5 ms·

Is there any information on what the upper bound might be on the infectivity of SARS-CoV-2? I think a lot of people just assume one big jump consumes most of th

Is there any information on what the upper bound might be on the infectivity of SARS-CoV-2? I think a lot of people just assume one big jump consumes most of the range, but we've seen at least three big jumps so far ("Doug", "Alpha", and "Delta").

softwaredoug 5y ago
There is a “Doug” variant?!? Asking for a friend… EDIT So there is! Ha > And you can imagine, it was quite a mouthful. So, we started to call this D to G mutation ‘Doug’, and then any of the other virus sequences that didn’t have this mutation … we called ‘Douglas’, so it was sort of a bit of a private joke within the lab,” she said. “As more mutations came about, we’d come up with a person’s name for them.” https://www.theguardian.com/world/2021/feb/17/nicknames-emerge-for-growing-list-of-covid-variants https://www.theguardian.com/world/2021/feb/17/nicknames-emer...
- deleted 5y ago
  [deleted]
- NullPrefix 5y ago
  >One of the first mutations to go global is known as D614G, or Doug for short
  - hahamrfunnyguy 5y ago
    Also the Nelly and Eeek variants. They would have called it Erik, but they worked closely with someone named Erik already.
- deleted 5y ago
  [deleted]
toiletaccount 5y ago
i was wondering this the other day. the next big mutations may not be more infectious because they can survive outside the body longer, but because they get around existing immunity or theres a longer asympomatic-but-still-transmissible phase. theres a lot of different paths this could take to mass infection.
- tehjoker 5y ago
  Receptor binding affinity can also increase too, or like Alpha did, further suppress interferon production. Lots of ways...
  - T-A 5y ago
    That reminds me of this scary preprint from January: https://www.biorxiv.org/content/10.1101/2021.01.06.425392v3 https://www.biorxiv.org/content/10.1101/2021.01.06.425392v3 "in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity" :/
    - tehjoker 5y ago
      I saw that yesterday and didn't post it because it was too scary lol
f38zf5vdt 5y ago
Measles is estimated to be about 300% more infectious than the delta variant, so if it surpassed measles it would be the most contagious viral disease known to man. It's already pretty close to what is assumed to be the "ceiling".
- tehjoker 5y ago
  300% is still a lot of room to grow. Delta is only about twice as bad as the wild type strain.
  - marricks 5y ago
    I'm not sure "only twice as bad" paints an accurate picture. - Herd immunity is much harder. Calculated as 1 - 1/r0 where r0 is defined in relation to transmissibility. So if r0 = 3 that's ~66% need to be immune to stop the virus. If r0 = 6 that's 83% needed, much higher threshold. - The virus is only getting more deadly. A preprint study found delta has "120% greater risk of hospitalization, 287% greater risk of ICU admission and 137% greater risk of death"[1] Also 225% more transmissible is 3x more unless I'm doing my math wrong?[2] [1] https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Virulence https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Virul... [2] https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Transmissibility https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Trans...
    - nradov 5y ago
      Right which is why achieving any meaningful level of herd immunity is now effectively impossible. Thus we're all likely to get infected eventually. https://www.businessinsider.com/delta-variant-made-herd-immunity-not-possible-astrazeneca-developer-2021-8 https://www.businessinsider.com/delta-variant-made-herd-immu... Fortunately the vaccines are very effective at preventing death for all variants.
      - Retric 5y ago
        Herd immunity happens long before we are all infected. Less than 40% of the US population is completely unvaccinated, which means we can open up more without overwhelming hospitals. That does put the unvaccinated at increased risks, but the general public is seemingly unwilling to continue lockdowns to protect people choosing not to be vaccinated. If ~85% is needed for herd immunity then we could be rapidly approaching that point. Though specific locations would likely have outbreaks even if it was less of a concern nationally.
bredren 5y ago
This is getting at “saying the quiet part out loud.” For a variety of reasons media and influential organizations have avoided considering the upper bound on virility and mortality (? Not sure the right term) of covid. But to think delta is it would be some kind of miracle. It would mean we are going through the worst of it, and that after we handle delta globally, people can worry about other things. But it doesn’t stand to reason that we are done here with covid. There are too many hotspots and I believe delta is older than most of the big ones right now. How likely is a nasty new variant not pop out of Iran or India, or Texas? What about variants created by non-human beings like rats? [1] Are we going to skate by on those? That would be great! I suspect the public is not ready to fully address the breadth and depth of covid’s impact. I also speculate that the “booster” shot suddenly being prescribed is intended to help ward off future variants as much or more so than delta alone. [1] https://www.nbcnewyork.com/news/local/researchers-find-covid-mutations-in-nyc-sewage-pointing-to-possible-dog-rat-infections/3185871/ https://www.nbcnewyork.com/news/local/researchers-find-covid...
- nradov 5y ago
