The Health Secretary Matt Hancock, recovered after also testing positive for coronavirus last week, insisted the PM was "OK" but still had a temperature.
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And he said he did not know whether the PM had been seen by a doctor.
Government aides said he had been "coughing and spluttering" on video conference calls over the last few days.
It sparked fears the PM's health is deteriorating, with doctors saying patients are at risk of developing pneumonia if a temperature persists for more than a week.
Mr Johnson was due to end his seven days of self-isolation last Friday but was still recording a high temperature so continued to stay holed up in his No11 flat in accordance with Public Health guidance.
Mr Hancock said the contrast in how he and Mr Johnson had suffered exposed how difficult to predict and dangerous the virus was.
Asked about the PM's health, the Health Secretary told Sky News: "He’s okay, I’ve been talking to him every day, often several times a day, throughout this, throughout the time that both of us
were off and so he has very much got his hand on the tiller but he has still got a temperature.
"In a way it shows this virus affects different people differently.
"I was lucky, I had two pretty rough days and then I bounced back and some people do get it pretty mildly, and then for others it’s very, very serious and the Prime Minister is not at that end of the spectrum."
Last night his pregnant fiance Carrie Symonds tweeted that she had been in bed for the last week with coronavirus symptoms – but was now "on the mend".
It's thought she is staying in the pair's South London flat while Boris stays in Downing Street.
Mr Hancock added of the PM: "He’s working away inside Downing Street but he is protecting others by making sure that he too follows the clear public health advice, which is to self-isolate if you have got symptoms."
Earlier the PM tweeted: "Thank you to everyone who is saving lives by staying at home this weekend. I know it's tough, but if we all work together and follow the guidance we will beat coronavirus."
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