20 ms·

SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility

146 points by MKais 6y ago

jlgaddis 6y ago
Off-topic: > ... made available under a CC-BY-ND 4.0 International license. I'm quite pleased to see more and more academic and scientific papers being licensed as such in recent times!
- anticensor 6y ago
  Why ND and not BY-SA?
  - ashleyn 6y ago
    Derivative works from a biology paper can result in disinformation.
    - anticensor 6y ago
      It should still be BY-SA. Ancillary and auxiliary sources are key to scientific criticism.
      - oh_sigh 6y ago
        What form of criticisms are possible with BY-SA that aren't with BY-CC? Criticism would usually come in the form of new papers which merely reference the previous one.
        deleted 6y ago
        [deleted]
        anticensor 6y ago
        Direct editing of offending paper while adding you to authors. (that derivative work should still be referenced to the same DOI et al.)
  - murphyslab 6y ago
    Use of the CC BY ND license is meant to reflect the common practice of sharing academic papers, which was often done informally, as opposed to a paywall. I can send you a copy of my paper; you can pass on copies to colleagues. But in doing so, you wouldn't edit it. That's not a freedom which is necessary for sharing a paper. The paper is a complete product. Moreover it would be a breech of the integrity of the work to edit it. If a correction is required, there is a proper route for that: erratum or corrigendum, published in the original venue. The first catch of "ND" is that this excludes translation, but that really is not considered to be an issue for two reasons: (1) Scientists are generally expected to be proficient in English and able to read a paper in English - as once was the case for chemists being proficient in German. (2) For popularization and dissemination, media outlets are able to write summaries in other languages. The second catch is that we really should have some kind of formal secondary license for images and figures within a paper (ideally CC-BY), to allow them to be used separately, since reuse of these should be as frictionless as possible. As a former grad student, it was a pain when writing the review section in a thesis! Though many journals & academic publishers achieve this through having blanket forms that an academic can download for permission to re-use images; for others one needs to consult with the authors of a paper which can be tricky. And to counter your other comment: > Ancillary and auxiliary sources are key to scientific criticism. The licensing does nothing whatsoever to prevent scientific criticism. The Berne Convention [1] explicitly allows for quoting from other works, even if not licensed whatsoever: > 10.1 It shall be permissible to make quotations from a work which has already been lawfully made available to the public, provided that their making is compatible with fair practice, and their extent does not exceed that justified by the purpose, including quotations from newspaper articles and periodicals in the form of press summaries. Criticism is never a matter of editing someone else's work; it's commenting about the work. You don't need a license to do that. If one has free access to the full text, which CC BY ND provides, then one has everything necessary to understand the criticism. [1] https://wipolex.wipo.int/en/text/283698 https://wipolex.wipo.int/en/text/283698
    - anticensor 6y ago
      I thought fair use was automatically disclaimed when you receive an explicit licence, reducing the baseline to taint=derivation (which is the main reason open source developers avoid looking at closed source software that performs similar function), unless your licence specifies otherwise. And some countries are not signatory to Berne convention, instead to Buenos Aires convention, which is much stricter and does not have a common fair use stipulation. > Criticism is never a matter of editing someone else's work; it's commenting about the work. It is. Every consumption is an edit. You edit to remove everything not related to your criticism and add your opinion.
omginternets 6y ago
One thing isn't clear to me, for lack of background knowledge: have there been several strains since the beginning of the pandemic, or is this study based on evidence of mutation in the wild? It sounds like the former, but since it wasn't explicitly addressed in the abstract, I thought I'd ask.
- melville 6y ago
  Doesn't the first phrase of the abstract state that the latter is the case: "During the evolution in humans ...."?
- remote_phone 6y ago
  There have been variants but none so dissimilar that they are considered a new strain. The terminology is very precise here but the media have been mixing it up, causing confusion. https://medium.com/swlh/variants-lineages-and-strains-of-coronavirus-7a71a0e699d7 https://medium.com/swlh/variants-lineages-and-strains-of-cor...
  - ismail 6y ago
    Thanks for this link. From the article she states: “Mutations that alter any of the following can lead to a new strain: pathogenicity virulence immunogenicity.” And “ Another way that the term strain is used is when a particular variant of the virus (the virus with a specific set of mutations) ” This sounds like the mutation referenced in the paper could be considered a “new strain” given the above? “ Until there is clear evidence supporting functional or immunogenic differences among the variants, it is appropriate to consider all of these lineages of the same virus.”
- Raidion 6y ago
  This is not my area of expertise, but I think I can help answer the question. Everything mutates a lot, so there is a lot of genetic variability. These are usually pretty minor, but really help with tracing, as you can correlate "family trees" of mutations. The big one early in the pandemic was you could see the difference in the genome between the China/West Coast USA and Europe/East Coast USA infections. I'm not sure of the strict scholastic definition of a strain, but I think they're derived from branches of that family tree. Most of those branches behave pretty similarly as they have mutations that aren't really impactful, but some of those behave differently, and those are the "strains/variants" we're talking about. On an interesting note on how genetics are used to target therapies, what researchers can do is look at all the different mutations and they can find parts of the genome that change a lot, and parts that change very little. The parts that change very little are often critical for the function of the virus. Mutations to those still happen, but because of the critical nature of the part that mutated, the virus isn't able to reproduce as effectively and so doesn't show up as often. Researchers can use those as targets for treatments, as disrupting those can impact the effectiveness of the virus. If I got any of that wrong (or I'm using the wrong vocabulary), I'd love to hear from someone with an actual background in this stuff.
