That is correct. They appear to have arrived in SARS2 by natural mutagenesis. In the alignment below you can see how as you move to more ancient ancestors, the number of mismatches slowly increases. I therefore stay away from the term "insert", but instead use homology region.
3
1
7
Good, so this completely invalidates the case for “HIV inserts”, right? As these are just spurious AA coincidences between HIV and SARS2’s ancestors — natural bat viruses.
3
1
2
The only issue I have with that is that most of those genomes might be fakes. I would prefer a more comprehensive alignment using the whole horseshoe bat coronavirus cohort (at least 40 sequences) before making a conclusion on conservation.
3
8
Yeah, I read that several of the genome sequences with the HIV “inserts” were updated within days of the HIV inserts preprint being published online (including RaTG13, CZ45, ZXC21). Sus timing at the very least. They lied about lab leak, why not lie about these genomes, too?
2
4
Is there any available evidence definitively showing that these bat virus genomes (or others) containing the HIV “inserts” existed prior to February 2020?
1
2
Thank you for the ref. Figure 3C is what I was looking for. Cryo EM, but still very helpful. No doubt that the 3 regions have evolved naturally. But their function remains unknown. Given their exposure, probably critical.
2
3
To answer @TyCardon's question, the Zhoushan viruses ZC45 and ZXC21 (deposited to GenBank in 2018) also has similar inserts.
3
7
That should resolve @pathogenetics concerns as well.
2
2
They don't look similar to me.
2
2
There are a lot of intermediate sequences between SARS1 and SARS2. It appears the region gets gradually filled in during evolution:

Jan 17, 2022 · 5:17 PM UTC

3
1
2
As I've pointed out, it gets filled in with viruses of dubious origin. If you accept RaTG13 et al are real then you may as well accept zoonosis. The only feature that can't be explained by this lot is the FCS. This is an elaborate fraud.
1