[krrrh]

It’s covered in the article and it’s called RaTG13 and no one can get a straight answer on where it was acquired or when. However independent researchers found it is identical to a virus previously known as RaBtCoV/4991 that made several miners ill in 2012.

It’s 96.2% similar not 98%. The issue is that coronaviruses in nature don’t mutate fast enough for that to be the missing link, and they have tested something like 80,000 animals since the outbreak without finding anything closer. One possibility is that the gap was closed through gain-of-function or serial passage research.

[seventytwo]

Where have you heard that CoVs don’t mutate fast enough in nature to close the missing 3.8% gap?

[krrrh]

It’s a claim that I’ve seen often referenced by people like Brett Weinstein and reporters who have been covering this story. I’m not sure where I first heard it, but here’s a quick reference published on a recent PLOS blog: [0]

> Clues to the transition from bat virus RaTG13 to human virus SARS-CoV-2 may lie within the 4% of the genome sequences that diverge. Evolutionary biologists estimate it would have taken at least 50 years for the bat virus to have mutated itself into SARS-CoV-2, considering known, natural mutation rates of viral genomes.

It goes on to say, that it’s possible this virus is just different.

This paper states 20-50 years an an estimate. [1]

> Bats belong to the usual suspects for zoonosis, and indeed, a bat virus that shared 96% sequence identity with SARS-CoV-2 was isolated in Yunnan /China in 2013. However, a 4% sequence difference (>1000 bp) would indicate 20 to 50 years of separation from SARS-CoV-2, making this bat isolate an unlikely direct source for the nascent epidemic. Chinese researchers explored tissue and faecal samples from 227 bats representing 20 species living in China, collected between May and October 2019 and analysed them by metagenome sequencing. This investigation found that the closest relative of SARS-CoV-2 in this sample set shared 93.3% sequence identity over the entire genome, less than the bat coronavirus isolated in 2013 from the same province, Yunnan (Zhou et al., 2020).

I’m not a virologist, just trying to keep up with this story. It seems like a consensus that 3.8% is a large chasm to cross in that time frame, but there could be things we don’t know or possibly viruses that are closer to SARS-CoV2 that we haven’t sequenced yet. I think the most important thing to note is that there hasn’t been enough evidence to rule out a gain-of-function lab leak hypothesis given what we know today about viruses and there wasn’t a year ago either.

[0] https://dnascience.plos.org/2021/04/15/3-possible-origins-of...

[1] https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/175...

[seventytwo]

Thanks much!

[jkelleyrtp]

I believe the furin cleavage site has been quoted to be an exceptionally rare mutation. It is extremely unlikely for this particular mutation to exist without being accompanied by other less-rare mutations in a natural-spread scenario. For this particular mutation, a gap of greater than 3.8% would be expected. It may (I'm not an expert) may be unlikely for a 3.8% drift, but is less likely for only a 3.8% drift given the rarity of the ACE2 spike.