20 ms·

Mutated Covid-19 strain confirmed in Japan as case tally hits record high

292 points by Circumnavigate 6y ago

rolph 6y ago
Mutation is simply a loaded term for variation, nothing horrible or shocking is happening. https://news.ycombinator.com/item?id=25538675 https://news.ycombinator.com/item?id=25538675 https://en.wikipedia.org/wiki/Mutation https://en.wikipedia.org/wiki/Mutation
- Volundr 6y ago
  Not horrible or shocking, but concerning. Mutation is expected but the more strains there are the more likely one turns out to be unaffected by the vaccine and we find ourselves back at square one.
  - rolph 6y ago
    there is considerable selective pressure upon the spike protien, very large changes to this protien are not frequently viable, as the virus would need to find a new trophic target or a new host altogether. We are tracking these changes closely and concommitantly can change the sequence of mRNA, responsively, and pre-emptively if desired.
  - UncleOxidant 6y ago
    I would hope that they could add coverage for new variants to the mRNA vaccines without having to go completely back to square one. Do they have to do full 3 phase testing on the flu vaccine every year?
    - rolph 6y ago
      first issue here is the differences in terminology regarding strains, vs variants. strains are signifigantly different from each other, variants are a nuance on the same theme. the virus strain that infects small mammals is separate from the trans specific strain that spilled over to humans. the virus with small changes to the spike sequence altering spike structure or function is a variant. under emergency conditions a 3phase trial is not mandatory , and would likely be a quick deliberation under normal conditions for small adjustments to the sequence, similar to seasonal influenza vaccines.
- yread 6y ago
  Note that here we're not talking about a single mutation but 17 non-synonymous (they change the protein) mutations with 3-4 with known effects on the interactions of the resulting proteins
  - rolph 6y ago
    yes, and this is also not a surpise, this is part of the character of this virus, the sequence is unstable due to size and due to RNA instability.
    - yread 6y ago
      What are you talking about? Sequence is unstable due to size? Coronavirus has proofreading mechanism that corrects most mutations due to errors, the estimate for mutation speed before this variant emerged was 2 mutations per month so this variant has ~10 months of evolution in them but probably evolved much faster for some reason. This is very much a surprise
      - rolph 6y ago
        This is what i am typing about. The error rate is in terms of the number of nucleotides addended to the polymerizing RNA during replication the mutation rate is primarily a result of RNA replication, _not_ time. this means more replication events leads to more "errors", this also means longer sequence has a higher rate of error than a shorter sequence. at a length of ~29k bp the coronavirus sequence is very error prone, so error prone that this is approaching the upper limit of stability. it seems you are mistaking DNA proofreading for an RNA proofreading mechanism, which happens to be negative selection upon nonfunctional mutant/variant. there is no recognized enzymatic [rdRNApol] error correction associated with the coronavirus. "the RNA polymerases of RNA viruses are the kings of errors – these enzymes screw up as often as one time for every 1,000 – 100,000 nucleotides polymerized. This high rate of mutation comes from the lack of proofreading ability in RNA polymerases. These enzymes make mistakes, but they can’t correct them. Therefore the mutations remain in the newly synthesized RNA." [0] none of these error prone generated mutations are surprising, they are to be expected espescially when the virus is given opportunity to replicate at a high cyle rate. this is very much not a surprise, if you are aware of the properties of +ssRNA virus. [0] https://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/ https://www.virology.ws/2009/05/10/the-error-prone-ways-of-r... you may find this interesting[1] however this is primarily post polymerization [RNA readout] modification mechanism not error correction. [1] https://www.pnas.org/content/103/13/5108 https://www.pnas.org/content/103/13/5108
- nabla9 6y ago
  This is incorrect. Mutation and variation are different concepts. Mutations affect the single organisms. Variations happens between individuals, groups or populations of an organism.
