[eganp]

IIRC, this is still true if you exclude the spike protein and use a higher similarity threshold.

Why would one do that? Well, two reasons. First, the spike more variable as it is subject to greater evolutionary pressure as the major component of the viral surface. Second, in coronavirus reverse genetics typically the virus is segmented into multiple pieces, most of which compose the non-spike backbone and a subset which compose the spike protein. This is intentional to enable the swapping of spike proteins. So, if SARS-CoV-2 is spike-swap or spike variant assembly, a RaTG13-like virus could be the "backbone" of SARS-CoV-2.

Moreover, a hypothetical SARS-CoV-2 backbone could exist in the viral sequences list the WIV took down in Sept. 2019. They sequenced RaTG13 a few years prior. The lab's raison d'etre is collecting and sequencing coronaviruses poised for spillover. And, with modern DNA synthesis technology, it's not difficult to print out arbitrary backbone contigs for a viral assembly.