tl;dr: mNGS [1]
Longer answer as I think you may need to be mansplained because you wrote a long post which could be answered by a simple Google search and Wikipedia article:
Step 1: Doctor wonder why their patients were so sick, looks like infection but no pathogens identified, this is actually not that rare as there are many obscure pathogens even for experienced doctors.
Step 2: Patients agrees to pay for mNGS. Nurse draw their blood, send to lab.
Step 3: mNGS matches every DNA "pieces" from the patients' blood against a database. One of those pieces matched the original SARS with about 90% similarity.
Step 4: Chaos in the lab, the hospital and the government.
Step 5: "We've detected a new virus"
[1] https://en.wikipedia.org/wiki/Clinical_metagenomic_sequencin...