Some viruses have specific sets of symptoms that would guide diagnosing them but I think for a definite confirmed diagnosis most modern tests would be trying to detect genetic material from the virus in a sample from the patient. We have tests like PCR for viruses that we already know about like flu or SARS-CoV-2, it uses small bits of genetic material that we know should match the virus we’re testing for to check if the virus is present. If a lot of people are sick and it isn’t any of the usual viruses that we can test for (like at the start of the pandemic, when we hadn’t seen SARS-CoV-2 before!) then we would have to do something more broad to figure it out. When we pull out all the genetic information from a sample without looking for something specific it’s called metagenomics, this lets us look at everything without knowing exactly what virus we’re looking for beforehand so we can work out what’s going on.
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