How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data? On GISAID they classified the coronavirus using 4 clades(S, G, V, Other).
I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging to one of the 4 clades(S, G, V, Other).
On the top left of the image below is the classification of the 3 clades(S, G, V).
More specifically, the three strains were classified based on three specific variants(This answer was taken from my previous question):

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).

My problem is that using this method of classification for the coronavirus genome I am seeking information on the protein products of the genes in the genome.
So to be more specific here are my concise questions:

How can I classify a genome as &quot;Strain S&quot; using only the complete genome assembly, without any information about its proteins?
How can I classify a genome as &quot;Strain G&quot; using only the complete genome assembly, without any information about its proteins?
How can I classify a genome as &quot;Strain V&quot; using only the complete genome assembly, without any information about its proteins?


This picture was taken from this PDF on GISAID
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).