How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
It seems to be explained right there in the image you posted:

So, the three strains were classified based on three specific variants:

Strain S, variant ORF8-L84S: a variant in the gene &quot;ORF8&quot; which changes the leucine (L) residue at position 84 of the gene's protein product to a serine (S).
Strain G, variant S-D614G: a variant in the gene &quot;S&quot; which changes the aspartic acid (D) residue at position 614 of the gene's protein product to a glycine (G).
Strain V, variant NS3-G251V: a variant in the gene &quot;NS3&quot; which changes the glycine (G) residue at position 251 of the  gene's protein product   to a valine (V).