On Apr. 12th, 2012, Dan Goodin reported for ars technica on Stuxnet. According to the article, Stuxnet made its way into the Iranian nuclear program through an infected USB stick planted by an Israeli double agent. From there, the virus spread throughout the Iranian networks. This story apparently came from U.S. intel officers.
For what it's worth, a few people have questioned the validity of the report. Notably, John Bumgarner (who theorized that the Conficker, Stuxnet, and Duqu viruses all worked together) was quick to tweet that "[t]he technical evidence doesn't support this theory."
You can find the ars technica source article here.
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