cephaslr 6y ago
Something I have been wondering about, wouldn't a virus naturally evolve to be less deadly and more contagious over time? I.e. virus's tend to achieve a steady state like the cold and flu in the long run. If you are too deadly it hinders spread so I would expect Covid to get less deadly and more contagious over time, which kind of fits the data?
- hamaluik 6y ago
  Generally, yes. But also we’re a bit unlucky that it isn’t very deadly: SARS was way deadlier To start with but as a result spread several orders of magnitude less (both naturally and because humans had a stronger reaction to “shut it down at all costs“). The H1N1 virus from the 1918 pandemic grew less deadly over time, and essentially evolved into a seasonal flu that is still affecting people around the world today. Personally, I expect COVID19 to go the same way.
  - packetlost 6y ago
    The h1n1 is a bit of a strange case though because it jumps species boundary very often and mutates very quickly. COVID-19 appears to evolve much, much slower. Based on my limited understanding of virology, I think this means it's unlikely to become a seasonal problem unless the general populations immune system does not retain immunity to the same strain for a significant period of time.
    - djsumdog 6y ago
      We already know CoV2 rarely causes any symptoms in children. I wonder if there was a time in prehistory where common Rhinoviruses and Coronaviruses wiped out larger populations of elderly. Even if our immune system memory doesn't last very long for these types of viruses, wouldn't young people getting exposed to it now likely reduce its impact long term? It also seems like >95% of people who die from this are over 55 years old. When you get into your 70s~80s, aren't common colds one of the things that result in natural deaths, due to an aging immune system allowing pneumonia to set in where it wouldn't in a younger person?
major505 6y ago
Is a shit thing when a virus got a firmware update in 2020, but not my android phone.
- herodotus 6y ago
  Thanks for the laugh. So needed for this crappy year of hell.
  - m101010 6y ago
    for me it helps to know that this pandemic (including all the lockdowns) would be way worse without all of the digital innovations from the last 10-20 years.
    - Loughla 6y ago
      Honestly, imagine how much worse the world would be (at least in 1st world countries) if we did not have the tech tools available to us. I legitimately do not know what would have happened, but I feel like it would be much more violent and much deeper despair. For all the headaches constant connection has brought, it has also alleviated an unknown number of them as well.
      - a_imho 6y ago
        I'm getting old. Last 20 years maybe, but I can't name a technology advancement that happened in the last 10 years that I would really miss. To me it seems like most technology is now done for the sake of doing it and solutions are looking for problems. Not to mention all the dystopian surveillance we have now. Rose tinted glasses and all that, the start of the millennium was a much happier time period imo.
        alexktz 6y ago
        Have you used a 10 year old phone lately?
baxtr 6y ago
AFAIK this is the variant that formed in northern Italy back in February and is since ruling the world
- libertine 6y ago
  That's why it's not good to have a new virus going around in among us. That's why the whole response should have been - isolate and eliminate the virus. Not, "hey, lets live with this guy until we can make a vaccine that works"...
  - ulfw 6y ago
    The Asian vs. the Euro-American model.
    - libertine 6y ago
      But that's the odd thing, isn't the procedure of the "asian model", which was used in NZ, on the "text manuals" of dealing with viruses? Specially after a first wave, we know how the virus behaved, how we behaved with the virus, and what cost it had (not only deaths, but the stress on health systems that gradually lose the ability to cope with infections, and evolve to the colapse of general health services, other than covid-19). Basically, the virus infection fatality rate might not be as high as we thought, but it ends up collapsing health services, so more deaths direct and indirect are accounted for. They were hammering us to live in the new normal, what kind of message is that for a population living in a pandemic?
    - adventured 6y ago
      Where has the virus been eliminated successfully in Asia by that model? New Zealand may be the only real success story, and it's a very tiny population island. India has seen a likely tens of millions of cases. Bangladesh, Indonesia and the Philippines have all seen bad outbreaks now. Nepal is currently being buried in cases. Case numbers are booming in Malaysia at present. Japan has never managed to eliminate it and continues to see persistent cases, despite their relative success. The same with Singapore. Did you mean to say that a few countries in Asia have managed to limit the virus, while the rest of Asia has entirely failed at doing so?
yomly 6y ago
Could someone with some background ELI5 this for those of us who lack expertise?
dehrmann 6y ago
This is what worries me a little about widespread mask use. It will start selecting strains that spread more through aerosols, touch, or are easier to contract.
- otherme123 6y ago
  Masks imposes such a hurdle on spreading that, even in the (incredible improbable) event that some virus strain gained a 20% more effectivity of transmission through masks, the mask itself would be restricting 99.99% of the spreading. Overall it means that in place of 1 transmission each 10,000 contacts with mask you'll have maybe 2-3 transmissions of this super-virus even with masks, but 5,000 transmissions without masks.
topbanana 6y ago
https://www.biorxiv.org/content/biorxiv/early/2020/10/27/2020.10.27.357558.full.pdf https://www.biorxiv.org/content/biorxiv/early/2020/10/27/202...
rr444rrr 6y ago
People with a weak immune system should die and that's OK. It's called NATURAL SELECTION.