  SARS-CoV-2 has multiple animal reservoirs, and that's one reason why it will be impossible to eradicate. But generally variants that evolve in animals will select for fitness in those different species. So those will probably have less impact on humans. This is one piece of circumstantial evidence why some virologists suspect the virus was produced in a lab doing gain of function research using transgenic mice with human like respiratory systems. When the virus first appeared in Wuhan it was already really good at infecting humans. That would be unlikely if it had evolved in wild bats or pangolins and then jumped straight to humans. But we don't know for sure, maybe it was just natural bad luck with no lab involved. https://pubmed.ncbi.nlm.nih.gov/25589660/ https://pubmed.ncbi.nlm.nih.gov/25589660/
  - DSMan195276 5y ago
    > When the virus first appeared in Wuhan it was already really good at infecting humans. That would be unlikely if it had evolved in wild bats or pangolins and then jumped straight to humans. But we don't know for sure. Just curious about this point - wouldn't this always be the case, since before it was good at infecting humans it would only be in a few if any of them? IE. My thinking is that even if it had existed for a while before that point, we'd be unlikely to know since it wasn't at that point good at infecting humans and thus not many had it.
johnchristopher 5y ago
> It may already be getting harder for SARS-CoV-2 to make big gains in infectiousness. “There are some fundamental limits to exactly how good a virus can get at transmitting and at some point SARS-CoV-2 will hit that plateau,” says Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center. “I think it’s very hard to say if this is already where we are, or is it still going to happen.” Evolutionary virologist Kristian Andersen of Scripps Research guesses the virus still has space to evolve greater transmissibility. “The known limit in the viral universe is measles, which is about three times more transmissible than what we have now with Delta,” he says. https://www.sciencemag.org/news/2021/08/new-sars-cov-2-variants-have-changed-pandemic-what-will-virus-do-next https://www.sciencemag.org/news/2021/08/new-sars-cov-2-varia...
tomrod 5y ago
It comes from the same family as SARS and MERS. Worst case, IMHO, would be that level of mortality combined with its current R0 of 6 to 9.
- sfink 5y ago
  Do absolute R0 numbers have meaning without a specified environment? As in, shouldn't there be various values for R0 within a fully vaccinated community, R0 within an age group, R0 relative to the prevalence of active infection in a community, etc.? I'm just wondering what complexity is concealed within an R0 figure. After all, if every infected person really infected 6 other people every 2 weeks or so, it would infect every person on Earth in about a year and a half. Which is probably why R0 is distinguished from R1. Since otherwise R1 would be R0**2, and I highly doubt it is. It could be higher if viral load was a large factor (you have x% chance of picking it up when around a single carrier, but >x% if surrounded by multiple). Far more likely, it would be lower as it burned out tightly-connected groups. Anyway, just thoughts triggered by seeing absolute R0 values.
  - raphlinus 5y ago
    It's best to think of R0 as a summary. For a detailed discussion, see TWiV [792] with epidemiologist Jeff Shaman. First link in this show notes is "A guide to R"[2]. [792]: https://www.microbe.tv/twiv/twiv-792/ https://www.microbe.tv/twiv/twiv-792/ [2]: https://www.nature.com/articles/d41586-020-02009-w https://www.nature.com/articles/d41586-020-02009-w
  - tomrod 5y ago
    Consider R0 a rough estimate of how many people each cade infects. It's an imperfect instrument but helps communicate the idea clearly that answers "how infectious is this virus?"
criticaltinker 5y ago
Here is a fantastic resource from the UK government that answers your question in great detail [1]. > As eradication of SARS-CoV-2 will be unlikely, we have high confidence in stating that there will always be variants. > We describe hypothetical scenarios by which SARS-CoV-2 could further evolve and acquire, through mutation, phenotypes of concern, which we assess according to possibility. > Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date. For example, with similar morbidity/mortality to other zoonotic coronaviruses such as SARS-CoV (~10% case fatality) or MERS-CoV (~35% case fatality). [...] Likelihood: Realistic possibility. Impact: High. > Scenario Two: A variant that evades current vaccines. [...] Likelihood: Realistic possibility. Impact: High. > Scenario Three: Emergence of a drug resistant variant after anti-viral strategies. [...] Likelihood: Likely - unless the drugs are used correctly. Impact: medium. > Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence. [...] Likelihood: Unlikely in the short term, realistic possibility in the long term. And here is one very relevant quote: > There is no historic precedent for the mass administration of antiviral medication in the community as prophylaxis, apart from the use of anti influenza Neuraminidase Inhibitors, which were used to a limited extent in this way in the early phases of Influenza Pandemic of 2009 in the UK. The safety and efficacy profile must be extremely well established for a mass administration strategy to work and poor compliance will likely rapidly lead to the selection of drug resistant variants, rendering such a strategy short lived. [1] Can we predict the limits of SARS-CoV-2 variants and their phenotypic consequences? https://www.gov.uk/government/publications/long-term-evolution-of-sars-cov-2-26-july-2021 https://www.gov.uk/government/publications/long-term-evoluti... https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1007566/S1335_Long_term_evolution_of_SARS-CoV-2.pdf https://assets.publishing.service.gov.uk/government/uploads/...
- tehjoker 5y ago
  Thank you!
  - bredren 5y ago
    Indeed, thank you for these links and quotes.

