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Welcome to the Virosphere

114 points by vo2maxer 7y ago

romanovcode 7y ago
Why link paywalled article?
- drivers99 7y ago
  Why don’t you just buy a subscription?
  - deleted 7y ago
    [deleted]
  - Sembiance 7y ago
    All coronavirus articles should be FREE and accessible without registration. Any company doing otherwise is socially irresponsible.
    - ryan_j_naughton 7y ago
      Firstly, this isn't about SARS-COV-2. It is about the more broad concept of viral classification. Secondly, journal articles, yes, I agree. And a lot of government funding should be pouring into research to be published and that needs to be available to help us fight this. Journalism articles though are more tricky. Because they need to pay their employees, the journalists, and cover their costs. Given that 90% is all news now (my guess) is about covid-19, then there would be significantly less revenue for journalism if it said it couldn't paywall articles covid-19 articles. Additionally, advertising revenue is likely to collapse as a second order effect of the recession this crisis is bringing. Finally, there is a lot of competition for news, so any major news story has multiple free articles about it that will be accessible to all (with ads of course). The highest quality journalism is currently coming from two places: paywalled websites and NPR. NPR is free and fulfills a comparable market position as BBC. That is your "public option". But not allowing paywalls would kill the quality reporting of the nytimes and Washington Post and turn them into CNN / Fox / MSNBC.
merricksb 7y ago
http://archive.is/VbTDd http://archive.is/VbTDd
dsign 7y ago
I think that "only 250 virus infect humans" means something like "so far, we only know of 250 viruses in record that cause notable diseases". In an ideal world, we should be sequencing viruses for each single patient, just like we measure blood pressure.
- alexpotato 7y ago
  Along these lines, I wonder if we will eventually see charts like this for ALL human viruses with a person by person trace: https://nextstrain.org/ncov https://nextstrain.org/ncov
  - sjg007 7y ago
    Yes we will
    - Ericson2314 7y ago
      Why so confident? We have the technical skills, but this also takes institutional cooperation we suck at. We don't even have a standard format for conventional medical records in the US!
      - sjg007 7y ago
        I expect legislation that will require CDC and DHHS to establish surveillance programs. We will be sequencing. This will be academic labs and clinic labs most likely. There might be a national sequencing center established. If we work together with China we might leverage their massive sequencing capacity.
  - leoedin 7y ago
    That chart is fascinating - especially the extent of which some countries apparently have virus strains from every branch, while others have 1 or 2 distinct lineages (Washington State being the biggest one). That does imply that the UK and Netherlands have seen the virus introduced from many sources, which suggests much more widespread transmission than eg New Zealand, which appears to have one lineage. However, there's probably a huge sampling bias present. Hopefully we can keep doing this sort of genetic lineage testing at greater rates - it's incredibly informative on how it spreads.
ppod 7y ago
Will the media ever understand the difference between "we underestimate tail risks all the time" and "we have been underestimating this specific tail risk"?
- nisa 7y ago
  That something like this would happen was clear for at least the last ten years. It was only not clear when it would happen.
  - cactus2093 7y ago
    Why 10? Why not the last 50 years, or last 100?
aasasd 7y ago
It generally seems like evolution is better described by continuums, not discrete entities: if one gene is changed among thousands, is the result worthy of a new name? Just like with languages vs dialects—those are the same thing, but on different scale. Edit: to clarify, I'm aware of the criterion of sexual incompatibility, and that genes don't usually work one-by-one, but still—slapping an arbitrary Latin-ish name on each of the millions of, say, fly species seems of dubious use, at least to an outsider.
- blauditore 7y ago
  First, it's important to distinguish between genotype and phenotype. Most genetic mutations don't cause any change in behavior or appearance, so the two individuals are phenotypically equal. With sexual reproduction, individuals can differ genetically but still be compatible, so there is some notion of a pool with a clear boundary. For viruses, this is of course a bit trickier because they "reproduce asexually"[0] and quite rapidly, so mutations happen at a high rate. But one useful property to distinguish them is which receptors (and thus which cells) they bind to, generally affecting what symptoms and diseases they cause. [0]: Viruses are not considered living things, so the concept of reproduction is already quite a stretch.