146 points by MKais 6y ago

Off-topic: > ... made available under a CC-BY-ND 4.0 International license. I'm quite pleased to see more and more academic and scientific papers being licensed as such in recent times!

anticensor 6y ago
Why ND and not BY-SA?
- ashleyn 6y ago
  Derivative works from a biology paper can result in disinformation.
  - anticensor 6y ago
    It should still be BY-SA. Ancillary and auxiliary sources are key to scientific criticism.
    - oh_sigh 6y ago
      What form of criticisms are possible with BY-SA that aren't with BY-CC? Criticism would usually come in the form of new papers which merely reference the previous one.
      - deleted 6y ago
        [deleted]
      - anticensor 6y ago
        Direct editing of offending paper while adding you to authors. (that derivative work should still be referenced to the same DOI et al.)
- murphyslab 6y ago
  Use of the CC BY ND license is meant to reflect the common practice of sharing academic papers, which was often done informally, as opposed to a paywall. I can send you a copy of my paper; you can pass on copies to colleagues. But in doing so, you wouldn't edit it. That's not a freedom which is necessary for sharing a paper. The paper is a complete product. Moreover it would be a breech of the integrity of the work to edit it. If a correction is required, there is a proper route for that: erratum or corrigendum, published in the original venue. The first catch of "ND" is that this excludes translation, but that really is not considered to be an issue for two reasons: (1) Scientists are generally expected to be proficient in English and able to read a paper in English - as once was the case for chemists being proficient in German. (2) For popularization and dissemination, media outlets are able to write summaries in other languages. The second catch is that we really should have some kind of formal secondary license for images and figures within a paper (ideally CC-BY), to allow them to be used separately, since reuse of these should be as frictionless as possible. As a former grad student, it was a pain when writing the review section in a thesis! Though many journals & academic publishers achieve this through having blanket forms that an academic can download for permission to re-use images; for others one needs to consult with the authors of a paper which can be tricky. And to counter your other comment: > Ancillary and auxiliary sources are key to scientific criticism. The licensing does nothing whatsoever to prevent scientific criticism. The Berne Convention [1] explicitly allows for quoting from other works, even if not licensed whatsoever: > 10.1 It shall be permissible to make quotations from a work which has already been lawfully made available to the public, provided that their making is compatible with fair practice, and their extent does not exceed that justified by the purpose, including quotations from newspaper articles and periodicals in the form of press summaries. Criticism is never a matter of editing someone else's work; it's commenting about the work. You don't need a license to do that. If one has free access to the full text, which CC BY ND provides, then one has everything necessary to understand the criticism. [1] https://wipolex.wipo.int/en/text/283698 https://wipolex.wipo.int/en/text/283698
  - anticensor 6y ago
    I thought fair use was automatically disclaimed when you receive an explicit licence, reducing the baseline to taint=derivation (which is the main reason open source developers avoid looking at closed source software that performs similar function), unless your licence specifies otherwise. And some countries are not signatory to Berne convention, instead to Buenos Aires convention, which is much stricter and does not have a common fair use stipulation. > Criticism is never a matter of editing someone else's work; it's commenting about the work. It is. Every consumption is an edit. You edit to remove everything not related to your criticism and add your opinion.

