"I am departing for Qatar but it is without the soul of a rider," the 26 year-old told La Gazzetta dello Sport ahead of his Tour of Qatar title defence.
"I feel that I have come [to Qatar] lacking stimulus and motivation. I am shocked and mortified."
A string of stories broke in the Belgian press on Tuesday accusing Lefevere of decades of doping activities, but the 2005 world champion said the charges against his mentor were ridiculous.
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"What's been told is impossible. I am not going to believe anything I am reading because a lot of it is just fabrication," Boonen told Belgian radio. "I've been involved with Lefevere for many years and he's always been very straight with me."
Adding to the drama surrounding the Quick Step squad, former world champion Johan Museeuw acknowledged that he had in fact taken performance enhancing drugs in his final year riding with the team in 2004.
Boonen also defended his former team-mate, saying that Museeuw's confession did not imply a larger pattern of doping for the "Lion of Flanders" or within the Quick Step team.
"What Johan talked about clearly happened only in the final year of his cycling career," Boonen said in the radio interview. "There's no organized doping on this team."
"I think that he did well to confess," Boonen also told Gazzetta. "It is the first pass for rehabilitation. But it is not enough to cast a shadow over his entire career, since they were referring to only one year and, practically, his last year."
After more charges came out in the Belgian press from an anonymous current rider against the entire Quick Step team, Boonen reacted angrily and even sounded a conspiratorial tone.
"I don't think that it is a coincidence," the two-time Tour of Flanders victor said. "I think that it is a political objective against Patrick via accusations against cycling. But do they know that they are playing with the jobs of 60 people?"
"But I don't believe this. It is bull****. I read the anonymous testimony, with many inaccuracies and inconsistencies."
The Tour of Qatar, Boonen's first race of the season, is set to start on Sunday.
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