softwaredoug 5y ago

There is a “Doug” variant?!? Asking for a friend… EDIT So there is! Ha > And you can imagine, it was quite a mouthful. So, we started to call this D to G mutation ‘Doug’, and then any of the other virus sequences that didn’t have this mutation … we called ‘Douglas’, so it was sort of a bit of a private joke within the lab,” she said. “As more mutations came about, we’d come up with a person’s name for them.” https://www.theguardian.com/world/2021/feb/17/nicknames-emerge-for-growing-list-of-covid-variants https://www.theguardian.com/world/2021/feb/17/nicknames-emer...

deleted 5y ago
[deleted]
NullPrefix 5y ago
>One of the first mutations to go global is known as D614G, or Doug for short
- hahamrfunnyguy 5y ago
  Also the Nelly and Eeek variants. They would have called it Erik, but they worked closely with someone named Erik already.
deleted 5y ago
[deleted]

toiletaccount 5y ago

i was wondering this the other day. the next big mutations may not be more infectious because they can survive outside the body longer, but because they get around existing immunity or theres a longer asympomatic-but-still-transmissible phase. theres a lot of different paths this could take to mass infection.

tehjoker 5y ago
Receptor binding affinity can also increase too, or like Alpha did, further suppress interferon production. Lots of ways...
- T-A 5y ago
  That reminds me of this scary preprint from January: https://www.biorxiv.org/content/10.1101/2021.01.06.425392v3 https://www.biorxiv.org/content/10.1101/2021.01.06.425392v3 "in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity" :/
  - tehjoker 5y ago
    I saw that yesterday and didn't post it because it was too scary lol

f38zf5vdt 5y ago

Measles is estimated to be about 300% more infectious than the delta variant, so if it surpassed measles it would be the most contagious viral disease known to man. It's already pretty close to what is assumed to be the "ceiling".

