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They found her alive “chained like a dog” to the inside of the box, a local sheriff told US media.
Ms Brown went missing in late August this year with her boyfriend, Charlie Carver, who is yet to be found.
Registered sex offender Todd Kohlhepp, 45, was arrested on Thursday in connection with the incident.
According to SLED records, Kohlhepp is a convicted sex offender who was added to the registry after being convicted of kidnapping in Arizona in 1987, when he was 16.
Spartanburg County Sheriff, Chuck Wright, said Brown and Kohlhepp were acquainted, but investigators are still looking into the connection.
Wright said Kohlepp is charged with kidnapping, and other charges are possible.
Kohlhepp will appear before a Spartanburg County magistrate judge for a bond hearing at 2 p.m. Friday.
Ms Brown told police that she had been fed twice a day but was “obviously traumatised” after her time in the container.
It was described by Spartanburg County Sheriff Chuck Wright as “a hellish place to be locked in hot weather. No lights, no windows, no air flow”.
Four people may be buried on the property, according to a testament given by Ms Brown to Sheriff Wright.
“We’re trying to make sure we don’t have a serial killer on our hands,” Sheriff Wright said. “It very possibly could be what we have.”
Sheriff Wright added that a cadaver dog, trained to smell human decomposition, had picked up on “something, it’s not clear what”, while searching.
Officers had been led to the 100-acre property thanks to a tip-off by a sex-crime investigator.
US broadcaster WYFF say a massive investigation is now underway.