U.S. Customs and Border Protection said in a news release that the boy died shortly after midnight.
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The death came during an ongoing dispute over border security and with a partial government shutdown underway over President Donald Trump's request for border wall funding. The White House referred questions to the U.S. Department of Homeland Security, CBP's parent agency. CBP officers and the Border Patrol remain on the job despite the shutdown.
The agency said the boy showed "signs of potential illness" on Monday and was taken with his father to a hospital in Alamogordo, New Mexico, where he was diagnosed with a cold and a fever. The boy was prescribed amoxicillin and Ibuprofen and released Monday afternoon after being held 90 minutes for observation, the agency said.
The boy was returned to the hospital Monday evening with nausea and vomiting and died there just hours later, U.S. Customs and Border Protection said.
The agency said the cause of the boy's death has not been determined and that it has notified the Department of Homeland Security's inspector general and the Guatemalan government.
The hospital - the Gerald Champion Regional Medical Center - declined to comment, citing privacy regulations.
CBP promised "an independent and thorough review of the circumstances."
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The agency has not yet said when or where the father and son entered the United States or how long they were detained, saying only in its statement that the boy had been "previously apprehended" by its agents. CBP typically detains immigrants when they cross the border for short periods of time before releasing them or turning them over to U.S. Immigration and Customs Enforcement.
Alamogordo is about 90 miles (145 kilometers) from the U.S.-Mexico border at El Paso, Texas. Ruben Garcia, director of El Paso's Annunciation House, said Tuesday that he had no reason to believe his shelter had served the family, but was waiting for further details about what happened.
A CBP spokesman declined to elaborate Tuesday, but said more details would be released shortly.
A 7-year-old Guatemalan girl died earlier this month after being apprehended by border agents, also in New Mexico. The body of the girl, Jakelin Caal, was returned to her family's remote village Monday for burial Tuesday.
Large numbers of Guatemalan families have been arriving in recent weeks in New Mexico, often in remote and dangerous parts of the desert. Jakelin and her father were with 161 other people when they were apprehended in Antelope Wells, about 230 miles (370 kilometers) southwest of Alamogordo.
CBP announced new notification procedures in response to Jakelin's death, which was not revealed until several days later.
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Democratic members of Congress and immigration advocates sharply criticized CBP's handling of the death and questioned whether border agents could have prevented it by spotting symptoms of distress or calling for an evacuation by air ambulance sooner. CBP has said that it took several hours to transport Jakelin and her father from a remote Border Patrol facility to a larger station and then a hospital in El Paso.
Xochitl Torres Small, a Democrat who will represent the district starting in January, called for a thorough and transparent investigation into the children's deaths and more medical resources along the border.
"This is inexcusable," she said in a statement Tuesday. "Instead of immediately acting to keep children and all of us safe along our border, this administration forced a government shutdown over a wall."
A spokeswoman for U.S. Rep. Steve Pearce, a Republican whose district along the U.S.-Mexico border includes Alamogordo, could not be reached Tuesday.
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