The 8-year-old Guatemalan migrant who died on Christmas Eve in the custody of US Customs and Border Protection had the flu, according to the New Mexico Office of the Medical Investigator.
An official cause of death for Felipe Gomez Alonzo has not yet been determined.
The boy, who was detained with his father, died shortly before midnight Monday at Gerald Champion Regional Medical Center in Alamogordo, New Mexico, about 90 miles north of the border crossing in El Paso, Texas.
His father, Agustín Gómez Pérez, was released from CBP custody on his own recognizance Thursday, Immigration and Customs Enforcement spokeswoman Liz Johnson said.
An autopsy showed Felipe tested positive for Influenza B, the medical examiner's office said Friday.
Influenza B is among the viruses that cause seasonal epidemics most winters in the United States, according to the US Centers for Disease Control and Prevention.
Felipe's half sister, Catarina Alonzo, 21, said the boy was healthy when he set out with his father for the United States in mid-December. He had vowed to work hard to send money to his mother in their small village in the highlands of western Guatemala, near the border with Mexico.
"This is not what we wanted for him," she told CNN in a phone interview Friday.
Alonzo described Felipe as a playful and respectful boy who liked soccer and eating fish from a lake near the family's thatched-roof home. She said the family received a phone call from a Guatemalan consular representative but government officials have not visited or offered assistance.
Felipe's father had planned the journey north for about two weeks, Alonzo said. She said she believes they rode buses to the US border. In addition to working, she said, Felipe was also eager to study in the United States.
On December 18, Felipe and his father were apprehended for illegal entry about 3 miles west of the Paso Del Norte port of entry in El Paso.
Monday, the boy was taken to the hospital after a border agent noticed signs of illness, and the medical staff first diagnosed him with a common cold and later detected a fever.
"The child was held for an additional 90 minutes for observation and then released from the hospital mid-afternoon on December 24 with prescriptions for amoxicillin and Ibuprofen," CBP said in a statement. Amoxicillin is a commonly prescribed antibiotic.
On Monday evening, the boy began vomiting and was taken back to the hospital for evaluation. He died hours later, the CBP said.
Felipe was the second Guatemalan child to die in US border patrol custody this month.
On December 8, Jakelin Caal Maquin, 7, died in a hospital two days after she was taken to a Border Patrol station.
Department of Homeland Security Secretary Kirstjen Nielsen traveled to El Paso, Texas, on Friday and with be in Yuma, Arizona, on Saturday, a DHS official said.
Nielsen's trips to the US cities near the Mexican border are intended "to see firsthand the medical screenings and conditions at Border Patrol stations."
The mayor of El Paso, Dee Margo, met with Nielsen Friday.
"I appreciate Secretary Nielsen taking the time to meet with me to discuss the El Paso region, and our immigration needs on the border. Our federal officials should visit the border when making decisions about our immigration system, and Secretary Nielsen's visit is most welcome," Margo said in a statement.
El Paso has faced the challenge this week of figuring out shelter for hundreds of undocumented immigrants that have been dropped off by ICE.