>Additionally, the closest relative to SARSCov2 that has been identified (RaTG13)
As of 2022, this is no longer true.
As of 2022, this is no longer true.
https://www.business-standard.com/amp/article/current-affair...
One of the things we know for sure is that that about 50 years of evolutionary changes separate RaTG13 and BANAL-52 from SARSCoV2, so they are not its direct ancestors.
Do you have a source for this?
Also, I'm no biologist, but is comparing the base rate of evolutionary changes still relevant if SARSCoV2 wasn't of natural origins? E.g. through creating chimeras or 'serial passaging' as described in this article? Wouldn't that create an environment where 50 years could pass in a way shorter timeframe?
>Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID- 19 pandemic
>Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879–1999), 1969 (95% HPD: 1930–2000) and 1982 (95% HPD: 1948–2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
https://www.nature.com/articles/s41564-020-0771-4
You should also know that SARSCoV2 1) is not a chimeric virus, and 2) that the present study includes viruses linked to RaTGP13 but more distant from SARSCoV2, i.e. it includes evidence from viruses unassociated with the pandemic.
There is no basis for this claim. Genomic evidence shows that SARS-CoV-2 is not a chimera of any two previously-known viruses. No possible genomic evidence could exclude a chimera of two previously-unknown viruses, and the WIV was the world's leading collector of such novel sarbecoviruses from nature. They proposed to make chimeras of them in DEFUSE. That proposal wasn't funded, but this article now reports explicit claims they did such work:
> They said the Wuhan scientists had inserted furin cleavage sites into viruses in 2019 in exactly the way proposed in Daszak’s failed funding application to Darpa.
You're basically rehashing Andersen's "Proximal Origins" here, and even he has moved on to more sophisticated (though still unconvincing) arguments like Pekar. As David Relman wrote almost three years ago:
> This argument [that SARS-CoV-2 must be natural since it doesn't use a known backbone] fails to acknowledge the possibility that two or more as yet undisclosed ancestors (i.e., more proximal ancestors than RaTG13 and RmYN02) had already been discovered and were being studied in a laboratory—for example, one with the SARS-CoV-2 backbone and spike protein receptor-binding domain, and the other with the SARS-CoV-2 polybasic furin cleavage site. It would have been a logical next step to wonder about the properties of a recombinant virus and then create it in the laboratory.
Of course such a virus could also have evolved naturally by a similar path; lots of sarbecoviruses are just a single mutation away from that FCS, and perhaps there's some yet-unknown natural animal host where that gets selected for. The point is that no genomic evidence can distinguish between these two cases, though.
For emphasis, it seems like you're assuming that we know all the natural viruses that the WIV was working with. Sampling of novel coronaviruses from nature was a core part of the WIV's research, so that's not a reasonable assumption. RaTG13 was sampled in 2013, but not fully published until 2020. At least one novel coronavirus was identified in contamination of rice samples sequenced on the same equipment that the WIV used:
https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2
That's a merbecovirus, so it couldn't possibly have any relationship to SARS-CoV-2; but if they had one unpublished novel virus, then it's hard to reject the possibility that they had more.
We don't know as for unknown reasons the database of specimens collected by the Wuhan lab was taken down in September 2019.
The distance in years between two viral strains you mention makes no sense at all, as the mutation rate is extremely dependent on environment.
The article is not suggesting that Covid19 evolved from RaTG13; it is suggesting that Covid19 is a chimaera made with RaTG13.
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.