omginternets 6y ago

One thing isn't clear to me, for lack of background knowledge: have there been several strains since the beginning of the pandemic, or is this study based on evidence of mutation in the wild? It sounds like the former, but since it wasn't explicitly addressed in the abstract, I thought I'd ask.

melville 6y ago
Doesn't the first phrase of the abstract state that the latter is the case: "During the evolution in humans ...."?
remote_phone 6y ago
There have been variants but none so dissimilar that they are considered a new strain. The terminology is very precise here but the media have been mixing it up, causing confusion. https://medium.com/swlh/variants-lineages-and-strains-of-coronavirus-7a71a0e699d7 https://medium.com/swlh/variants-lineages-and-strains-of-cor...
- ismail 6y ago
  Thanks for this link. From the article she states: “Mutations that alter any of the following can lead to a new strain: pathogenicity virulence immunogenicity.” And “ Another way that the term strain is used is when a particular variant of the virus (the virus with a specific set of mutations) ” This sounds like the mutation referenced in the paper could be considered a “new strain” given the above? “ Until there is clear evidence supporting functional or immunogenic differences among the variants, it is appropriate to consider all of these lineages of the same virus.”
Raidion 6y ago
This is not my area of expertise, but I think I can help answer the question. Everything mutates a lot, so there is a lot of genetic variability. These are usually pretty minor, but really help with tracing, as you can correlate "family trees" of mutations. The big one early in the pandemic was you could see the difference in the genome between the China/West Coast USA and Europe/East Coast USA infections. I'm not sure of the strict scholastic definition of a strain, but I think they're derived from branches of that family tree. Most of those branches behave pretty similarly as they have mutations that aren't really impactful, but some of those behave differently, and those are the "strains/variants" we're talking about. On an interesting note on how genetics are used to target therapies, what researchers can do is look at all the different mutations and they can find parts of the genome that change a lot, and parts that change very little. The parts that change very little are often critical for the function of the virus. Mutations to those still happen, but because of the critical nature of the part that mutated, the virus isn't able to reproduce as effectively and so doesn't show up as often. Researchers can use those as targets for treatments, as disrupting those can impact the effectiveness of the virus. If I got any of that wrong (or I'm using the wrong vocabulary), I'd love to hear from someone with an actual background in this stuff.

cephaslr 6y ago

Something I have been wondering about, wouldn't a virus naturally evolve to be less deadly and more contagious over time? I.e. virus's tend to achieve a steady state like the cold and flu in the long run. If you are too deadly it hinders spread so I would expect Covid to get less deadly and more contagious over time, which kind of fits the data?