  - littlestymaar 7y ago
    > so there is some notion of a pool with a clear boundary. That's a model that kind of works most of the times, but not always: the most known example are Bisons and Cows which can breed together and the offsprings are fertile : https://en.m.wikipedia.org/wiki/Beefalo https://en.m.wikipedia.org/wiki/Beefalo In fact, most of today's bisons have cows' genes in their genome.
  - dragontamer 7y ago
    > With sexual reproduction, individuals can differ genetically but still be compatible, so there is some notion of a pool with a clear boundary. The boundary isn't very clear. https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species A can breed with B, B can breed with C, C can breed with D, and D can breed with A. But A cannot breed with C. Are A and C part of the same species, or not? These "ring species" occur around geographic rings, such as the Arctic Circle, so each population remains genetically compatible with its neighbors... but not "across the ring". https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ring_species_seagull.svg/800px-Ring_species_seagull.svg.png https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ri...
globular-toast 7y ago
I studied viruses for a job a few years ago. I looked at RNA viruses mostly and specifically influenza. The way they work is truly astonishing but you quickly realise it's an unfortunate inevitability given the way our genetics works. One interesting thing I remember is that virtually every human over a year old or so is "infected" with at least a handful of viruses for life. The scare quotes are because we really don't know what effect these viruses have on us. They could be beneficial for all we know. To add further complexity consider that bacteria get infected by viruses (called bacteriophages). All those bacteria inside you are in turn "infected" by viruses. Phages are so numerous that a drop of seawater contains about ten million of them. Also they are literally like microscopic genome injection machines. Look up some pictures and electron microscope images.
- packetlost 7y ago
  Could you expand on the statement: > virtually every human over a year old or so is "infected" with at least a handful of viruses for life That sounds like a very interesting concept, and it's one that I haven't heard of before. If you don't want to write yourself, linking me to some reputable sources would be awesome too.
  - durkie 7y ago
    Not entirely sure what GP is talking about, but just off the top of my head, this is the situation for anyone who's ever had chickenpox: you get chickenpox, the sores appear and then go away, but the virus stays in you. If you become immunocompromised/stressed later on in life it can re-emerge as shingles (decades later even).
  - DoingIsLearning 7y ago
    I simple example of this is chicken pox (Varicella Zoster). A large proportion of adults have had it as kids. The immune system fights it off but virus particles can still 'hide' from it and lay dormant inside pheripheral nerve tissue. A proof of this is 'shingles' in adults. i.e. a virus which probably infected the host +50 years ago and went dormant in their nerves finds the host immune system weak enough to come out again and start replicating.
ajnin 7y ago
How is a virus species defined ? As I understand it a species is a group of organisms that can reproduce viably with each other. But a virus doesn't reproduce like that, they clone themselves by hijacking a cell's machinery, so there is no notion of compatibility between viruses. The article says that Covid-19 is "similar" to SARS so it was put in the same species, but that seems a rather soft definition. Especially if there are trillions of different viruses like the article says, some objective criterion is needed. Not to mention viruses mutate all the time, at what point does it become a new species?
- nvrspyx 7y ago
  The International Committee on Taxonomy of Viruses (ICTV) is responsible for classifying viruses and they use a bunch of different criteria, such as chemical characteristics, structure (e.g. look at Covid-19 vs a bacteriophage), type of nucleic acid, mode of replication, host organisms, and the types of diseases they cause. They also group them based on common ancestors. In other words, it becomes a new species when there's a change to the phenotypic traits above.
- dekhn 7y ago
  Many human concepts only approximate the underlying physical reality, and the concept of "species" is a great example of that, especially when applied to a population of viruses. It's unclear whether having a truly accurate concept of species is even an achievable or desirable goal.
- Ericson2314 7y ago
  Yeah species is exta. hard for asexually reproducing species. Sometimes two different viruses infect the same cell and we get a hybrid. Doing that in a lab and looking at the offspring vitality rate would be interesting, and mathematically coherent.
neonate 7y ago
https://archive.md/V7wvl https://archive.md/V7wvl

