Doctors associated with Harvard and Johns Hopkins called for an investigation into health care at border facilities in a letter to members of Congress Thursday. The letter comes in response to the deaths of six migrant children either in government custody or soon after their release.

At least three of the children died from the flu, according to autopsies. The doctors wrote in their letter that flu deaths "are fairly rare events for children living in the United States." Domestically, the U.S. experiences a rate of about one flu death per 600,000 children, according to the doctors. Among migrants children in custody, the numbers are far higher, they wrote.

"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," they wrote.

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The letter includes a list of topics and questions that the doctors suggest be posed to each facility holding migrant children, ranging from health screening to treatment and surveillance for infectious illnesses like the flu.

"We suspect that the Department of Homeland Security (DHS) and Department of Health and Human Services (HHS) may not be following best practices with respect to screening, treatment, isolation, and prevention of influenza," the doctors wrote.

In a statement to CBS News, a spokesperson for HHS's Office of Refugee Resettlement (ORR), which houses unaccompanied migrant children, said every child in the agency's care receives a complete medical examination in the first 48 hours. In addition, the agency "requires all care providers to report incidents affecting a child's health, well-being and safety."

"As such, ORR provides routine and emergency medical and mental health care for all unaccompanied alien children (UAC) in its care, including an initial medical examination, appropriate follow-up care, and weekly individual and group counseling sessions with care provider clinicians," the spokesperson said.

The letter was sent to Rep. Rosa DeLauro, D-Connecticut, who chairs the subcommittee that oversees HHS, and Rep. Lucille Roybal-Allard, D-California, who chairs the subcommittee on Homeland Security.

"This 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," DeLauro said in a statement to CBS News. "Even under the best circumstances, the flu is a dangerous threat to people. This Administration continues to exacerbate this crisis to an untenable degree. Much of the problem stems from the lack of coordination, the lack of basic standards of care and procedures to ensure children are screened for health issues, treated quickly and safely, and get the proper vaccinations."

Prior to September 2018, it had been a decade since any children had died in Border Patrol custody, according to government figures. Since then, five Guatemalan children and one child from El Salvador have died either in custody or soon after their release to hospitals.

Rep. Roybal-Allard said in an email to CBS News that the deaths of children in U.S. custody that she will "seek a thorough accounting of (the children's) deaths."

"As a mother and grandmother, I have been heartbroken by the deaths of migrant children in our government's custody," Roybal-Allard said.

In a statement to CBS News, a CBP official said its facilities were not designed to hold children for long periods of time.

"As DHS and CBP leadership have noted numerous times in testimony to Congress and in numerous media engagements that our short-term holding facilities were not designed to hold vulnerable populations," the official said.

Autopsies performed on three of the children, who died at ages 2, 6 and 16, revealed flu as the cause. The doctors called for independent forensic reviews of the deaths of two other children who were not subject to autopsies. In one of those cases, the September 2018 death of a 10-year-old girl from El Salvador was not publicly acknowledged by the government until a CBS News report in May revealed she succumbed to long-term heart problems in a Nebraska hospital.

The most recent death was that of 16-year-old Carlos Hernandez Vásquez, just a week before what would have been his 17th birthday. The boy had been apprehended a week earlier in the Rio Grande Valley, near the southern U.S. border. When unaccompanied migrant children are taken into Border Patrol custody, the agency is mandated to notify HHS' Office of Refugee Resettlement (ORR) via an online portal within 72 hours. Instead, Vasquez remained for six days at the crowded McAllen Processing Center.

A month earlier, 2-year-old Wilmer Vasquez succumbed to complications from the flu in a hospital bed. The earliest verified case of a migrant child's death from the flu shortly after being in government custody was on Christmas Eve, Dec. 24, 2018. In that case, 8-year-old Felipe Alonzo died just six days after being apprehended with his father by Border Patrol.