The former Alnwick athlete, who is now based in Leeds, was left heartbroken after sustaining a hamstring injury in training just days before the Championships, which were held in Manchester at the weekend.
It means Weightman, who is 30 this week, is now sweating over whether or not she will be on the plane to Tokyo.
She already holds the qualification time for the 5000m, but her fate now lies in the hands of the British Athletics selectors.
In a message posted on Twitter before Manchester she wrote:
“Sadly it breaks my heart to say I won’t be on the start line of this weekends Olympic trials. Just when things were coming together I sustained a small hamstring injury in training on Tuesday.
“Life seems like it’s against me right now after a number of challenges this last year. But one thing I do know, whatever happens in the coming weeks I will be stronger for this.”
Weightman, who is coached by Steve Cram, has already competed in two Olympic Games, at London in 2012 and Rio de Janeiro in 2016.
She started out as a 1500m runner, winning a bronze medal at the 2018 European Championships in Berlin, but later moved up to the 5000m, also winning bronze in the 2018 Commonwealth Games in Australia.
Another Northumberland athlete, Berwick’s Guy Learmonth has also seen his Olympic hopes dashed due to the effects of COVID.
Learmonth, who is a 400m runner, was hoping to qualify for his first Olympics, but like Weightman, was forced to withdraw from the trials due to effects of the virus.
He was suffering from a respiratory problem and said: "I didn't want to admit anything was wrong.
"I was one of many that got Covid at the Euro Champs in March and after initially getting through it, I just cracked on with training almost immediately, raced a lot across America and Europe and put so much stress and strain on my body without the proper recovery … but I will be back, hopefully by September.”