114 points by vo2maxer 7y ago

romanovcode 7y ago

Why link paywalled article?

drivers99 7y ago
Why don’t you just buy a subscription?
- deleted 7y ago
  [deleted]
- Sembiance 7y ago
  All coronavirus articles should be FREE and accessible without registration. Any company doing otherwise is socially irresponsible.
  - ryan_j_naughton 7y ago
    Firstly, this isn't about SARS-COV-2. It is about the more broad concept of viral classification. Secondly, journal articles, yes, I agree. And a lot of government funding should be pouring into research to be published and that needs to be available to help us fight this. Journalism articles though are more tricky. Because they need to pay their employees, the journalists, and cover their costs. Given that 90% is all news now (my guess) is about covid-19, then there would be significantly less revenue for journalism if it said it couldn't paywall articles covid-19 articles. Additionally, advertising revenue is likely to collapse as a second order effect of the recession this crisis is bringing. Finally, there is a lot of competition for news, so any major news story has multiple free articles about it that will be accessible to all (with ads of course). The highest quality journalism is currently coming from two places: paywalled websites and NPR. NPR is free and fulfills a comparable market position as BBC. That is your "public option". But not allowing paywalls would kill the quality reporting of the nytimes and Washington Post and turn them into CNN / Fox / MSNBC.

merricksb 7y ago

http://archive.is/VbTDd http://archive.is/VbTDd

dsign 7y ago

I think that "only 250 virus infect humans" means something like "so far, we only know of 250 viruses in record that cause notable diseases". In an ideal world, we should be sequencing viruses for each single patient, just like we measure blood pressure.

alexpotato 7y ago
Along these lines, I wonder if we will eventually see charts like this for ALL human viruses with a person by person trace: https://nextstrain.org/ncov https://nextstrain.org/ncov
- sjg007 7y ago
  Yes we will
  - Ericson2314 7y ago
    Why so confident? We have the technical skills, but this also takes institutional cooperation we suck at. We don't even have a standard format for conventional medical records in the US!
    - sjg007 7y ago
      I expect legislation that will require CDC and DHHS to establish surveillance programs. We will be sequencing. This will be academic labs and clinic labs most likely. There might be a national sequencing center established. If we work together with China we might leverage their massive sequencing capacity.
- leoedin 7y ago
  That chart is fascinating - especially the extent of which some countries apparently have virus strains from every branch, while others have 1 or 2 distinct lineages (Washington State being the biggest one). That does imply that the UK and Netherlands have seen the virus introduced from many sources, which suggests much more widespread transmission than eg New Zealand, which appears to have one lineage. However, there's probably a huge sampling bias present. Hopefully we can keep doing this sort of genetic lineage testing at greater rates - it's incredibly informative on how it spreads.

ppod 7y ago

Will the media ever understand the difference between "we underestimate tail risks all the time" and "we have been underestimating this specific tail risk"?

nisa 7y ago
That something like this would happen was clear for at least the last ten years. It was only not clear when it would happen.
- cactus2093 7y ago
  Why 10? Why not the last 50 years, or last 100?

aasasd 7y ago

It generally seems like evolution is better described by continuums, not discrete entities: if one gene is changed among thousands, is the result worthy of a new name? Just like with languages vs dialects—those are the same thing, but on different scale. Edit: to clarify, I'm aware of the criterion of sexual incompatibility, and that genes don't usually work one-by-one, but still—slapping an arbitrary Latin-ish name on each of the millions of, say, fly species seems of dubious use, at least to an outsider.

