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Both Cunego, who finished seventh in last month’s Tour de France, and Ballan, world champion in 2008, are accused of having consumed doping products.
The charges relate to an investigation conducted in Mantova in Lombardy from 2008 until April this year.
Cunego and Ballan are among 32 people, including Marzio Bruseghin and Denmark’s Michael Rasmussen, accused of having doped.
Cunego’s Lampre team manager Guiseppe Saronni is similarly accused of having bought such products.
They are due to appear at the CONI offices in Rome on September 7.