▶ Watch Video: Suspected human-smuggling boat capsizes, killing at least 3

Antonio Hurtado, accused of piloting the boat that capsized off the coast of San Diego in an apparent human smuggling operation, has been charged in San Diego federal court. Hurtado faces charges of attempting to bring in undocumented migrants at a place other than a port of entry, and an assault on a federal officer. Both charges are considered felonies.

Several of the 29 survivors identified Hurtado in a photo lineup, according to the complaint obtained by CBS News. Hurtado is alleged to have struck a U.S. Border Patrol agent in the head with his knee while being shackled at the ankle. The agent “suffered slight redness on his forehead and a burning sensation,” per the charging document.

The “severely overcrowded” boat overturned Sunday in the choppy waters near Point Loma in San Diego. Thirty-three people, including the alleged captain, were pulled from the ocean, and three of them died. Those who were injured ranged in age from 15 to 39.

All but one of the 28 survivors were from Mexico. They remain in federal custody as material witnesses in the case.

Details, including Hurtado’s exact role, age, hometown and citizenship status, were not detailed in court documents, but law enforcement previously said the suspected captain is a U.S. citizen. Several of the passengers told law enforcement that they paid $15,000 to $18,000 to be smuggled into the U.S., according to the charging document.

Hurtado made his first virtual court appearance Thursday afternoon. He didn’t enter a plea. His next hearing is scheduled for May 11.

Antonio Hurtado is seen in a virtual court appearance in this court sketch dated Thursday, May 6, 2021.

Krentz Johnson

Rick Romero, a lifeguard lieutenant with the city of San Diego, said on Sunday that there were a “wide variety of injuries,” including hypothermia. Lifeguards made seven water rescues and a cliff rescue. There was one major trauma and three people needed CPR at the scene. He said many people were able to walk themselves to an ambulance.

“Our goal was just to rescue everyone we can from the water and down along on the beach and get them up safely transported to the hospital as quickly as we can,” Romero said.

The lieutenant said the conditions in the ocean “were pretty rough” with 5 to 6 feet of surf. He said the 40-foot cabin cruiser “slowly disintegrated” as it hit the ocean reef, and there were several people who were sucked out to sea by rip currents.

A total of 96 personnel responded to the incident, officials said, including personnel from the Coast Guard, U.S. Border Protection, U.S. Park Rangers and U.S. Department of the Interior. Officials said the emergency was located near the Cabrillo National Monument in Point Loma, some 130 miles south of Los Angeles.

Wreckage and debris from a capsized boat washes ashore at Cabrillo National Monument near where a boat capsized just off the San Diego coast on Sunday, May 2, 2021, in San Diego.

Denis Poroy / AP

Nicole Sganga contributed to this report.