Wayde van Niekerk struggled as much with the chilly weather as with his rivals as he completed the first stage of a likely double at these world championships with victory in the 400m – but the night was mired in controversy after his main rival, the Botswanan Isaac Makwala, was barred from running.

The 25-year-old Van Niekerk is known for throwing up after his races, such is the all-out effort he always gives. But it was Makwala’s sickness that dominated the evening, especially after the world’s second best 400m runner was denied entry to the London Stadium because he was suffering from an infectious disease that required him to be quarantined in his room for 48 hours.

That seemed a logical decision given Makwala had been ill before the 200m heats on Monday and these championships have been hit by more than 30 cases of gastroenteritis, particularly to Canadian and German athletes. But it was angrily criticised by Makwala, who took to Facebook to claim that, when he arrived at the stadium, he was the victim of a “government trap”.

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“We fought all day for the truth to come out,” he added. “I still maintain I have never been sick and not tested by any doctor.” Speaking to the BBC earlier on Tuesday, he added: “I am heartbroken. I feel like it is sabotage. I am feeling good to run.”

However last night Dr Pam Venning, the head of medical services for the IAAF, athletics’ governing body, insisted that Makwala had come into their medical centre of his own accord on Monday and was seen by one of their volunteer doctors and examined.

“When he was told he had a gastrointestinal disease he tried to leave but one of my other senior members of staff brought him back in because we have an outbreak of gastroenteritis in the hotels and it is highly infectious,” she said.

“He had taken a history, examined him, pulse, respiratory and the history from this gentleman is very clear that he had symptoms similar to all the other athletes classified as having this gastro-intestinal disease.”

In a statement the IAAF said it had sympathy with Makwala but it had to think of the welfare of all the athletes given the outbreak of gastroenteritis which has plagued these championships. “The team doctor, team leader and team physio had been informed following the medical examination that the athlete should be quarantined for 48 hours and would therefore be missing the 400m final,” it said in a statement. “The IAAF is very sorry that the hard work and talent of Isaac Makwala won’t be on display tonight but we have to think of the welfare of all athletes.”

Whatever the rights and wrongs of the case, it made one of the most-hyped races of the championships a desperately flat and one-sided contest, with Van Niekerk barely celebrating his victory, which went alongside his 2015 world championships and 2016 Olympic titles.

Indeed he was able to win easing down in 43.98 secs, nearly half a second clear of the silver medallist, Steve Gardiner of the Bahamas, with the Qatari Abdalelah Haroun finishing rapidly to take bronze in 44.48, even though he struggled with the plummeting temperatures.

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“It was quite freezing,” explained the South African. “For 200m I was doubting my momentum. In the last 150m I was trying to get an extra gear but when I knew I was winning I slowed down. I thought if the times were not going to come there was no reason to push it to the finishing line.”

Van Niekerk, who also revealed that he has been struggling with a back injury for much of the season, added: “When I knew I was going to take gold it was such a massive relief. It is such a massive honour to say I have three global gold medals in three years. But I know this is not my best and I am actually looking forward to the off-season.” The 25-year-old, who will run in the 200m semi-finals on Wednesday, also expressed his best wishes to Makwala – and said he wished he could give him his medal.

“I really wish him a speedy recovery,” he said. “On Monday I saw him just before the 200m heats and the only thing I could think of was wrapping my arms around him and saying get well soon because I wouldn’t wish that on anyone. It is such a massive pity. Obviously there are a lot of fingers that are being pointed right now. I would allow him to have his fair opportunity. I wish he could have run. I have so much sympathy for him. I wish I could give him my medal to be honest. But this is sport. We all have disappointments, we all have tough times – we just have to fight back even harder.”

It was a classy thing to say, from the classiest of athletes. And despite Makwala’s angry outburst it was easy to understand his pain. Victory would have earned him his first world title and substantial sponsors’ bonuses. Instead, like the rest of us, he could only admire another Van Niekerk procession.