  - rolph 6y ago
    you dont seem to understand either concept. mutation is passed from individuals by vertical or horizontal transmission. variation of a gene [alleles] are mutations, mutations are the index variation. mutation is a change in the gene sequence, this is variation, this has created a mutant, also known as a variant. mutation is also a term loaded with connotations due to popular depictions. sexual reproduction is the mechanism of verticall transmission of variation of genetic sequence through a population. genetic drift is also a mechanism of variation of a population. the long and short of it is that mutation and variation, are tied together, they are the same thing. you also seem to have overlooked the abuse of the term mutation, by the original article title, the use of mutation is slicker, than the use of error prone generated variant. the use of the term strain is also erroneous in this context.
RcouF1uZ4gsC 6y ago
There are two important things to temper how worried you should be: 1. Many times there is an inverse relationship between ease of transmission, and severity of symptoms. There is a good chance that this new more transmissible mutant is likely to make people less sick. 2. So far all the available evidence seems to indicate that the vaccines will be effects against this strain as well.
- saberdancer 6y ago
  You shouldn't speculate about 1. especially as this is a virus that is new. It didn't have wave after wave where the "deadly" strains would lose out in evolution. Death rate in London and Kent didn't seem very different to other affected areas which would imply that the virus has same severity of symptoms but it is easier to transmit/contract.
  - irq11 6y ago
    It’s not remotely clear that this strain is easier to transmit. It’s entirely hypothesis and speculation. We have seen strains quickly accelerate because of founder effect several times in 2020, and particular strains dominate in particular regions. The experimental studies that are needed to confirm a claim of evolutionary advantage have not been done, and the observational evidence is weak. Those who would panic about this should be just as circumspect in their their claims as those who would dismiss it.
    - jibbit 6y ago
      I'm guessing you're not living in Kent right now?
    - Jabbles 6y ago
      It is a hypothesis with a small prior, yes. But when considering the data - that the strain has grown faster than all others in the UK at the time - the likelihood becomes significant. Not certain, but not worthy of your casual dismissal. You dismiss their observational evidence as weak, but offer no further analysis. Please do so.
ethbr0 6y ago
> The people who tested positive with the new strain, which is said to spread more easily and was blamed for a recent spike in infections in the U.K., returned to Japan this month — two at Tokyo's Haneda airport and and three at Kansai International Airport in Osaka. This is talking about the SARS-CoV-2 VOC 202012/01 variant [0], aka B.1.1.7., aka carrying the N501Y mutation. No news here, other than confirmed spread to Japan. [0] https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-emerging-variant.html https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-br...
- dnautics 6y ago
  That's interesting that it's an N -> Y mutation, if it's a surface mutation, that AA shift is typically associated with tighter specificity in binding to it's target, e.g. and in antibody studies. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829252/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829252/
  - ethbr0 6y ago
    I think this is a NextStrain link to it. There's probably more information, jumping off from there. https://nextstrain.org/groups/neherlab/ncov/S.N501?animate=2019-12-19,2020-12-23,0,0,30000&c=gt-S_501&f_region=Europe&s=Germany/BY-ChVir-1017/2020 https://nextstrain.org/groups/neherlab/ncov/S.N501?animate=2...
- lbeltrame 6y ago
  N501Y itself has already appeared around the world. By itself, it does look that it is not more transmissible (see Prof. Francois Balloux's Twitter for some explanations). The deletion, again by itself is not new, and also in this case it doesn't seem it has (on its own) increased fitness over the others. N50Y has also a similar antibody neutralization profile as the non-mutated version. Of course, these data refer to the mutations on their own, not together. More on the deletion (on its own, again): while it is supposedly tied to a faster entry into the cells (twice as efficient in experimental assays), it look like it has lower fitness in absence of an ongoing immune response (it would lower in presence - but not disappear - in the immunocompromised patient it was first found into between treatments with convalescent serum).
