Ok, Don, here’s the quick and dirty.

When you do this kind of sequencing, you sequence everything in the mix. Before you sequence you isolate all the DNA (or RNA and convert it to DNA with reverse transcriptase) and then you shear it into small pieces of a few hundred nucleotides plus or minus. Or longer if the sequencing technology you use can do longer reads.

Then, when you sequence you have a whole mess (literally millions) of these “short reads” which are then put through a computer program that “assembles” them into longer reads by matching overlaps at the ends of the reads.

Now, the virus genome is WAY smaller than the human one and so it will have a start and a finish that’s much smaller than the human and again, database comparisons (again by computer programs) will find the sequences that resemble other viruses with genes not normally found in humans. And because the viruses are much more numerous than the human cells and DNA, there will also be a lot greater number of copies of those reads.

Does that give you a better picture of how that is done? I’ve left out some of the finer details but I think that’s enough for you to see how it’s done, yes?