The world champion notched his second win of the race after conquering the Laguna Seca raceway ahead of Greg Van Avermaet (BMC) and Nathan Haas (Dimension Data).
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For Sagan it may mark a turning point, having finished second behind Van Avermaet on several occasions, including at the Tour de France stage 13 in 2015 and stage six of Tirreno-Adriatico this season.
A mostly uphill stage follows on Thursday, with riders rising from Lodi – 7m above sea level – to the 2,615m summit of Carson Pass over the first 164km. The category three climb to South Lake Tahoe could see some attacks on Alaphilippe’s lead.