sigil 6y ago
As discussed on TWiV yesterday, B.1.1.7 isn't a "strain," which has demonstrably different biological properties, but is still considered a "variant." https://www.microbe.tv/twiv/twiv-697/ https://www.microbe.tv/twiv/twiv-697/ Any biological differences are theorized solely from the genome at this point. In the episode, Racaniello is at pains to point out that genomic differences alone don't imply biological differences in say transmission, and things like founder effects might also explain the variant's prevalance. We simply don't know yet. There's a neat cautionary example at 35:10 which I'll try to summarize here. Polio was endemic, with low incidence, for thousands of years. Around 1900 it went from endemic to epidemic. Why? Did it suddenly mutate into a deadlier or more transmissable strain? While we don't have polio sequences from before and after 1900 to compare, we do know that rapid improvements in sanitation delayed exposure to the polio virus. Babies were now encountering the virus after maternal antibodies to it had waned! And it turns out this adequately explains the spike in polio a century ago. Goes to show how complex the dynamics of these systems can be!
- trebligdivad 6y ago
  [edited to add newer doc] The UK NERVTAG had other measures of transmissability that got them to the conclusion it did have higher transmissability; https://khub.net/documents/135939561/338928724/SARS-CoV-2+variant+under+investigation%2C+meeting+minutes.pdf/962e866b-161f-2fd5-1030-32b6ab467896?t=1608470511452 https://khub.net/documents/135939561/338928724/SARS-CoV-2+va... and have a newer one where they're more confident: https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/756964987830 https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/...
  - sigil 6y ago
    They discuss these in that TWiV episode as well!
  - randomsearch 6y ago
    Worth noting that you can’t test a hypothesis from the data you used to formulate it. I haven’t seen any work on this variant that doesn’t fall into that trap.
Lin99 6y ago
I can see very easily how Japan could be the first epicenter of this new Covid-19 mutation.
laydn 6y ago
People appear to be expecting there will be "weaker" variant/strains/mutations of this virus as time goes on. I am not sure why this is the mainstream thought. Shouldn't these viruses get selectively better at fighting human immune systems? And we're throwing 750.000 new hosts to this virus worldwide every day.
- pakeha 6y ago
  What is the evolutionary value of killing the host (potentially) before transmission can occur? I’d have thought the sweet spot is weak enough to minimise fatality/maximise accidental transmission while strong enough to ensure minimal symptoms that result in increased transmission vectors (eg coughing) But. I have no training.
- smichel17 6y ago
  I am not an expert and have no special knowledge of this particular situation. In general, a "weaker" virus has an evolutionary advantage. Killing or disabling the host means fewer opportunities to spread.
- rq1 6y ago
  They shouldn’t as they have no will whatsoever, nor it is “fighting” our immune system. If any (will), it shouldn’t be killing its host. These are anthropomorphic reasoning and antagonisms.
  - throwaway2245 6y ago
    I know that some people consider it poor practice to anthropomorphise virus particles, but isn't this just an abstraction - a reasonable illustration - of what is happening? What would you say instead, to capture these ideas, that are equally clear to everyone?
- guscost 6y ago
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/ > Trade-offs between different components of parasite fitness provide the dominant conceptual framework for understanding the adaptive evolution of virulence (Alizon et al. 2009). ... > By far, the most widely studied trade-off involves transmission and virulence (Anderson and May, 1982; Frank, 1996; Alizon et al. 2009).
Threeve303 6y ago
What happens if the world gets into a situation where the virus mutates rapidly and we find the vaccines becoming less effective? We assume the drug companies will be able to adapt the vaccine quickly to the new variants. If this happens then it creates a few problems.. One problem is having to continuously distribute a new vaccine to people indefinitely. Another problem is only certain countries are capable of manufacturing the vaccine. So you have a kind of supply chain scarcity develop where only certain people in certain countries will be able to get one. I've seen mixed reports about whether the current vaccine will hold up as variants appear.