tehjoker 5y ago
300% is still a lot of room to grow. Delta is only about twice as bad as the wild type strain.
- marricks 5y ago
  I'm not sure "only twice as bad" paints an accurate picture. - Herd immunity is much harder. Calculated as 1 - 1/r0 where r0 is defined in relation to transmissibility. So if r0 = 3 that's ~66% need to be immune to stop the virus. If r0 = 6 that's 83% needed, much higher threshold. - The virus is only getting more deadly. A preprint study found delta has "120% greater risk of hospitalization, 287% greater risk of ICU admission and 137% greater risk of death"[1] Also 225% more transmissible is 3x more unless I'm doing my math wrong?[2] [1] https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Virulence https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Virul... [2] https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Transmissibility https://en.wikipedia.org/wiki/SARS-CoV-2_Delta_variant#Trans...
  - nradov 5y ago
    Right which is why achieving any meaningful level of herd immunity is now effectively impossible. Thus we're all likely to get infected eventually. https://www.businessinsider.com/delta-variant-made-herd-immunity-not-possible-astrazeneca-developer-2021-8 https://www.businessinsider.com/delta-variant-made-herd-immu... Fortunately the vaccines are very effective at preventing death for all variants.
    - Retric 5y ago
      Herd immunity happens long before we are all infected. Less than 40% of the US population is completely unvaccinated, which means we can open up more without overwhelming hospitals. That does put the unvaccinated at increased risks, but the general public is seemingly unwilling to continue lockdowns to protect people choosing not to be vaccinated. If ~85% is needed for herd immunity then we could be rapidly approaching that point. Though specific locations would likely have outbreaks even if it was less of a concern nationally.

bredren 5y ago

This is getting at “saying the quiet part out loud.” For a variety of reasons media and influential organizations have avoided considering the upper bound on virility and mortality (? Not sure the right term) of covid. But to think delta is it would be some kind of miracle. It would mean we are going through the worst of it, and that after we handle delta globally, people can worry about other things. But it doesn’t stand to reason that we are done here with covid. There are too many hotspots and I believe delta is older than most of the big ones right now. How likely is a nasty new variant not pop out of Iran or India, or Texas? What about variants created by non-human beings like rats? [1] Are we going to skate by on those? That would be great! I suspect the public is not ready to fully address the breadth and depth of covid’s impact. I also speculate that the “booster” shot suddenly being prescribed is intended to help ward off future variants as much or more so than delta alone. [1] https://www.nbcnewyork.com/news/local/researchers-find-covid-mutations-in-nyc-sewage-pointing-to-possible-dog-rat-infections/3185871/ https://www.nbcnewyork.com/news/local/researchers-find-covid...

nradov 5y ago
SARS-CoV-2 has multiple animal reservoirs, and that's one reason why it will be impossible to eradicate. But generally variants that evolve in animals will select for fitness in those different species. So those will probably have less impact on humans. This is one piece of circumstantial evidence why some virologists suspect the virus was produced in a lab doing gain of function research using transgenic mice with human like respiratory systems. When the virus first appeared in Wuhan it was already really good at infecting humans. That would be unlikely if it had evolved in wild bats or pangolins and then jumped straight to humans. But we don't know for sure, maybe it was just natural bad luck with no lab involved. https://pubmed.ncbi.nlm.nih.gov/25589660/ https://pubmed.ncbi.nlm.nih.gov/25589660/
- DSMan195276 5y ago
  > When the virus first appeared in Wuhan it was already really good at infecting humans. That would be unlikely if it had evolved in wild bats or pangolins and then jumped straight to humans. But we don't know for sure. Just curious about this point - wouldn't this always be the case, since before it was good at infecting humans it would only be in a few if any of them? IE. My thinking is that even if it had existed for a while before that point, we'd be unlikely to know since it wasn't at that point good at infecting humans and thus not many had it.

