Amit Singh, 32, was extradited to the US from India last week and has been arraigned on a grand jury indictment charging him with rape in the first and second degrees, sexual abuse and endangering the welfare of a child.
He was remanded by Judge Angelo Delligatti and is due back in court on October 11, Nassau County District Attorney Kathleen Rice said. He faces 25 years in prison.
Singh fled the country five days after the attack and one day before the victim positively identified him in a photo array presented by police. His return to the US to face charges is a result of an international manhunt.
Members of the US Marshal's Service travelled to India last week and brought Singh back to New York's JFK International Airport where he was arrested by detectives from the Nassau County Police Department's Special Victims Unit.
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"The persistence and dedication exhibited by multiple law enforcement agencies, however, guaranteed that there was no corner of the globe where this predator could safely hide," Rice said.
DNA evidence from the attack matched Singh's in April 2009. His DNA profile was in the system from a prior felony drug conviction, Rice said.
A grand jury indicted Singh in August 2009. An international warrant was issued by Interpol in February 2011.
The US Department of Justice notified Nassau authorities in July that year that Singh had been arrested while trying to board a plane to Thailand. He had been imprisoned in New Delhi and fighting extradition since then. Indian authorities agreed to extradite him earlier this month.