Hi Everyone!! Is it possible to detect RNA viruses from shotgun metagenomics data except for the retroviruses? I am curious because we have found retroviruses from our shotgun metagenome data but that is explainable because the retroviruses have the machinery to integrate into the DNA (genome) and replicate so they can be detected but other RNA viruses can't be detected from the shotgun metagenomics data. I just want to know if I am thinking correctly.

Thanks in Advance!!