico’s jungles before deploying it in Vietnam.  Medical groups joined the opposition, including the largest, the Puerto Rican College of Physicians and Surgeons. Dr. Iván González Cancel, a surgeon famous for performing the island’s first heart transplant, denounced the plan, saying: “I don’t believe in conspiracy theories, but I think this is an experiment with the C.D.C. using Puerto Rico as a laboratory.”  On July 21, a local TV station revealed that the C.D.C. had quietly imported naled. The next day, Gov. Alejandro García Padilla accused the agency of “blackmail” and emphatically killed the idea. The agency apologized, saying it was only trying to be prepared. But it was too late.  That same week, Dr. Johnny Rullán, a former health secretary advising Governor Padilla on the epidemic, gave up his post, saying the whole atmosphere had become too vicious. Since January, he had held town meetings explaining the mosquito control plans to skeptical audiences. “I felt like a scratched record saying the same things over and over,” he said. When he endorsed aerial spraying, he was falsely accused of plotting to make millions by basing planes at a remote airport he was accused of owning. (It is owned by someone with a similar name.)  He ultimately decided the spraying would be a public relations disaster. “Any microcephaly cases that occur now will be blamed on the spray, not the virus,” he said.  He resigned and left for a vacation in Spain. “In October,” he said, “I’ll write something saying, ‘I told you.’ ”  Skepticism of the danger remains high. Local papers still refer to the “theory” that the Zika virus causes microcephaly, although the World Health Organization considers it a fact.  Seventy-two apparently healthy babies have been born to infected mothers while only one stillborn fetus has shown evidence of microcephaly, so no disturbing pictures of tiny-headed babies, like those in Brazil, have appeared. Although officials have explained that most of the 72 mothers were infected late in pregnancy, the sense that the danger is remote persists.  Alba Sanchez, 25, and nearing the end of her fourth pregnancy, attended a hospital Zika-prevention workshop wearing the skimpiest of maternity dresses. Asked if she used repellent, she wrinkled her nose.  “Never!” she said loudly. “It’s stinky. And I don’t know anyone who’s had Zika.”  Asked how she protected herself, she mimed slaps to her bare arms and legs. “I smack every one I see.”  Her husband, Jandy Vasquez, 22, a mountainous man towering over her, rolled his eyes and smiled ruefully. “I’d spray a whole can on her every day,” he said. “But she does what she wants.”  Indeed, the fight against birth defects is taking place largely in face-to-face meetings between doctors and patients like Ms. Sanchez.  Many obstetricians said they were urging women to put off pregnancy. And through the CDC Foundation, pharmaceutical companies like Bayer, Allergan and Merck have donated or discounted more than 100,000 sets of IUD’s, implants, vaginal rings and other contraceptives.  “I tell my patients: ‘If you can avoid pregnancy for one year, please do,’ ” said Dr. Carmen D. Zorrilla, founder of the University of Puerto Rico’s Maternal-Infant Studies Center, the territory’s leading maternal H.I.V. unit, which now holds workshops in Zika-related care.  The doctors also remind patients whose fetuses show signs of brain damage that abortion is available in major hospitals and, for the uninsured, through Profamilias, a reproductive-rights group.  Some religious women will say, “‘But this is God’s gift,’ ” Dr. Zorrilla said. “But at the same time, they’re afraid to have a baby they know will need assistance 24/7 for life.”  How many women are terminating pregnancies is unknown. Although the health department tabulates legal abortions, current figures are unavailable, a department spokeswoman said.  “Anecdotally, they’re on the increase,” Dr. Rullán said. “One doctor told me he did 15 in a period where he normally would have done one or two.”  Making that choice is excruciating. Danelle, a patient of Dr. De la Vega’s who agreed to be interviewed on the condition that only her middle name be used, wept as she described her predicament.  Her fetus is 23 weeks along. On sonograms, Danelle, 36, can see a face, even hair: To her, the outlines resemble a small, sleeping child, nestled against the placenta as if it were a pillow.  Danger signs have appeared since Danelle was infected with the virus in late April. The fetus’s growth abruptly slowed and is now well below normal. An enlarged brain artery indicates that too little nutrition is crossing the placenta.  Because she herself is a doctor, Danelle knows what that means: Severe mental deficits are possible. Her husband, a train dispatcher who held her hand as she spoke, “is the more positive one of us — and he’s also in denial,” she said.  “But I’m the G.I. one,” she added, using a local term for hewing strictly to the book.  She was having ultrasounds every 14 days and must decide very soon whether to abort.  “The window is closing,” she said, wiping her eyes. “I don’t sleep at night. I don’t want to do this, but I don’t want her to come into this world and then suffer.  “And when I’m not here, who’s going to take care of her?”  Omaya Sosa Pascual contributed reporting.  A version of this article appears in print on July 31, 2016, on page A1 of the New York edition with the headline: As Zika Rages in Puerto Rico, Chaos Hobbles Response to Crisis. Order Reprints| Today's Paper|Subscribe
Thousands of islanders — and up to 50 pregnant women — are getting infected every day with the mosquito-borne virus.