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Konta was ruled out of Wimbledon after being forced to self-isolate when a member of her team tested positive.
The 30-year-old has now revealed that she, too, developed systems while in isolation and subsequently tested positive.
Explaining her absence, Konta said in a tweet: “As a result, I have been unable to train for the last two-and-half weeks and sadly, this has put my body in a situation where I am unable to ask it to be fully ready in time for the Olympic Games in Tokyo.
“This is a heart-breaking reality for me, as representing Team GB at the Olympic Games in Rio in 2016 is one of my most treasured memories from my career so far,
“I’ll be doing my best to get myself back to full health and fitness and ready to be competing again soon. During this time, I’ll also be glued to my TV cheering on my fellow Team GB athletes competing in Tokyo and I hope you will all join me.”
Konta’s withdrawal comes on the same day as Roger Federer pulled out of the Games because of a knee injury.