Yes, that is the process basically for new virus discovery- sequencing and then looking for similarity to known viral sequences. That is still an expensive and time consuming research project, and it fails if the virus is too different to identify any sequence homology. We still find a lot of DNA and RNA we can’t make any sense of in almost every sequencing experiment- there’s a ton of stuff out there undiscovered and unexplained. I suspect a lot of currently mysterious diseases and health problems may have viral origins.

That’s why I’m saying we can’t rule out a virus here easily- not until some other cause is proven.

You can also have more complex mechanisms that also involve a virus plus generic or environmental factors- for example the recent finding that implicates HSV in Alzheimers, despite the fact that most people with the virus still never get Alzheimers.