The closest relative of SARS-CoV-2

In the absence of an obvious animal on which to pin the origin of the COVID19 virus, we return to what the genetic code of the virus can tell us. Is this virus, for instance, from the same source as its four bears, the original SARS or MERS viruses. That genetic code says not…

Julia - These viruses are very different. When comparing SARS-Cov-2 to the original SARS virus, their genetic codes are 79.4% similar. While that sounds like a pretty high number, in genetic terms that is about as similar as a human is to a cow. And when compared to MERS, this similarity drops to around 50%. So in order to find a closer relative, the genetic sequence of SARS-Cov-2 was compared to other documented coronaviruses already discovered in the wild.

Chris - Jesse Bloom studies viral evolution at the Fred Hutchinson Cancer Research Centre.

Jesse - The two closest known relatives of SARS-Cov-2 are two different coronaviruses that were isolated from bats. So one of these viruses, the first one that was known is called RATg13, and that was a virus that was sequenced at the Wuhan Institute of Virology and they had collected it from a bat cave in Yunnan province. More recently, another virus similarly close to SARS-Cov-2 was discovered in Laos. These viruses are both about 96 to 97% identical to SARS-Cov-2.

Chris - 96% the same is a lot closer. But how far apart in evolutionary terms is that missing 4%? In other words, given the rate at which coronaviruses evolve, how long would it take to fill that genetic gap? The answer is still a very long time.

Jesse - That corresponds at sort of the evolutionary timescale of a number of decades, say 30 to 50 years of time from which they diverged. It's also really important to emphasise that something like RATg13 is not the ancestor of SARS-Cov-2. The relationship between SARS-Cov-2 and these bat viruses is like the relationship between, let's say you and your cousin. Neither you or your cousin are descended from each other, but you have a common ancestor.

Chris - I was just going to say, it's a bit like we know chimpanzees and humans share a very high fraction of our genetic material. It's not that we have descended from them. It's just that we have descended from a common ancestor. We both shared an ancestor back in history. So that argues, then there must be some kind of virus back in history that gave rise to SARS-Cov-2 and to these viruses you've just mentioned. So where is it then?

Jesse - It's not known. These two closest known relatives to SARS-Cov-2 were from bats that were in Laos or Yunnan province, both of which are actually fairly far away from Wuhan. So it's believed that the ancestor of SARS-Cov-2 is probably a bat coronavirus that existed somewhere in this geographic area. But how that bat coronavirus got to Wuhan is what remains unclear.