In sequencing a RNA strand, you use an enzyme called reverse transcriptase (RT), which allows you to go from RNA to DNA (recall that most genes, when making proteins, go from DNA to RNA not vice versa). With RT, you get a copy of the RNA virus in DNA form, called copy-DNA (cDNA). So in sequencing what you'd be actually measuring and sequencing is the cDNA produced by RT from the viral RNA.
^^^^^^I'm pretty sure that's generally correct, though I could be wrong.
More generally, I find it amazing that different combinations of A's, C's, T's, G's direct and specify all life forms and their traits, from eye color we find alluring to viruses that can wipe out half the earth.