SARS-CoV-2 looks like a hybrid of viruses from two different species - Ars Technica

Analysis of the virus' genome was ambiguous?

How do pieces of virus from different species end up being mashed together.

Recombination can also take place in simpler cells, where it's been the primary tool that we've used to engineer new or altered genes into the genome of bacteria?

And, since the molecules that perform the recombination aren't especially picky about which DNA molecules they work with, DNA viruses that infect cells can sometimes recombine if more than one strain of virus infects a single cell.

Those of you who have followed the virus closely, however, may be wondering what's going on here.

For example, the influenza virus spreads its genome across eight different molecules, allowing cells infected by more than one strain of flu virus to produce viral particles that have a random assortment of molecules from the two strains.

As a result, this process can allow recombination among viruses that are relatively distantly related from an evolutionary perspective.

So, for the new analysis, the research team started with a collection of 43 different coronaviruses from a variety of species, including humans, bats, and the pangolin sequences known to be similar to SARS-CoV-2.

The basic genome analysis confirmed that SARS-CoV-2 is most closely related to a number of viruses that had been isolated from bats.

But different areas of the virus were more or less related to different bat viruses.

In other words, you'd see a long stretch of RNA that's most similar to one virus from bats, but it would then switch suddenly to look most similar to a different bat virus.

This sort of pattern is exactly what you'd expect from recombination, where the switch between two different molecules would cause a sudden change in the sequence at the point where the exchange took place.

But there was a notable exception to this mixing of bat viruses: the spike protein that sits on the virus' surface and latches on to human cells.

Here, the researchers found exactly what the earlier studies had suggested: a key stretch of the spike protein, the one that determines which proteins on human cells it interacts with, came from a pangolin version of the virus through recombination.

SARS-CoV-2 is most closely related to bat viruses and most closely related to pangolin viruses.

And, while exchanges are more common among viruses that infect the same species, it's entirely possible that contributions can come from much more distantly related ones.

The authors find evidence that the viruses from different species may experience distinct selective pressure, which isn't really surprising.