The doctors, who wrote to Congress on Thursday, said autopsy reports show that at least three of the children — ages 2, 6 and 16 — died in part as a result of having the flu, a far higher incidence of such deaths than across the general population. Child flu deaths are rare, the doctors said, and should be preventable.

“Poor conditions at the facilities may be amplifying the spread of influenza and other infectious diseases, increasing health risks to children,” according to the letter, submitted by Harvard pediatrics professor Jonathan Winickoff; Johns Hopkins public health professors Joshua Sharfstein and Paul Spiegel and two of their master’s students; and San Francisco forensic pathologist Judy Melinek. “With so many lives at risk, these issues are worthy of congressional investigation. Another influenza season is around the corner, and there are other types of infectious diseases that pose a threat to detained populations. Timely action is critical.”

The letter, dated Thursday, alleges that the Department of Homeland Security and the Department of Health and Human Services — which supervises longer-term custody of unaccompanied migrant minors — might not be following best practices in regard to screening, treatment, isolation and prevention of the flu.

Sharfstein said in an interview that with all of the problems at the southern border, “people may be overlooking the risks of outbreaks that are entirely preventable.”

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The expression of concern by the doctors comes as the U.S. government has been struggling to deal with a record influx of Central American families and unaccompanied minors at the border, a shift in migration patterns that has at times put enormous stress on the nation’s immigration infrastructure. Children have spent days or even weeks in Border Patrol stations that are not meant for long-term housing, and the crush has meant people have been jammed into cage-like holding pens and even have had to stay in outdoor fenced encampments without access to showers or beds.

U.S. officials have said they are doing their best to care for everyone they take into custody but have acknowledged numerous times that Border Patrol stations are not designed to handle the number of migrants crossing the border in recent months. Even with a downturn in June and July, some facilities are still overcrowded.

Detainees with the flu, including children, “are handled as appropriate depending on the specific circumstances,” a Customs and Border Protection spokeswoman said. Children who test positive for flu are placed together “as best as possible” to separate them from other children, Kelly Cahalan, the spokeswoman, said in an email.

Five Guatemalan children who had been taken into Border Patrol custody died between December and May. At least three of the deaths involved the flu, according to autopsy reports obtained by The Washington Post. A sixth child, a 10-year-old girl from El Salvador with a history of heart problems, died in September 2018 after a long illness, administration officials disclosed in May.

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Before the recent deaths, it had been 10 years since a child died in Border Patrol custody, officials have said.

Border Patrol facilities had little to no health-care resources before the deaths in December of Jakelin Caal Maquin, 7, and Felipe Gomez Alonzo, 8. DHS officials then deployed Coast Guard medical personnel to border stations and contracted with health-care providers.

“CBP has approximately 200 medical personnel engaged along the Southwest border. This is a significant increase from just a few months ago, and a dramatic increase from about 20 medical personnel a year ago,” Cahalan said.

The 200 medical personnel include a mix of nurse practitioners, physician assistants, emergency-medicine technicians, certified medical assistants and other medical support personnel, the spokeswoman said.

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“Medical personnel on site conduct initial intake interviews to identify health/medical issues as well as more detailed medical assessments on juveniles or persons identified with medical issues,” she said. “Medical personnel on site are available 24/7 to provide medical diagnosis and treatment, address infectious disease issues, and coordinate referral to and follow up from local health system/emergency rooms.”

Cahalan declined to address whether children are vaccinated for the flu when taken into custody.

The Office of Refugee Resettlement, an HHS agency responsible for children who cross the border without parents or guardians, gives flu vaccines to children when they are transferred from Border Patrol or other agencies, a spokesman said.

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Unaccompanied children are supposed to be moved from Border Patrol to ORR within 72 hours under a long-standing court order, but the Trump administration has routinely violated that edict during the migration surge.

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The Border Patrol’s internal standards call for individuals and families to be held for no longer than 72 hours in the agency’s temporary holding facilities, but that standard also has not been followed. Two of the children whose deaths involved the flu had been held by Border Patrol for six days before falling ill.

“The key point is that these problems are created to a certain extent by poor planning,” Sharfstein said.

He said the U.S. government should have been prepared for the health concerns that accompany an increase in migration, as numbers steadily rose, especially from rural areas of Guatemala, Honduras and El Salvador.

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Migrant children are at greater risk of flu because of lower immunization rates, higher rates of other infectious diseases and inadequate access to health care earlier in their lives, the letter said. And detention centers are at higher risk for flu outbreaks.

The Centers for Disease Control and Prevention reported 124 child flu deaths in the United States last flu season, a rate of about one death per 600,000 children, according to the letter.

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“While comparisons are difficult for many reasons, this rate of death from influenza appears to be substantially less than the rate in detention facilities, with at least three deaths in as many as 200,000 children detained — many for less than the length of the season,” the letter said.

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The doctors outline a number of steps for protecting detained children from the flu, including vaccinating children against the disease when they are taken into custody, aggressive screening for flu symptoms, isolation of symptomatic children, prompt treatment with antiviral medication for children with positive flu tests and prophylactic use of antivirals for people exposed to others with positive flu tests.

“One important step is obviously for the kids to be moved out as quick as possible,” Sharfstein said. “Just the very fact of living with so many other kids in close quarters creates some level of risk.”

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The doctors and public health experts addressed the letter to Reps. Rosa L. DeLauro (D-Conn.) and Lucille Roybal-Allard (D-Calif.), who chair the House Appropriations subcommittees overseeing, respectively, HHS and DHS. They wrote the letter after reviewing the autopsy reports for four of the six children who died after being taken into Border Patrol custody.

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The letter expressed concern that autopsies were not performed in two of the deaths and called for an independent forensic review of migrant child deaths.

DeLauro said the letter “is alarming, but unfortunately not surprising, given the way the departments of Health and Human Services and Homeland Security are responding to the crisis on the border.” She vowed more oversight of the agencies.

Roybal-Allard said she is committed to providing CBP with the resources needed to protect children.