Julian Alaphilippe dug deep to keep the overall Tour de France lead on Sunday as Simon Yates captured his second stage of this year’s race and defending champion Geraint Thomas kept his title hopes alive after a late surge.

Few believed Frenchman Alaphilippe would emerge from two daunting summit finishes in the Pyrenees with the lead, but at the Foix Prat d’Albi finish he donned the yellow jersey for an astonishing 11th time as reward for his swashbuckling performances that have lit up this tour.

“I expected to lose a bit of time today. I’m delighted that I’m still in the yellow jersey. I gave my best to fight and retain the lead,” said the 27-year-old world No1 Alaphilippe.

“We knew it would be a hard day, I paid for my efforts in the finale,” admitted Alaphilippe of the Deceunick Quick-Step team who turned up at the Tour after multiple wins including the Fleche Wallonne and Milan-San Remo.

Thomas struggled on the final climb into the clouds, but then closed the gap on the leader to 1min 35sec by dropping him with a late burst afer initially looking like he was going to lose precious time on the overall leader.

Ineos sports director Nicolas Portal said the British team were “fine” with where they were so far.

“We’re in second place with G [Thomas]” said Portal. “We were not expecting this from Alaphilippe, he’s been imperious.”

“It’s exciting, he’s the man of the tour so far, but there’s a long way to go and we are hoping he blows,” he said.

Thomas singled out Thibaut Pinot for praise after the 2018 champion lost 49sec to the Frenchman.

Pinot, who won Saturday’s stage and then left all the chief contenders behind him after attacking halfway up the Prat d’Albi 11km ascent, now stands only 15sec behind the Welshman.

“We’ll have to really keep an eye on him now, we don’t want to lose too much time to him. He’s in great form, but look, he’s not the only one,” said the 33-year-old Ineos captain.

Simon Yates also won Thursday’s stage, also on a long distance breakaway, but his twin brother Adam’s Tour de France chances look completely cooked as he lost time again.

Vuelta a Espana champion Simon said he had mixed feelings about his performance.

“I came here to help my brother Adam, and that hasn’t gone to plan,” he admitted after his twin had a poor time in the Pyrenees. “But I had a second objective and that was to win a stage.