About the origin of SARS-CoV-2

[Michael_Okoko]

@BrianLopez

@Michael_Okoko

In addition, I am also curious why you accept virus phylogenies but not that of organisms? (@BrianLopez, do you see another example of an ID proponent accepting phylogenetic evidence in one context but ignoring it in another)

Yes I see it with my eyes, but I dont understand shizzle

Oh its quite simple. Gill is not convinced by the phylogenetic evidence that humans and chimps shared a common ancestor, but he is convinced that SARS-CoV-2 and RATG13 shared a common ancestor, despite the fact that the phylogenetic evidence in both cases are essentially derived the same way. This shows he accepts phylogenetic evidence only when it lends some degree of support to his beliefs (in this case, a lab leak).

@Giltil

@Michael_Okoko

There, my friend, is the evidence for recombination between SARS-CoV-2 (a sarbecovirus) and merbecoviruses (which are phylogenetically distant). As a bonus, they indicated some of these detected recombination was between SARS-CoV-2 and merbecoviruses in Wuhan, China .

The evidence for recombination between sars-cov-2 and merbecoviruses is not as compelling as you seem to think for it leaves room for another less likely but still plausible possibility.

Are we looking at the same data? If we are, then you should know this is a ridiculous statement. The h/m ratio for recombination between SARS-CoV-2 with other sarbecoviruses and merbecoviruses in the study was essentially the same. Look at the data in case you have forgotten:

@Rumraket

@Michael_Okoko

Yes this seems to be the general trend but there are exceptions and SARS-CoV-2 is one of them.

I’m not sure I follow you here.

In what way is SARS-Cov2 an exception to the general trend?

According to the paper, genetic exchange between strains of the various subgenera is quite rare and rare enough to consider them as biological distinct species. This means we shouldn’t detect recombination between SARS-CoV-2 and other betacoronavirus subgenera. However, it turns out there was significant recombination between SARS-CoV-2 and merbecoviruses (but not embevoviruses). This makes SARS-CoV-2 an exception to the general observation that strains from one subgenus of betacoronaviruses does not recombine with strains in other subgenera.

@Rumraket

The origin of SARS-Cov2 is the case we are trying to assess, so it would be begging the question to simply invoke it as a virus who’s FCS originated by recombination from a more distantly related betacoronavirus.

Did I miss something?

I am not arguing that the FCS of SARS-COV-2 derived from recombination with some other distantly related betacoronavirus (although this would be the case for several segments of its NSP genes). I was rebutting Gil’s claim that only phylogenetically close strains could have recombined with SARS-CoV-2 and as the paper he cited showed, that is clearly false (but he didn’t realize this and went ahead to cite it).

With regards to the origin of its FCS, we should look more to recombination with other sarbecoviruses as that is the most frequent. As the paper showed, there is plentiful recombination between SARS-CoV-2 and other sarbecoviruses in the spike protein region, so it’s quite likely it got its FCS (or a pre-FCS which would go on to mutate to the current form) via recombination with another unknown sarbecovirus.