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The Jumbo-Visma rider was dropped out of the back of peloton with 8.5km to go as Ineos Grenadiers pushed the pace on the front.
It was a long way to the top for Dumoulin and he crossed the line over 6:30 behind the main group of favorites.
“I’m just not feeling good, it’s like that. I worked hard to get here in the best shape possible. Everything is ok, but I just don’t have the legs at the moment. I don’t know why, but it is like it is,” Dumoulin said.
Dumoulin came into the first major mountain test, and the first stage on Italian soil, well positioned in the overall standings and with plenty to play for.
He started the day in third place overall, just 16 seconds behind the maglia rosa Mathieu van der Poel (Alpecin-Fenix) and five seconds behind Simon Yates (BikeExchange-Jayco).
This year’s Giro d’Italia was Dumoulin’s first attempt at a GC challenge since he took his sixth-month sabbatical from cycling at the beginning of last year. He had looked strong in the stage 2 time trial, though he was beaten by Yates, but he couldn’t keep the pace on the difficult slopes of the Sicilian volcano.
Jumbo-Visma’s GC hopes took another hit with Tobias Foss also losing touch with the main group favorites and giving away over two minutes to it.
The Norwegian started the day 28 seconds behind the race lead and 17 seconds back on Yates, but he is now about 2:42 behind the BikeExchange rider.
“When it got really steep and the guys went fast, I was missing the last percentage but it’s still early and a long way to go in the race, but it’s not the best, for sure,” Foss said.
“To me [Dumoulin] looked good, but it is what it is, it was a hard stage in general so if you don’t have the extra percentages then you struggle. There are still a lot of races left so we will take it day by day and see what our chances are.”