It is understood Andrew saw the Queen in the last few days but has been undertaking regular testing and has not seen her since he tested positive.
The monarch's son was due to attend a thanksgiving service at St Paul's on Friday. Even before his test results came back, Andrew was unlikely to attend any other events over the long weekend.
The duke was cast out of the working monarchy after Virginia Giuffre, a woman trafficked by paedophile Jeffrey Epstein, accused Andrew of sexually assaulting her when she was 17. The duke denied the claims, but paid millions to Ms Giuffre to settle a civil sexual assault case in February.
Before the Jubilee festivities, the Archbishop of Canterbury, the Most Rev Justin Welby, told ITV News that Andrew was “seeking to make amends”, adding: “I think that’s a very good thing.” This bank holiday's events will see members of the monarchy, celebrities, and people from all parts of the UK gather to recognise the Queen’s legacy.
To launch the four-day long celebrations, Royal family members joined The Queen to watch the RAF flypast over Buckingham Palace.
A delayed cheer went up as the Queen appeared on the balcony from the thousands who had gathered in The Mall and in the stands for the Trooping the Colour parade.
In the evening, more than 3,000 beacons will be set ablaze across the UK and the Commonwealth in tribute to the Queen, who will lead the lighting of the principal Jubilee beacon in a special ceremony at Windsor Castle.
The thanksgiving service at St Paul's will be held on Friday, but the Queen’s planned visit to Epsom for the Derby the following day is off, with members of the Royal family attending on her behalf.
On Saturday evening, the BBC’s Party at the Palace – set on three stages in front of Buckingham Palace – will entertain a live crowd of 22,000 people and a television audience of millions.
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The line-up includes Diana Ross, Queen + Adam Lambert, Alicia Keys, Nile Rodgers and Andrea Bocelli.
Millions will gather on Sunday for patriotic street parties, picnics and barbecues. A Jubilee Pageant will make its way through the streets of London, with a cast of 6,000 performers and close to 200 celebrities joining the procession.
It is hoped the monarch will make a final appearance on the Buckingham Palace balcony to round off the weekend and see Ed Sheeran singing the national anthem.