blauditore 7y ago
First, it's important to distinguish between genotype and phenotype. Most genetic mutations don't cause any change in behavior or appearance, so the two individuals are phenotypically equal. With sexual reproduction, individuals can differ genetically but still be compatible, so there is some notion of a pool with a clear boundary. For viruses, this is of course a bit trickier because they "reproduce asexually"[0] and quite rapidly, so mutations happen at a high rate. But one useful property to distinguish them is which receptors (and thus which cells) they bind to, generally affecting what symptoms and diseases they cause. [0]: Viruses are not considered living things, so the concept of reproduction is already quite a stretch.
- littlestymaar 7y ago
  > so there is some notion of a pool with a clear boundary. That's a model that kind of works most of the times, but not always: the most known example are Bisons and Cows which can breed together and the offsprings are fertile : https://en.m.wikipedia.org/wiki/Beefalo https://en.m.wikipedia.org/wiki/Beefalo In fact, most of today's bisons have cows' genes in their genome.
- dragontamer 7y ago
  > With sexual reproduction, individuals can differ genetically but still be compatible, so there is some notion of a pool with a clear boundary. The boundary isn't very clear. https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species A can breed with B, B can breed with C, C can breed with D, and D can breed with A. But A cannot breed with C. Are A and C part of the same species, or not? These "ring species" occur around geographic rings, such as the Arctic Circle, so each population remains genetically compatible with its neighbors... but not "across the ring". https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ring_species_seagull.svg/800px-Ring_species_seagull.svg.png https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ri...

globular-toast 7y ago

I studied viruses for a job a few years ago. I looked at RNA viruses mostly and specifically influenza. The way they work is truly astonishing but you quickly realise it's an unfortunate inevitability given the way our genetics works. One interesting thing I remember is that virtually every human over a year old or so is "infected" with at least a handful of viruses for life. The scare quotes are because we really don't know what effect these viruses have on us. They could be beneficial for all we know. To add further complexity consider that bacteria get infected by viruses (called bacteriophages). All those bacteria inside you are in turn "infected" by viruses. Phages are so numerous that a drop of seawater contains about ten million of them. Also they are literally like microscopic genome injection machines. Look up some pictures and electron microscope images.

packetlost 7y ago
Could you expand on the statement: > virtually every human over a year old or so is "infected" with at least a handful of viruses for life That sounds like a very interesting concept, and it's one that I haven't heard of before. If you don't want to write yourself, linking me to some reputable sources would be awesome too.
- durkie 7y ago
  Not entirely sure what GP is talking about, but just off the top of my head, this is the situation for anyone who's ever had chickenpox: you get chickenpox, the sores appear and then go away, but the virus stays in you. If you become immunocompromised/stressed later on in life it can re-emerge as shingles (decades later even).
- DoingIsLearning 7y ago
  I simple example of this is chicken pox (Varicella Zoster). A large proportion of adults have had it as kids. The immune system fights it off but virus particles can still 'hide' from it and lay dormant inside pheripheral nerve tissue. A proof of this is 'shingles' in adults. i.e. a virus which probably infected the host +50 years ago and went dormant in their nerves finds the host immune system weak enough to come out again and start replicating.

ajnin 7y ago

How is a virus species defined ? As I understand it a species is a group of organisms that can reproduce viably with each other. But a virus doesn't reproduce like that, they clone themselves by hijacking a cell's machinery, so there is no notion of compatibility between viruses. The article says that Covid-19 is "similar" to SARS so it was put in the same species, but that seems a rather soft definition. Especially if there are trillions of different viruses like the article says, some objective criterion is needed. Not to mention viruses mutate all the time, at what point does it become a new species?

nvrspyx 7y ago
The International Committee on Taxonomy of Viruses (ICTV) is responsible for classifying viruses and they use a bunch of different criteria, such as chemical characteristics, structure (e.g. look at Covid-19 vs a bacteriophage), type of nucleic acid, mode of replication, host organisms, and the types of diseases they cause. They also group them based on common ancestors. In other words, it becomes a new species when there's a change to the phenotypic traits above.
dekhn 7y ago
Many human concepts only approximate the underlying physical reality, and the concept of "species" is a great example of that, especially when applied to a population of viruses. It's unclear whether having a truly accurate concept of species is even an achievable or desirable goal.
Ericson2314 7y ago
Yeah species is exta. hard for asexually reproducing species. Sometimes two different viruses infect the same cell and we get a hybrid. Doing that in a lab and looking at the offspring vitality rate would be interesting, and mathematically coherent.

neonate 7y ago

https://archive.md/V7wvl https://archive.md/V7wvl