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It was Kipchoges first defeat since 2013. He came in 8th in 2:06.49.
In cold, wet conditions, Kitata edged clear to win in a relatively slow two hours, 05.41 minutes.
Sisay Lemma of Ethiopia was third. with Kipchoge eighth.
In the women’s race, Kenyan world record holder and defending champion Brigid Kosgei cruised to a dominant victory, overcoming her rivals on an unfamiliar multi-lap course in relentless rain to triumph in two hours, 18.58 minutes.
Running her first marathon since setting the world record of 2:14.04 in Chicago a year ago, Kosgei ran alongside compatriot Ruth Chepngetich until around the 20-mile mark, when she forged clear to open a lead of about 50 metres within a couple of minutes.
She then ran strongly for the rest of the race to finish around three minutes clear.
American Sara Hall produced an incredible finish, wiping out a huge deficit over the last few hundred metres to sweep past world champion Chepngetich almost on the line to finish in 2:22.01 to the Kenyan’s 2:22.05.
Wrapped in a huge coat at the finish area, the tiny Kosgei said it had been a tough day.
“It was wonderful to race but we haven’t been able to prepare well because of COVID, and because of the weather today it was a struggle up to the moment I finished,” she said.