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Most of the other royals sat in their family groups dotted at a safe social distance throughout St George’s Chapel at Windsor Castle.
Although Andrew’s two daughters were present, he sat apart from them in accordance with Covid-19 guidelines as they do not share a household.
He was however seated closest to the Queen who also sat alone throughout the ceremony.
Andrew has often been described as her favourite son.
At one point, an emotional-looking duke could be seen pulling his mask down with his eyes cast downwards.
Andrew moved to follow immediately behind his mother as she left the chapel at the conclusion of the service.
He did drop back however, to allow his brother the Prince of Wales and the Duchess of Cornwall to go ahead of him.
As the family left the chapel and made their way up the hill towards the royal apartments, Andrew could be seen walking close to his eldest daughter Princess Beatrice and her husband Edoardo Mapelli Mozzi.
Earlier, Andrew walked with his siblings and nephews behind the Duke of Edinburgh’s coffin as it travelled from Windsor Castle to St George’s chapel.
He walked beside his younger brother the Earl of Wessex and immediately behind Charles and in front of the Duke of Cambridge.
Andrew’s presence is believed to be one of the reasons behind the decision to have all the male royals wear morning coats rather than traditional military uniform.
His military status has been ambiguous since stepping back from his former duties in the wake of his disastrous Newsnight interview about his friendship with convicted sex offender Jeffrey Epstein.
He was made an honorary vice-admiral in the Royal Navy on his 55th birthday in 2015, and had been due to be promoted to admiral on his 60th birthday last year but offered to defer the role indefinitely.
The Duke of Sussex is also not entitled to wear military dress due to his own decision to step away from royal life.
The no-uniform rule was seen to be “the most eloquent solution to the problem”, a military source told The Sun.
Andrew – who saw active service in the Falklands War piloting a Sea King helicopter – did wear his military medals, which include the South Atlantic Medal 1982 and the Long Service and Good Conduct Medal for his time in the Royal Navy.
His relationship with Epstein has cast a long shadow over his years of royal service and led to questions about his future role, if there was to be any, in the monarchy.
Virginia Giuffre, who says she was trafficked by Epstein as a teenager, said she was left “horrified and ashamed” after an alleged sexual encounter with the duke in London in 2001.
Andrew, who was previously dubbed Air Miles Andy amid criticism of his globe-trotting, denies he had any form of sexual contact or relationship with Ms Giuffre.
His ex-wife Sarah Ferguson, with whom he shares a home, was not invited to the funeral.
Harry was also left sitting alone after his heavily pregnant wife Meghan was advised against flying to the UK by her doctors and could have watched the events of the day unfold as the funeral was screened live on three of America’s major television networks.
Other members of the royal family appeared dignified and reserved at the funeral service, but showed glimpses of affection and emotion during the course of the day.
The Countess of Wessex had her arms around her children, Lady Louise Windsor and James, Viscount Severn.
Sophie is being described as a great source of comfort to the Queen, who has been visiting the Queen at Windsor in the days following Philip’s death.
She was pictured in the service with her face mask pulled down around her chin and looked to be wiping her nose with a tissue.
Other members of the royal family standing at the Galilee Porch included the Duchess of Cornwall, the Duchess of Cambridge, Princesses Beatrice and Eugenie and their cousin Zara Tindall.
Standing in a row, they painted a solemn picture as they watched the coffin go by, some with their heads bowed.
Beatrice and her husband Edoardo Mapelli Mozzi held hands as they made their way to the funeral on Saturday.
Those in the procession quickly put on their face masks as they entered St George’s Chapel, but the Queen’s nephew, the Earl of Snowdon, was last to do so after he initially struggled to unfold his face covering.
Most of the family wore plain black masks, with the exception of the Queen and Charles, who wore black masks edged in white, and Camilla, whose mask was embroidered with a floral gold pattern.
After the service, Beatrice appeared to be holding a tissue in her left hand which she raised to her face as she left the chapel, with her husband’s arm around her waist for comfort.
Members of the royal family walked away from the chapel in small groups, chatting as they walked through the sunlit grounds.
The Earl of Wessex and his family walked together, closely followed by the Duke of Sussex who was chatting to the Duke and Duchess of Cambridge.
The Duke of York stayed close to his daughter Beatrice and her husband, while Charles and Camilla walked behind them.