But there is little evidence of recent major recombination in the history of this particular virus, since its common ancestor with the 2013 virus. It looks like it has a pretty much vertical inheritance from its common ancestor with the 2013 bat sequence.
Check out the paper “Evolutionary origins of the SARS‐CoV‐2 sarbecovirus lineage responsible for the COVID-19 pandemic” (https://www.biorxiv.org/content/10.1101/2020.03.30.015008v1). They run a sliding window along the SARS-CoV-2 sequence and compare it to the sequence of many other viruses. The conservation is not constant across the genome, but different regions are under different evolutionary constraint, and the *relative* conservation across the genome looks more or less consistent rather than there being big sharp jumps in homology as you would expect from distant recombination and see in other more distantly related viruses.
Some have argued that recombination could account for the origin of the specific receptor binding domain since it seems very similar to that found in a pangolin virus. But overall there is very little recombination evidence.
The only idea that is really open at all is ‘Poor procedure resulting in viral transfer from a wild lab animal’, not ‘recombination experiments in the lab creating something unusual’.
But there is little evidence of recent major recombination in the history of this particular virus, since its common ancestor with the 2013 virus. It looks like it has a pretty much vertical inheritance from its common ancestor with the 2013 bat sequence.
Check out the paper “Evolutionary origins of the SARS‐CoV‐2 sarbecovirus lineage responsible for the COVID-19 pandemic” (https://www.biorxiv.org/content/10.1101/2020.03.30.015008v1). They run a sliding window along the SARS-CoV-2 sequence and compare it to the sequence of many other viruses. The conservation is not constant across the genome, but different regions are under different evolutionary constraint, and the *relative* conservation across the genome looks more or less consistent rather than there being big sharp jumps in homology as you would expect from distant recombination and see in other more distantly related viruses.
Some have argued that recombination could account for the origin of the specific receptor binding domain since it seems very similar to that found in a pangolin virus. But overall there is very little recombination evidence.
The only idea that is really open at all is ‘Poor procedure resulting in viral transfer from a wild lab animal’, not ‘recombination experiments in the lab creating something unusual’.