How can a viral amino acid sequence be used to identify a virus?
The same way that pretty much any amino acid sequence (or better yet, nucleotide sequence) of sufficient length can be used to identify any organism. 🙂
Protein sequences are not so well used for organism identification, since you cannot multiply them. Nucleic acids are better for that.
Anyway, if you get some proteins, you identify them with mass spec (either MALDI or digest on LC-MS) and this information you use for the identification.