US Customs and Border Protection identified the teenager as Carlos Gregorio Hernandez Vasquez. CBP said the Border Patrol apprehended the teenager in South Texas' Rio Grande Valley on May 13. He was found to be unresponsive during a welfare check Monday morning.
Carlos was detained for six days at the Border Patrol's processing centre in McAllen, Texas, despite federal law and CBP's guidelines generally requiring the transfer of an unaccompanied youth within three days to a facility operated by the US Department of Health and Human Services. The agency said Carlos was "due for placement" in an HHS facility at the time of his death.
CBP said Carlos reported early Sunday morning that he was not feeling well and diagnosed with the flu.
He was prescribed the medicine Tamiflu, then transferred later Sunday to the Border Patrol station at Weslaco, Texas, to prevent his flu from spreading to other detainees. He was not hospitalised.
An agency official who briefed reporters on the condition of anonymity said Carlos had last been checked an hour before he was found unresponsive. The FBI is investigating the case.
On April 30, a 16-year-old Guatemalan boy died after officials at an HHS detention facility noticed that he was sick. He was hospitalised in intensive care for several days before his death.
After the deaths of two children aged 7 and 8 in December, the Department of Homeland Security ordered medical checks of all children in its custody and expanded medical screenings.
John Sanders, the acting commissioner of US Customs and Border Protection, said in a statement that his agency was "saddened by the tragic loss of this young man and our condolences are with his family.
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