The seven-time world champion has revealed he returned three negative tests this week only for a fourth to come back positive and ruling him out of the penultimate race of the season.
He is now self-isolating in his hotel room for the next 10 days putting his participation at the season-ending Abu Dhabi Grand Prix in doubt.
"I'm devastated that I won't be racing this weekend", Hamilton said in a post on social media. "Since we started the season in June my team and I have been taking all the precautions we possibly can and following the regulations everywhere we have been in order to stay safe.
"Unfortunately, even though I returned three negative results this past week, I woke up yesterday morning with mild symptoms and requested another test which came back positive. I have immediately gone into self-isolation for 10 days.
"I am gutted not to be able to race this weekend but my priority is to follow the protocols and advice to protect others.
"I am really lucky that I feel OK with only mild symptoms and will do my best to stay fit and healthy.
"Please look after yourselves out there, you can never be too careful. These are worrying times for everyone and we need to make sure we are looking after ourselves and each other."
It remains to be seen whether he will be able to line up for the final race of the campaign in Abu Dhabi next weekend
Due to strict Covid-19 rules in Abu Dhabi, all personnel involved in the F1 event must travel from Bahrain on 7 December.
Yas Island, where the race is being staged on 13 December, will then effectively be locked down.
With Bahrain laws dictating Hamilton must quarantine for 10 days, it is anticipated that the world champion will not be eligible to fly until 9 December at the earliest.
Hamilton, who wrapped up the title in Turkey last month, is the third driver to have contracted the illness.
Sergio Perez missed the British and 70th Anniversary Grands Prix at Silverstone in August, while his Racing Point team-mate Lance Stroll also tested positive following October's Eifel Grand Prix in Germany.
Sunday's race will be the first Hamilton has missed since his debut at the 2007 season-opening race in Australia.
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