johnchristopher 5y ago

> It may already be getting harder for SARS-CoV-2 to make big gains in infectiousness. “There are some fundamental limits to exactly how good a virus can get at transmitting and at some point SARS-CoV-2 will hit that plateau,” says Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center. “I think it’s very hard to say if this is already where we are, or is it still going to happen.” Evolutionary virologist Kristian Andersen of Scripps Research guesses the virus still has space to evolve greater transmissibility. “The known limit in the viral universe is measles, which is about three times more transmissible than what we have now with Delta,” he says. https://www.sciencemag.org/news/2021/08/new-sars-cov-2-variants-have-changed-pandemic-what-will-virus-do-next https://www.sciencemag.org/news/2021/08/new-sars-cov-2-varia...

tomrod 5y ago

It comes from the same family as SARS and MERS. Worst case, IMHO, would be that level of mortality combined with its current R0 of 6 to 9.

sfink 5y ago
Do absolute R0 numbers have meaning without a specified environment? As in, shouldn't there be various values for R0 within a fully vaccinated community, R0 within an age group, R0 relative to the prevalence of active infection in a community, etc.? I'm just wondering what complexity is concealed within an R0 figure. After all, if every infected person really infected 6 other people every 2 weeks or so, it would infect every person on Earth in about a year and a half. Which is probably why R0 is distinguished from R1. Since otherwise R1 would be R0**2, and I highly doubt it is. It could be higher if viral load was a large factor (you have x% chance of picking it up when around a single carrier, but >x% if surrounded by multiple). Far more likely, it would be lower as it burned out tightly-connected groups. Anyway, just thoughts triggered by seeing absolute R0 values.
- raphlinus 5y ago
  It's best to think of R0 as a summary. For a detailed discussion, see TWiV [792] with epidemiologist Jeff Shaman. First link in this show notes is "A guide to R"[2]. [792]: https://www.microbe.tv/twiv/twiv-792/ https://www.microbe.tv/twiv/twiv-792/ [2]: https://www.nature.com/articles/d41586-020-02009-w https://www.nature.com/articles/d41586-020-02009-w
- tomrod 5y ago
  Consider R0 a rough estimate of how many people each cade infects. It's an imperfect instrument but helps communicate the idea clearly that answers "how infectious is this virus?"

criticaltinker 5y ago

Here is a fantastic resource from the UK government that answers your question in great detail [1]. > As eradication of SARS-CoV-2 will be unlikely, we have high confidence in stating that there will always be variants. > We describe hypothetical scenarios by which SARS-CoV-2 could further evolve and acquire, through mutation, phenotypes of concern, which we assess according to possibility. > Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date. For example, with similar morbidity/mortality to other zoonotic coronaviruses such as SARS-CoV (~10% case fatality) or MERS-CoV (~35% case fatality). [...] Likelihood: Realistic possibility. Impact: High. > Scenario Two: A variant that evades current vaccines. [...] Likelihood: Realistic possibility. Impact: High. > Scenario Three: Emergence of a drug resistant variant after anti-viral strategies. [...] Likelihood: Likely - unless the drugs are used correctly. Impact: medium. > Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence. [...] Likelihood: Unlikely in the short term, realistic possibility in the long term. And here is one very relevant quote: > There is no historic precedent for the mass administration of antiviral medication in the community as prophylaxis, apart from the use of anti influenza Neuraminidase Inhibitors, which were used to a limited extent in this way in the early phases of Influenza Pandemic of 2009 in the UK. The safety and efficacy profile must be extremely well established for a mass administration strategy to work and poor compliance will likely rapidly lead to the selection of drug resistant variants, rendering such a strategy short lived. [1] Can we predict the limits of SARS-CoV-2 variants and their phenotypic consequences? https://www.gov.uk/government/publications/long-term-evolution-of-sars-cov-2-26-july-2021 https://www.gov.uk/government/publications/long-term-evoluti... https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1007566/S1335_Long_term_evolution_of_SARS-CoV-2.pdf https://assets.publishing.service.gov.uk/government/uploads/...

tehjoker 5y ago
Thank you!
- bredren 5y ago
  Indeed, thank you for these links and quotes.