The indictment accuses Butina of conspiring with the unnamed "Russian official" to "infiltrate organizations active in American politics in an effort to advance the interests of the Russian federation".
It was apparent Butina was getting ready to leave Washington, the U.S. said.
Prosecutors outlined in a court document seeking her continued detention how she had maintained a web of people to support her mission in the United States, and was in touch with employees of the Russian FSB, the spy agency that succeeded the KGB.
The U.S. Justice Department asked a federal court on Wednesday to detain alleged Russian agent Maria Butina pending her trial, saying she poses a serious flight risk, has ties to Russian intelligence and will likely appeal to people in the Russian government to help her flee.
She lived with the 56-year-old man, but appeared to "treat it as simply a necessary aspect of her activities", the USA said. She is known as a protege of Alexander Torshin, a Russian former state banker, who met Donald Trump Jr for dinner at the NRA's 2016 convention.
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Schnatter is still on the board and is the company's largest shareholder - meaning he remains a key presence. The pizza chain founder claimed that Papa John's marketing agency tried to "extort" him over the remarks.
The gun rights organization is nearly certainly the National Rifle Association, whom Butina began reaching out to in 2013 and meeting with both in the USA and Russian Federation.
In the 29-page filing, prosecutors said Butina has ties to Russian oligarchs, including one with a net worth of $1.2 billion, and that she was previously was in touch with oligarchs about funding her trip to the United States.
Russia's Foreign Ministry on Wednesday said there were no grounds for her arrest, and that its embassy in Washington has requested a meeting with Butina. The filing also says that Butina viewed her relationship with "U.S. Person 1" as a "necessary aspect of her activities" and that she expressed disdain for having to live with him.
Her lawyer has called the allegations overblown and has denied that Butina is a Russian agent.
Citing her intelligence ties, the government is arguing that Butina poses an "extreme" risk of fleeing the US, where she has been living on a student visa.
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Broken shop windows, pillage and other destruction lined a section of the Champs-Elysees, the postgame site for revelers. But eventually the French players - who had remained silent, perhaps bemused by the row, felt compelled to speak out.
Butina was arrested over the weekend amid signs that she planned to leave the country.
In March 2017, following news coverage of Butina, the Russian official wrote, "Are your admirers asking for your autographs yet?" This Russian official was sanctioned by the U.S. Department of the Treasury, Office of Foreign Assets Control in April 2018.
The FBI said it has determined that even though Butina had a personal relationship with someone described in court papers as Person 1 - identified by NPR as political fundraiser Paul Erickson - she "offered an individual other than Person 1 sex in exchange for a position with a special interest organization". He and the Russians sought to use the imprimatur of the NRA in order to meet US political leaders and Trump, citing a "back channel" he had forged with the Kremlin. The filings allege that she undertook her activities without officially disclosing the fact that she was acting as an agent of Russian government, as required by law.
Prosecutors say the official directed Butina to use her contacts with the NRA and other conservative causes to gather intelligence on American officials and political organizations.
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He said that he had taken the "very hard decision" to resign "to express discontent" in votes. It remains far from clear whether Brussels will accept her plans.