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I think the closest natural virus was 95% similar. 5% seems pretty far for mutations. Is there a historical track record for finding the natural virus to a 99.9

I think the closest natural virus was 95% similar. 5% seems pretty far for mutations. Is there a historical track record for finding the natural virus to a 99.9% similarity?

deleted 6y ago
[deleted]
cma 6y ago
We see around one base pair mutation per host transmission, so that would likely already put us outside 99.9% similarity even among humans with coronavirus wouldn't it? Rough estimate: (29,000 base pairs, just assuming 3.5 days between generations, 395 days since first affected person (probably it was a bit more), would be 112 mutations = 99.6% similarity) And I think we'd expect more changes to be selected for in the early period of host adaptation.
- andi999 6y ago
  Your first sentence is missing the number, did you mean 'one bas pair'?
  - cma 6y ago
    Yes thanks, fixed
mabbo 6y ago
Two answers. First, it was 96% identical. But that was in 2013. Presume it's being passed bat to bat every few days for 6 years, then at some point made the jump to another species, most likely in a wet market. It's really not unreasonable to imagine a 4% drift in that time. Second, we don't identify every virus or every strain of every virus. Just because we found one that was 96% similar doesn't mean that all the other bats carry an identical virus. It's quite likely we found a distant cousin of the umpteenth-grand-parent of covid-19, and sequenced it.
- esja 6y ago
  Can you explain how that evolutionary path led to the virus becoming better adapted to humans than it is to bats, and can you explain how all the samples we have ever found, from the very beginning of this outbreak, are uniquely adapted to humans? https://arxiv.org/abs/2005.06199 https://arxiv.org/abs/2005.06199
  - robbiep 6y ago
    You’ve asked the same question in 3 spots. You’re asking the question backwards and not reading the other comments here (for example, the particular response you responded to) There are some very good reasonable answers for why and how this could have happened, unless you’re a biologist and are going to tell us how it happened (which the paper you cited doesn’t) you’re beating on a painful drum
    - esja 6y ago
      Ok, if there are very reasonable answers, perhaps you can point to them?
  - mabbo 6y ago
    It's not an unreasonable question. But my own guess? Selection bias applies. Viruses grow by the millions, billions, and mutations occur frequently. This virus's ancestor might have hopped around civets for months. Then, a few random mutations on one got lucky and made it really good at infecting humans. That's when it made the leap. We don't see the billions of attempts and mutations that sucked at infecting humans. We see the one that did. Now, my own bias is that my honours thesis was on evolutionary algorithms and I spent a lot of time being amazed at how well random mutations can lead to optimal answers.
sradman 6y ago
> Is there a historical track record for finding the natural virus SARS-1 [1]: > The viral outbreak was subsequently genetically traced to a colony of cave-dwelling horseshoe bats in Yunnan, China. The Guardian reference [2] states: > Hence the efforts of Chinese scientists – led by Shi Zheng-Li and Cui Jie of the Wuhan Institute of Virology, China – to trace the source of the outbreak. Scientists initially suspected that civet cats, sold in markets in China, were the source of the virus but later turned their attention to bats, which they realised were the prime source of the virus. Civets were merely an intermediary. [1] https://en.m.wikipedia.org/wiki/Severe_acute_respiratory_syndrome https://en.m.wikipedia.org/wiki/Severe_acute_respiratory_syn... [2] https://www.theguardian.com/world/2017/dec/10/sars-virus-bats-china-severe-acute-respiratory-syndrome https://www.theguardian.com/world/2017/dec/10/sars-virus-bat...

I think the closest natural virus was 95% similar. 5% seems pretty far for mutations. Is there a historical track record for finding the natural virus to a 99.9% similarity?

deleted 6y ago

[deleted]

cma 6y ago

We see around one base pair mutation per host transmission, so that would likely already put us outside 99.9% similarity even among humans with coronavirus wouldn't it? Rough estimate: (29,000 base pairs, just assuming 3.5 days between generations, 395 days since first affected person (probably it was a bit more), would be 112 mutations = 99.6% similarity) And I think we'd expect more changes to be selected for in the early period of host adaptation.

andi999 6y ago
Your first sentence is missing the number, did you mean 'one bas pair'?
- cma 6y ago
  Yes thanks, fixed

mabbo 6y ago

Two answers. First, it was 96% identical. But that was in 2013. Presume it's being passed bat to bat every few days for 6 years, then at some point made the jump to another species, most likely in a wet market. It's really not unreasonable to imagine a 4% drift in that time. Second, we don't identify every virus or every strain of every virus. Just because we found one that was 96% similar doesn't mean that all the other bats carry an identical virus. It's quite likely we found a distant cousin of the umpteenth-grand-parent of covid-19, and sequenced it.

esja 6y ago
Can you explain how that evolutionary path led to the virus becoming better adapted to humans than it is to bats, and can you explain how all the samples we have ever found, from the very beginning of this outbreak, are uniquely adapted to humans? https://arxiv.org/abs/2005.06199 https://arxiv.org/abs/2005.06199
- robbiep 6y ago
  You’ve asked the same question in 3 spots. You’re asking the question backwards and not reading the other comments here (for example, the particular response you responded to) There are some very good reasonable answers for why and how this could have happened, unless you’re a biologist and are going to tell us how it happened (which the paper you cited doesn’t) you’re beating on a painful drum
  - esja 6y ago
    Ok, if there are very reasonable answers, perhaps you can point to them?
- mabbo 6y ago
  It's not an unreasonable question. But my own guess? Selection bias applies. Viruses grow by the millions, billions, and mutations occur frequently. This virus's ancestor might have hopped around civets for months. Then, a few random mutations on one got lucky and made it really good at infecting humans. That's when it made the leap. We don't see the billions of attempts and mutations that sucked at infecting humans. We see the one that did. Now, my own bias is that my honours thesis was on evolutionary algorithms and I spent a lot of time being amazed at how well random mutations can lead to optimal answers.

sradman 6y ago

> Is there a historical track record for finding the natural virus SARS-1 [1]: > The viral outbreak was subsequently genetically traced to a colony of cave-dwelling horseshoe bats in Yunnan, China. The Guardian reference [2] states: > Hence the efforts of Chinese scientists – led by Shi Zheng-Li and Cui Jie of the Wuhan Institute of Virology, China – to trace the source of the outbreak. Scientists initially suspected that civet cats, sold in markets in China, were the source of the virus but later turned their attention to bats, which they realised were the prime source of the virus. Civets were merely an intermediary. [1] https://en.m.wikipedia.org/wiki/Severe_acute_respiratory_syndrome https://en.m.wikipedia.org/wiki/Severe_acute_respiratory_syn... [2] https://www.theguardian.com/world/2017/dec/10/sars-virus-bats-china-severe-acute-respiratory-syndrome https://www.theguardian.com/world/2017/dec/10/sars-virus-bat...