Assange has been evicted from the Ecuadorian embassy in London, where he sought political asylum in 2012, on April 11, and shortly after sentenced by the Westminster Magistrates' Court to 50 weeks of jail for breaking bail.
The Justice Department has announced 17 new charges against Julian Assange.
The new indictment alleges that Assange conspired with Manning to steal classified government documents, including State Department cables and classified reports about the Iraq and Afghanistan war efforts.
The case presents immediate questions about media freedom, including whether the Justice Department is charging Assange for actions - such as soliciting and publishing classified information - that journalists do as a matter of course.
Those charges including unlawfully obtaining and disclosing classified documents, the Justice Department said Thursday. Prosecutors say his actions "risked serious harm" to the United States.
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The indictment specifically addresses Assange's exchanges with Manning, alleging that "after agreeing to receiving classified documents from Manning and aiding, abetting, and causing Manning to provide classified documents", Assange then published those documents on WikiLeaks - an act they say put confidential sources used by the USA government overseas in potential danger.
Multiple news outlets cited Assistant Attorney General for National Security John Demers as saying in an interview accompanying the indictment's release that, "the department takes seriously the role of journalists in our democracy and we thank you for it". Department officials said Thursday they believe Assange strayed far outside First Amendment protections.
One of the counts included in the superseding indictment includes a charge of conspiracy between Manning and and Assange to obtain receive and disclose national defense information in violation of Espionage Act, a rare charge for a person who has never served inside the USA government.
Manning, who was convicted in military court for providing a trove of classified documents to Wikileaks, is now in a northern Virginia jail on a civil contempt charge.
Manning spent two months in the Alexandria Detention Center beginning in March after she refused to testify to a grand jury investigating Wikileaks. Manning was convicted in 2013 and sentenced to 35 years in prison before her sentence was commuted by President Barack Obama.