- IAmGraydon 6y ago
  The vaccine creates broad protection against the virus’s spike protein structure. If the virus mutated enough to evade this protection, it would have to develop a structure so radically different that it would likely no longer be able to attach to the ACE2 receptor. What is going on right now is mass anxiety. The vaccine is out, so humanity is imagining how things could still go wrong. The easiest thing to imagine is a version of the virus that doesn’t respond to antibodies. Luckily, they imagine this because they don’t understand how the vaccine works. It’s fantasy, and it is highly unlikely that any of this would play out.
  - enraged_camel 6y ago
    >> What is going on right now is mass anxiety. The vaccine is out, so humanity is imagining how things could still go wrong. Not enough anxiety, in my opinion. Tons and tons of people are still behaving as if everything is normal, or that they are somehow special.
    - nradov 6y ago
      So you think we need more irrational anxiety to control behavior? Mental health is just as important as physical health.
      - throwaway2245 6y ago
napier 6y ago
B.1.1.7 bodes stealthily and percussively enough, but I propose it be re-designated the Great Barrington Variant.
- throwaway2245 6y ago
  Regarding Great Barrington: I wonder if we'll ever see people apologise for their contribution towards this mess.
  - bluescrn 6y ago
    The cost/benefit of lockdowns will be argued about for decades. Assuming we ever get out of them...
DebtDeflation 6y ago
Has there ever been any genomic sequencing done to pinpoint what made SARS and especially MERS so much more deadly than SARS-CoV-2?
- AdrianB1 6y ago
  I don't know if we are that advanced in medicine to figure out from the genome of the virus what will be the impact on a human being.
- klondike_ 6y ago
  The lethality of a virus is inversely proportional to its transmissibility. In other words, a virus won't spread very far if it kills its host.
  - jliptzin 6y ago
    I don’t really understand why this is a “rule.” Say there’s two viruses and it takes both 3 weeks to run their course. They are both equally contagious during the 3 weeks, however the first virus results in death for 50% of those infected (50% recover after 3 weeks and are no longer contagious), and in the second the death rate is only 1% (99% recover after 3 weeks). Is such a virus not possible to exist?
    - rolph 6y ago
      the rule being discussed doesnt apply to a virus that reproduces and transmits to another host before causing illness. the basis of the lethality and transmissibility are inversely related is dependent upon dead or ill hosts having down time and not interacting with other hosts. thus if you are sick and febrile, you contact fewer individuals thus less opportunity for virus transmission between individuals. in the case of the coronavirus the dynamic is different. you contact the virus, virus replicates, and becomes transmissible, you still feel fine and behave as always transmitting the virus to other individuals, Then you begin to feel ill and bedridden. the virus has reproduced, transmitted and even if it kills you, it has escaped the selection pressure of the first case, where lethality or morbidity must be decreased for maximization of transmission. here is a slightly difficult read but is is a classic example of the rule you are asking about. https://en.wikipedia.org/wiki/Myxomatosis https://en.wikipedia.org/wiki/Myxomatosis
CWuestefeld 6y ago
How is this news at all? The virus has been mutating and throwing off different strains all along. There are entire websites devoted to tracking these, e.g., [1] Perhaps this is just the normal operation of American media to exaggerate the negative side of the situation? [2] [1] https://nextstrain.org/sars-cov-2/ https://nextstrain.org/sars-cov-2/ [2] PDF link: https://www.nber.org/system/files/working_papers/w28110/w28110.pdf https://www.nber.org/system/files/working_papers/w28110/w281...
- totaldex 6y ago
  The title requires context - although given recent events we can infer that it is referring to the specific mutation seen in the UK. This particular mutation is of note since it has postulated as being more transmissible than other variants.
- ethbr0 6y ago
  Not sure Japan Times [0] qualifies as "American media." [0] https://www.japantimes.co.jp/about-us/ https://www.japantimes.co.jp/about-us/
- jackmodern 6y ago
  Bingo, media overhyping this thing at every turn.
