The incident happened shortly before 7 a.m. in waters about 175 yards from Beacon's Beach, leaving the teenager with traumatic injuries to his upper torso, said Capt. Larry Giles of the city's Marine Safety department.
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According to the captain, the water was about 9 feet deep at the location where the violent encounter occurred. Three good Samaritans rushed to the injured boy's aid and transported him to the shore on a kayak.
VIDEO: Officials give updates on teen attacked by shark
Shark attack at beach in Encinitas leaves 13-year-old hospitalized
Encinitas lifeguards and sheriff's deputies who were in the area responded to the scene and a rescue helicopter was summoned.
A witness's video shows the chopper landing on the sand as emergency personnel attend to the teen, who was carried away from the water on a stretcher.
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The victim, who suffered multiple shark bites, was medevaced to Rady Children's Hospital in San Diego, according to a spokesperson for the medical center.
Beaches in the area were closed after the incident and will remain so for at least 48 hours, Giles said at a morning news conference.