Buckingham Palace said she is well, and "following all the appropriate advice with regards to her welfare".
She last met with the PM on March 11 at their regular weekly audience, more than two weeks before his positive result.
Mr Johnson has been conducting his weekly audiences with the Queen by telephone for "at least the last fortnight".
The Queen was last with her son Prince Charles on March 12, when he went to Buckingham Palace to carry out an Investiture on her behalf.
Last night Prince George, Princess Charlotte and Prince Louis joined the nation in applauding NHS workers.
At 8pm, millions across the country took part in Clap for our Carers, a movement which was a chance to say thank you to all NHS workers as Britain continues its fight against coronavirus.
Prince William and Kate posted a video taken before bedtime of the three royal children applauding at once for several seconds.
The Queen's Trooping the Colour will not go ahead in line with government advice, it has been confirmed.
Buckingham Palace said in a statement: "In line with Government advice, it has been agreed that The Queen's Birthday Parade, also known as Trooping the Colour, will not go ahead in its traditional form.
"A number of other options are being considered, in line with relevant guidance."
It was due to be held on June 13 in London although the Queen's actual birthday is April 21.
Trooping the Colour is usually a large parade of soldiers through central London.
The Palace today confirmed that the Queen remains in "good health" despite recently spending time with Prime Minister Boris Johnson and her son Prince Charles - who have both tested positive for coronavirus.