- orblivion 6y ago
  It's news if there's anything notable about the strain. More deadly, faster spreading, potentialy resistant to the vaccines. So far UK and South Africa have two strains that are faster spreading (and hopefully that's the only difference). If there's nothing special about the one from Japan, I bet that this is just getting attention because the other two are in the news. Either news orgs jumping on a bandwagon or HN readers expecting that it's similar when it's not. But maybe this one actually is notable too, I don't know.
  - jsnell 6y ago
    This is not a report about a new variant, but that they found 5 cases of B.1.1.7 (the UK one) in Japan.
sjg007 6y ago
Just wait until it mutates and starts killing kids. Kids are currently the last to be vaccinated. I know this is morbid but this does not bode well but there is precedent. Spanish flu first only killed the elderly and then on its return killed young adults and kids disproportionately. Now the Spanish flu was influenza and this is coronavirus but this specific coronavirus should not be underestimated. I’ve said this from the beginning and I hope I’m wrong.
- ketamine__ 6y ago
  > I’ve said this from the beginning Is that relevant and who are you?
  - breitling 6y ago
    It's just a figure of speech
  - hombre_fatal 6y ago
    It's just a low effort rhetorical device where the speaker hopes to boost their signal. Much like "I don't normally say this but."
- jMyles 6y ago
  I have found myself concerned about this as well (and thinking about what decision-making for parents must have been like in late summer when this characteristic started to become evident). Ask yourself: if you're that parent, do you wish that your kid had already been exposed and run a complete course of the virus prior to this mutation? It seems obvious that the answer is 'yes', and, at least to my way of thinking, is an indictment of the purely horizontal approach to pandemic control so far displayed by states.
- capkutay 6y ago
  There’s no evidence that it’s more deadly at this time. In the words of Derek Lowe... “Many infectious pathogens, in fact, gradually evolve versus a given animal host to be more infectious and less virulent over time. Remember, it’s not the job of a virus to make people deathly ill: it’s the job of a virus to make more virus.”
mancerayder 6y ago
It's not too surprising to anyone following the events. Retroactive blood testing of donated blood should the original strain (the phrase original variant sounds like an oxymoron) having reached places like France and NY months earlier than we realized, certainly November if not September of 2018. The magic of the virus is its ability to travel and spread undetected due to asymptomatic carriers. At least now widespread testing is available and we're able to track new variants in geography and time. Looks like the mutated one mentioned just hit France a couple of days ago.
- sokoloff 6y ago
  > November if not September of 2018 Presumably you mean 2019?
  - mancerayder 6y ago
    Yup :-)
ehnto 6y ago
Would a tally not necessarily be at record highs after any additional cases?
landemva 6y ago
It is difficult to know what sources of information to trust. I already have antibodies, and thought I would be ok for a while. If this is a new strain, how would they know to make a vaccine for it, and how many vaccines will I need each year? Also, the article here says "case count". I'm really interested in the count of "excess deaths".
- space_fountain 6y ago
  I'm also a lay person so take this with a grain of salt. There isn't evidence that this new variant can reinfect people who previously had covid and all the expert speculation I've heard is that it probably won't break out of immunity. It's better to be cautious, but also no need to think the worst
- GoldenStake 6y ago
  The current vaccine is a new technology, which codifies the spike protein in mRNA. SAR-COV-2 works by using their spike protein to attach to your body's ACE2 receptors, This new vaccine time is targeting something that is invariant and integral to SAR-COV viruses (the spike protein which gives it entrance) and almost certainly covers the new variant
  - landemva 6y ago
    I already have the antibodies (from June), so it seems I won't need that vaccine. Right? Or in other words, my antibodies would almost certainly cover the new variant.
Animats 6y ago
New paper on transmissiblity in the UK: [1] NYT article on paper: [2] [1] https://cmmid.github.io/topics/covid19/reports/uk-novel-variant/2020_12_23_Transmissibility_and_severity_of_VOC_202012_01_in_England.pdf https://cmmid.github.io/topics/covid19/reports/uk-novel-vari... [2] https://www.nytimes.com/2020/12/23/health/coronavirus-uk-variant.html https://www.nytimes.com/2020/12/23/health/coronavirus-uk-var...
lumberingjack 6y ago
I traveled to Florida for the holidays nobody wears masks here nobody's sick. Back in California in the office retarded people were scared out of their minds on lockdown wondering if their mask their glove and the new plexiglass over their desk is enough precaution. Land of the free home of the brave only in Florida now I guess. This whole thing is just red pilling people by the millions creating a massive amount of anti-vaxxers.

