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The Olympic and world 400-metre champion and world record-holder has cut short his honeymoon after getting married two days ago so that he can have surgery in the United States.
“This is sport and these things (injuries) happen,” he said in a statement.
Among the events Van Niekerk will miss is the Commonwealth Games on the Australian Gold Coast next April.
His management company confirmed he will have surgery in Colorado town Vail, then recuperate there, in Qatar capital Doha and in South Africa.
Van Niekerk sustained the injury playing in a touch rugby match that was a curtain-raiser to a Test between South Africa and New Zealand in Cape Town earlier this month.
He quit the game after hurting himself, but the 25-year-old did not immediately realise the seriousness of the injury.
“I trust that the team I have around me, including the medical professionals, will make this process as smooth as possible,” he said.
“I have faith that, God willing, I will be able to race again later next year.
“A full recovery is going to be crucial so I will be patient, but I will work as hard as I can to get back on the track as soon as possible.”
In a tweet, Van Niekerk said: “Thanks to all for the kind wishes. Sadly, I announce that I will be off the track for a while. Will be back stronger.”
A spokesman for Van Niekerk said the Vail clinic was “the best” for knee injuries and he hoped the athlete would be back in action next July or August.
Van Niekerk, who hails from central South African city Bloemfontein, won gold at the 2016 Rio Olympics in 43.03 seconds, smashing a record set by American Michael Johnson in 1999.
The South African is the only athlete to run under 10 seconds in the 100m, under 20 seconds in the 200m and under 44 seconds in the 400m.
He planned to compete in the 100m, 200m and 400m at the 2018 Commonwealth Games.
News of the injury was kept under wraps so as not to detract from the wedding of Van Niekerk to childhood sweetheart Chesney Campbell in Cape Town.
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