I mean yes, that would be the assumption. DNA/RNA analysis is a bunch of probabilistic trickery for the most part. One good way they could make this assumption is through a differential expression analysis. Normal cells constantly make mRNA so ribosomes in the cytoplasm can make proteins. This particular virus (from my understanding) injects its own RNA into the cytoplasm. Ribosomes read this indiscriminately as there should be no foreign mRNA in the cell. They make what they find. If we do RNA seq and compare uninfected vs. infected, we can see difference between "normal" RNA vs. those that appear in infected people.