hamaluik 6y ago
Generally, yes. But also we’re a bit unlucky that it isn’t very deadly: SARS was way deadlier To start with but as a result spread several orders of magnitude less (both naturally and because humans had a stronger reaction to “shut it down at all costs“). The H1N1 virus from the 1918 pandemic grew less deadly over time, and essentially evolved into a seasonal flu that is still affecting people around the world today. Personally, I expect COVID19 to go the same way.
- packetlost 6y ago
  The h1n1 is a bit of a strange case though because it jumps species boundary very often and mutates very quickly. COVID-19 appears to evolve much, much slower. Based on my limited understanding of virology, I think this means it's unlikely to become a seasonal problem unless the general populations immune system does not retain immunity to the same strain for a significant period of time.
  - djsumdog 6y ago
    We already know CoV2 rarely causes any symptoms in children. I wonder if there was a time in prehistory where common Rhinoviruses and Coronaviruses wiped out larger populations of elderly. Even if our immune system memory doesn't last very long for these types of viruses, wouldn't young people getting exposed to it now likely reduce its impact long term? It also seems like >95% of people who die from this are over 55 years old. When you get into your 70s~80s, aren't common colds one of the things that result in natural deaths, due to an aging immune system allowing pneumonia to set in where it wouldn't in a younger person?

major505 6y ago

Is a shit thing when a virus got a firmware update in 2020, but not my android phone.

herodotus 6y ago
Thanks for the laugh. So needed for this crappy year of hell.
- m101010 6y ago
  for me it helps to know that this pandemic (including all the lockdowns) would be way worse without all of the digital innovations from the last 10-20 years.
  - Loughla 6y ago
    Honestly, imagine how much worse the world would be (at least in 1st world countries) if we did not have the tech tools available to us. I legitimately do not know what would have happened, but I feel like it would be much more violent and much deeper despair. For all the headaches constant connection has brought, it has also alleviated an unknown number of them as well.
    - a_imho 6y ago
      I'm getting old. Last 20 years maybe, but I can't name a technology advancement that happened in the last 10 years that I would really miss. To me it seems like most technology is now done for the sake of doing it and solutions are looking for problems. Not to mention all the dystopian surveillance we have now. Rose tinted glasses and all that, the start of the millennium was a much happier time period imo.
      - alexktz 6y ago
        Have you used a 10 year old phone lately?

baxtr 6y ago

AFAIK this is the variant that formed in northern Italy back in February and is since ruling the world

libertine 6y ago
That's why it's not good to have a new virus going around in among us. That's why the whole response should have been - isolate and eliminate the virus. Not, "hey, lets live with this guy until we can make a vaccine that works"...
- ulfw 6y ago
  The Asian vs. the Euro-American model.
  - libertine 6y ago
    But that's the odd thing, isn't the procedure of the "asian model", which was used in NZ, on the "text manuals" of dealing with viruses? Specially after a first wave, we know how the virus behaved, how we behaved with the virus, and what cost it had (not only deaths, but the stress on health systems that gradually lose the ability to cope with infections, and evolve to the colapse of general health services, other than covid-19). Basically, the virus infection fatality rate might not be as high as we thought, but it ends up collapsing health services, so more deaths direct and indirect are accounted for. They were hammering us to live in the new normal, what kind of message is that for a population living in a pandemic?
  - adventured 6y ago
    Where has the virus been eliminated successfully in Asia by that model? New Zealand may be the only real success story, and it's a very tiny population island. India has seen a likely tens of millions of cases. Bangladesh, Indonesia and the Philippines have all seen bad outbreaks now. Nepal is currently being buried in cases. Case numbers are booming in Malaysia at present. Japan has never managed to eliminate it and continues to see persistent cases, despite their relative success. The same with Singapore. Did you mean to say that a few countries in Asia have managed to limit the virus, while the rest of Asia has entirely failed at doing so?

yomly 6y ago

Could someone with some background ELI5 this for those of us who lack expertise?

dehrmann 6y ago

This is what worries me a little about widespread mask use. It will start selecting strains that spread more through aerosols, touch, or are easier to contract.

otherme123 6y ago
Masks imposes such a hurdle on spreading that, even in the (incredible improbable) event that some virus strain gained a 20% more effectivity of transmission through masks, the mask itself would be restricting 99.99% of the spreading. Overall it means that in place of 1 transmission each 10,000 contacts with mask you'll have maybe 2-3 transmissions of this super-virus even with masks, but 5,000 transmissions without masks.

topbanana 6y ago

https://www.biorxiv.org/content/biorxiv/early/2020/10/27/2020.10.27.357558.full.pdf https://www.biorxiv.org/content/biorxiv/early/2020/10/27/202...

rr444rrr 6y ago

People with a weak immune system should die and that's OK. It's called NATURAL SELECTION.