There are various ways of doing this. Remember that you can search for specific organisms using by adding "organism"[ORGN] to your search (e.g. "Murine Hepatitis virus"[ORGN], "sars coronavirus"[ORGN] or "coronavirus"[ORGN]), although you will see that it is not always easy to find viruses this way as most do not have a scientific name. Once you find one spike protein the other ones are most easily found by performing a BLAST search. Limit your BLAST search to viruses only. When BLAST search is finished scroll down to alignments and select the sequences you want to retrieve. At the end of the page you will see "Get selected sequences" button. Once you have your sequences in a file in FASTA format edit the header lines (the first line) so that the first word indicates which virus this spike protein is from. You should use unique names. You need this renaming to be able to see in your phylogentic tree which sequences belong to which viruses. If you are finished with preparing this dataset, move to sequence alignments and phylogeny. If you are stuck with preparing this dataset, you can also use Spikes file that is ready made for this exercise. In the parameters there is also a setting called CORRECT DIST. This is the same as the Kimura 2-parameter correction (see your reader), which corrects the evolutionary distances for multiple substitutions. See whether setting this has an effect on the phylograms you produce.