Sometimes, you can't stay friends with people.
Sometimes, they change and can no longer be reasoned with.

Not everyone who comes into our life is meant to stay in it.
This person sounds like a really good example of that fact.

You said he is very bright. Sure about that ?

My first thought is mental illness. How old is this person? He is in a science field and rejecting science. There are ways to view the virus, such as electron microscopy. I didn't take time to read the facebook stuff.

If he is rebelling against his father, chances are that eventually he will come back around to atheist, providing there is no mental illness involved.

I think there are still enough people who are able to think, reason and are interesting that wasting even a minute's attention on this person is an act of ingratitude for both the human ability to reason and life itself.

I think he is a very confused individual and probably nobody can help him, or perhaps some very strong medication.

I understood from my time studying biology that viruses were visible by electron microscopes. Regardless, we can't see atoms either, but we have plenty of ways of detecting facts to verify their existence and their configuration. Viruses are no different.
[ncbi.nlm.nih.gov]

I thought the reason you suspect your friend converted to Islam of interest. Michael Shermer in his book "How We Believe" examined a number of factors influencing the beliefs of individuals. One factor he wrote about ws the beliefs of parents; a person very often maintains the beliefs taught to them by their parents with an exception. If the parents have a difficult or hostile relationship with one another or with the child. Under these conditions, the offspring will change their belief system from their parents. Shermer noticed that offspring of believing parents would become nonbelievers at higher percentages when their relationships with parents were seen as unsatisfactory. I see no reason why the opposite wouldn't also be the case.

There's lots of things we can't see but know they are there. Electron microscopes can see viruses.

I thought they did image it with a Scanning Electron Microscope (SCM) ?

It's a misuse of a brain and of time.

Hardly anyone on Facebook can prove COVID exists with the level of proof he is probably going to require.

My best friend works at a hospital and says he sees it every day. This anecdotal evidence is good enough for me, but I’m not trying to get it passed peer review or anything.

I haven't had time to read your entire post yet but one thing struck me...
He doesn't think viruses are real because they can't be seen in a microscope.
Before the invention of the microscope he'd probably say the same things about germs.
And wwhat about atoms?

If the virus happens to you, it is fake.
If I get sick by it, then it is real

I wonder how long his faith in the Quran would last if he applied that type of thinking to it?

He is an idiot that knows nothing about ELECTRON MICROSCOPES that photograph the virus covered in proteins surrounding single cells like the corona around the sun

It's simple.
We have evidence that viruses exist.
We have no evidence God exists

What does one say to someone who claims to be some kind of researcher yet denies the evidence based existence of viruses? You're fucked in the head!

I see nothing wrong with asking for proof. Seems like a smart guy.

He can (mis)use philosophy the way he wants! It's nobody's knowledge! You shouldn't care! You shouldn't neither care whether he will go back to his senses or not! If you consider hem a 'friend' and you are truly worried, you've advised and told! Leave it there. If it's a fase, it will most likely pass(if he's 'bright' as you mentioned), if it doesn't he's free to fuck up his own life trying to get back at his parents! Unless you know for sure that he's planning on doing something violent! You know then who to call! (Not Ghostbusters)! If you and others try to haunt him, with good intentions, to deconvert, his subconscious mind would probably make him believe that his 'faith' "is true, otherwise you wouldn't bother!" Tell him to read more into that wrongly collected full of mistakes stuff called Islam and see how many times Killing is encouraged in his 'holy book', and no these are no interpretations! Kill the nonbelievers means Kill! And how at lease on 86 different occasions in his 'holy book' Muslim men are instructed on the how-to trade, obtain and use (underage) females! He doesn't mind his mum to be sold if a group of muslims were able to have the upper hand in his hometown? I'll go for a Vodka with Ice!

Real Atheist parents would teach a child basic science obvious for the last 50 years

Notice he does not dare himself to prove his allah exists anywhere in any shape ....he is a flat earther measuring flat elevation areas as if the planet is orbited by the sun