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The alert was first issued by the California Highway Patrol shortly after 2 p.m. Friday for 1-year-old Makai Bangoura, who was abducted at 3 p.m. Thursday.
After just four hours, the alert became active in Southern California counties, including Los Angeles, Orange and San Diego.
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Makai, was suspected to be with 30-year-old Jason Lam, his father. The man has joint custody of his son but did not return the child to his mother as scheduled on Thursday evening, according to the San Francisco District Attorney's Office.
CHP officials said Lam appeared to be suicidal. The suspect's sister, Mary Lam, disputed that claim in an interview with San Francisco's KGO-TV.
"He's never had any cuts on his arms, never shown any signs of being suicidal," she said, adding that she tried to stop her brother from taking the boy.
The father and son were said to be in a tan 2000 Toyota Corolla. They were spotted by a surveillance camera Thursday at a store in the Bay Area's Menlo Park.
About 8:20 p.m., Los Angeles police said the child was found safe in the area of Sepulveda and National boulevards and Lam was taken into custody.
"Today's a great day. We have a child that's going to be reunited with his loving mother," said San Francisco Deputy District Attorney Alex Bastian, adding that a tip led to Makai being found. "The Amber Alert did play a vital role."
Charges have not been announced in the incident.