Flavinkins (@Flavinkins)

When a synthetic recombinant genome for a coronavirus is constructed, fragments are selected from relevant natural bat isolates with a requirement that the type IIS restriction pattern using the planned enzymes on the resulting assembly should enable easy cloning and efficient manipulation—a less than 1 in 100 chance for this to happen randomly by chance for recombination outside the S1 region of the genome, and completely irrelevant to spillover. When a natural virus spills over, there is very little effect (within 1 order of magnitude) on the chance that some specific strain would end up becoming the pandemic strain for recombination ancestry outside the S1 region. There is no requirement that a strain that spills over must be a strain that is easy to clone by the 2 most popular type IIS restriction enzymes that were used in CoV genome assemblies, and the chance given natural spillover of an ancestry that had an efficient type IIS RGS system without modification is the same chance as finding one such strain in nature just by 1 single random sampling—so far no specimen from Asia satisfy this on their individual genomes. Again, which sequence on the ReCCA graph were not sampled from nature? Unfortunately, the so-called “natural recombination ancestry” argument may well just be one of the many ways workable coronavirus genomes are “recovered” from a set of otherwise unisolated samples. Whatever you reconstruct out of natural isolates for a clone, it must be easy to clone. It can be from one of the rare samples you find with an easy-to-clone pattern, or it could be one of the combinations of various contigs from sequencing a pooled sample. It could also be a chimeric genome constructed using fragments selected from related wild isolates with a requirement that the result is easy to clone. When a strain spills over naturally, there is no requirement that it must be easy to clone—restriction enzymes work on DNA not on RNA, and there is no reason why the specific combination with an easy to clone site pattern must be selected other than the posterior claim “it happened” (ReCCA construction used SARS-CoV-2 genome as reference). This is a circular argument as the claim that “the SARS-CoV-2 genome with its unusual combination of type IIS sites is the result of a natural spillover” assumed P(spillover|strain have good site combination)>=0.5 while P(strain have good site combination)<<0.5 with the only justification “we observe that the SARS-CoV-2 genome is easy to clone and can be constructed using a combination of fragments from some 8+ different “bat virus strains”” only able to justify this implied probability assumption with the assumption “SARS-CoV-2 is the result of a natural spillover”, a hypothesis that is being tested in the type IIS RE site analysis paper in stead of an underlying assumption. In conclusion, while a ReCCA with an easy to clone type IIS site combination with the go-to enzymes used for assemblies of this length is a possible combination of the bat coronavirus sequences known from sampling, there is no justification for this hypothetical and still unsampled ReCCA to be the only possible combination where a spillover is possible or that a spillover strain will have a probability that it will be easy to clone being >0.5 while the chance of finding such a strain from a random sampling from the wild being only about ~0.01.