The boy crossed the border near El Paso, Texas, on April 19, and was taken to a shelter in Brownsville a day later, according to Guatemala's Foreign Ministry.
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He did not appear ill when he was transferred to the care of the U.S. Department of Health and Human Services, according to a statement from the Administration for Children and Families, the division within HHS that cares for migrant children who cross the border alone. But the next morning, he had fever, chills and a headache and was taken to a hospital, where he was treated and released that day.
When the teen didn't recover, he was taken to a second hospital and transferred to a children's hospital. Guatemalan officials said he had a severe infection in his brain and had emergency surgery, but never stabilized and died Tuesday.
The cause of death was under review, as was the incident. His name was not released.
SEE ALSO: 8-year-old Guatemalan boy dies in custody of ICE
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The boy's brother and Guatemalan consular officials visited him while he was hospitalized, and hospital staff frequently updated his family in Guatemala, according to Evelyn Stauffer, a spokeswoman for the Administration for Children and Families.
It was the third death in government custody since December, as the U.S. deals with a surge of unaccompanied children and Central American families arriving at the southern border. Two other children died while in U.S. Customs and Border Protection custody shortly after they arrived at the border.
Trump administration officials have said the surge has strained resources beyond the breaking point, but immigrant advocates and some Democrats say part of the crisis is due to President Donald Trump's own hardline rhetoric and failed border policies.
The 16-year-old was from the municipality of Camotan in the eastern area of Chiquimula. The Guatemalan Consulate in McAllen tried to get humanitarian visas so the parents could be with their son, but they were too old to travel, the foreign ministry said. The boy's body will be repatriated, but it's not clear when.
In December, 8-year-old Felipe Gomez Alonzo died on Christmas Eve from influenza and a rapid, progressive infection that led to organ failure shortly after crossing the border. His death was two weeks after that of 7-year-old Jakelin Caal Maquin, who also had a bacterial infection that quickly led to sepsis and organ failure.
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Both of those children were also from Guatemala but arrived with a family member and were in Customs and Border Protection custody, not the care of HHS. The agency also managed the children who were separated from their parents by the Trump administration last summer.
The last time a child died in the custody of HHS was 2015.
The teen's death comes as the Trump administration asks for $4.5 billion in supplemental funding for the border, mostly for humanitarian aid. The official request said HHS will exhaust its resources by June. The funding request includes $2.8 billion to increase shelter capacity to about 23,600 total beds for unaccompanied children.
There were 50,036 unaccompanied children encountered during the last budget year, and so far this budget year there have been 35,898 children. The highest number was in 2014: 57,496.
Their average length of stay in a government shelter is 66 days, up from 59 during fiscal year 2018 and 40 in 2016's fiscal year.