CIUDAD JUREZ, Mexico Tania Bonilla arrived in this Mexican border city on Wednesday determined to apply for asylum in the United States.

With her 1-year-old in tow, she had defied the odds evading a death sentence by a Honduran gang at home, she said, as well as deportation by the Mexican authorities at the southern border and kidnapping by smugglers en route.

But now, in eyeshot of an international bridge connecting the Mexican city of Ciudad Jurez to the United States, a new and even more serious obstacle presented itself: the coronavirus.

In response to its rapid spread, which has claimed about 13,000 lives worldwide, the United States government announced on Friday that in addition to closing the Mexican border to nonessential traffic, it would shut off access for anyone trying to claim asylum from the border.

In practice, the United States will deport anyone caught crossing between official ports of entry, including those hoping to turn themselves in, denying them access to asylum and potentially sending them back into harms way.

Mexico has not only agreed to accept Mexicans returned under this policy. Its government acknowledged on Saturday that it would take back most Central Americans as well, potentially adding thousands more to the migrant populations already swelling along the border.

The Trump administration decision will also put an end, at least for now, to the hopes of asylum seekers who want to legally enter the United States at official border crossings. That includes thousands who have been waiting, some for months, for the chance to present themselves.

Analysts said this was the first time in memory since the creation of the current asylum system 40 years ago that the United States had shut down access to its program along the border a sign of the deep-seated fear that has prompted the president to close both the northern and southern borders to nonessential traffic.

But others viewed it as an attempt to use a global pandemic as a pretext to summarily block access to the U.S. asylum system for those coming from the south.

I think when you have a crisis of these proportions, its possible to get away with a lot, and thats possibly what they are doing here, said Sarah Pierce, an analyst at the Migration Policy Institute in Washington.

For some migrants, the move felt existential, as though what little hope remained had been plundered by a virus that is far more widespread in the United States than in their own countries.

Right now, I dont know what Im going to do, said Ms. Bonilla, 22, seated on a cinder block outside the state of Chihuahuas migrant affairs offices. Her son played with another group of children whose parents were also fleeing violence. The one thing I cant do is go back.

Equally worrisome are the implications of such a move along the border, particularly in terms of health care, with communities of asylum seekers already writhing under the weight of overcrowding and poor sanitary conditions.

On Saturday, the Mexican government was encouraging migrants to leave a large encampment in the border city of Matamoros, where some 2,000 have been living in tents on a muddy strip of land next to the international bridge.

At least 150 migrants boarded buses at the camp on Saturday and were taken away, though it was unclear whether that was related to the coronavirus. From time to time in recent months, the federal government has provided bus service to migrants seeking to leave northern Mexico and return to Central America.

Mexican officials said the buses on Saturday were provided by the government in response to requests from migrants living at the camp.

Fridays decision by the Trump administration to wall off the border from potential infections seems, for the moment, to fly in the face of transmission patterns.

Helen Perry, executive director of Global Response Management, a nonprofit that runs a clinic at the migrant encampment in Matamoros, said there had been no transmissions of the virus among the migrant population so far, and none of those residing in the camp appeared to show symptoms.

Similarly, in Tijuana and Ciudad Jurez, medical professionals reported no suspected cases.

Meanwhile, the number of confirmed cases in the United States dwarfs those in every nation in Latin America and the Caribbean, combined.

Experts say the most likely scenario is that someone coming from the United States will bring the virus into migrant communities living south of the border, sowing devastation among already vulnerable populations.

The migrants havent passed through major cities, airports or been hanging out at cafes, said Mrs. Perry.

What is certain, however, is that the bulk of the new policys burden will be felt on the Mexican side of the border, where shelters are bracing for the new reality.

At a meeting this week in Ciudad Jurez, shelter operators met to discuss group strategies to protect their populations from the virus. Increased use of hand sanitizer, face masks and screening were among the most obvious.

At the Casa del Migrante in Ciudad Jurez, the largest and longest-running shelter in the city, new arrivals will be housed in a separate facility for at least two weeks. But even they cant follow all best practices.

They suggest we put one meter of spacing between the beds, said Blanca Rivera, an administrator there. But we dont have that kind of space.

Sister Adelia Contini, the director of the Madre Asunta Institute shelter in Tijuana, said she was caring for 70 migrants in a center with only 45 beds.

Were not going to receive more people, she said by telephone.

Father Julio Lpez, who runs the Casa del Migrante Nazareth shelter in the city of Nuevo Laredo, said his center lacked basic safety equipment.

We dont have anything, he said.

Dirvin Luis Garca, the deputy director of the Chihuahua population council, which oversees migrant issues for the state, was more blunt still: We are not prepared for this scenario.

In the Matamoros camp, migrants bathe and wash their clothes in the Rio Grande.

Families of four or five occupy tents intended for two people; some are already weakened by respiratory and gastrointestinal ailments.

The crowded conditions, lack of hygiene and dearth of medical supplies practically guarantee that when the virus strikes, it will spread quickly and brutally.

We are preparing the community for what will inevitably happen, said Andrea Leiner, a nurse practitioner who is director of strategic planning for Global Response.

To prepare, the organization has begun distributing vitamin D and zinc in an attempt to boost migrants immune systems.

They are being told to position their tents at least six feet apart, and to open ventilation flaps to let in fresh air.

While many blame the United States for the already difficult conditions along the border, it is not solely responsible for the overcrowding.

Mexicos president, Andrs Manuel Lpez Obrador, has taken heat for bending to the will of the United States in ways once unthinkable for a leftist leader, especially one who had vowed to protect migrant rights.

His public assent has helped push shelters beyond capacity, taxed local and state governments, exhausted the resources of charitable groups and strained the good will of residents.

Yet the president has hardly paid a political cost.

His approval ratings remain high among Mexicans, who seem to have given little thought to his migration policy. His administration has been clear that its policy is to maintain good relations with the Trump administration.

For Ms. Bonilla, that policy is a crushing counterpoint to the hope that brought her hundreds of miles north in search of a better life.

Even last October, when thousands of migrants were being sent back to Mexico, her partner had managed to make it across with their daughter. He was living and working in Florida.

She hadnt planned to join him so soon, but in February, she said, Honduran gang members began extorting her. She had started a small business selling coffee, and they wanted her to pay them $400, a relative fortune.

She refused and filed a complaint with the police. Five days later, after the gang found out, they threatened to kill her son in front of her.

An hour later, she fled with her son, carrying their documents, her meager savings and a cellphone. Since then, she has been denied asylum in Mexico, deported and then robbed when she finally did make it to Ciudad Jurez.

In less than a week, she had come to understand the migrants burden: persistence in the face of cruel setbacks and total uncertainty. That felt truer than ever now, as she waited for the new policy to go into effect.

Weve suffered so much on the road, trying to get to this point, to ask for asylum, she said, clutching her son as he tried to wriggle free. To be met with this news, its just devastating.

Right now, I dont know what Im going to do, she added. Like I said, I cant go back. Thats the only thing I cant do.

Caitlin Dickerson contributed reporting from New York.

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A Closed Border, Dashed Hopes and a Looming Disaster - The New York Times