Mutation is simply a loaded term for variation, nothing horrible or shocking is happening. https://news.ycombinator.com/item?id=25538675 https://news.ycombinator.com/item?id=25538675 https://en.wikipedia.org/wiki/Mutation https://en.wikipedia.org/wiki/Mutation

Volundr 6y ago
Not horrible or shocking, but concerning. Mutation is expected but the more strains there are the more likely one turns out to be unaffected by the vaccine and we find ourselves back at square one.
- rolph 6y ago
  there is considerable selective pressure upon the spike protien, very large changes to this protien are not frequently viable, as the virus would need to find a new trophic target or a new host altogether. We are tracking these changes closely and concommitantly can change the sequence of mRNA, responsively, and pre-emptively if desired.
- UncleOxidant 6y ago
  I would hope that they could add coverage for new variants to the mRNA vaccines without having to go completely back to square one. Do they have to do full 3 phase testing on the flu vaccine every year?
  - rolph 6y ago
    first issue here is the differences in terminology regarding strains, vs variants. strains are signifigantly different from each other, variants are a nuance on the same theme. the virus strain that infects small mammals is separate from the trans specific strain that spilled over to humans. the virus with small changes to the spike sequence altering spike structure or function is a variant. under emergency conditions a 3phase trial is not mandatory , and would likely be a quick deliberation under normal conditions for small adjustments to the sequence, similar to seasonal influenza vaccines.
yread 6y ago
Note that here we're not talking about a single mutation but 17 non-synonymous (they change the protein) mutations with 3-4 with known effects on the interactions of the resulting proteins
- rolph 6y ago
  yes, and this is also not a surpise, this is part of the character of this virus, the sequence is unstable due to size and due to RNA instability.
  - yread 6y ago
    What are you talking about? Sequence is unstable due to size? Coronavirus has proofreading mechanism that corrects most mutations due to errors, the estimate for mutation speed before this variant emerged was 2 mutations per month so this variant has ~10 months of evolution in them but probably evolved much faster for some reason. This is very much a surprise
    - rolph 6y ago
      This is what i am typing about. The error rate is in terms of the number of nucleotides addended to the polymerizing RNA during replication the mutation rate is primarily a result of RNA replication, _not_ time. this means more replication events leads to more "errors", this also means longer sequence has a higher rate of error than a shorter sequence. at a length of ~29k bp the coronavirus sequence is very error prone, so error prone that this is approaching the upper limit of stability. it seems you are mistaking DNA proofreading for an RNA proofreading mechanism, which happens to be negative selection upon nonfunctional mutant/variant. there is no recognized enzymatic [rdRNApol] error correction associated with the coronavirus. "the RNA polymerases of RNA viruses are the kings of errors – these enzymes screw up as often as one time for every 1,000 – 100,000 nucleotides polymerized. This high rate of mutation comes from the lack of proofreading ability in RNA polymerases. These enzymes make mistakes, but they can’t correct them. Therefore the mutations remain in the newly synthesized RNA." [0] none of these error prone generated mutations are surprising, they are to be expected espescially when the virus is given opportunity to replicate at a high cyle rate. this is very much not a surprise, if you are aware of the properties of +ssRNA virus. [0] https://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/ https://www.virology.ws/2009/05/10/the-error-prone-ways-of-r... you may find this interesting[1] however this is primarily post polymerization [RNA readout] modification mechanism not error correction. [1] https://www.pnas.org/content/103/13/5108 https://www.pnas.org/content/103/13/5108
nabla9 6y ago
This is incorrect. Mutation and variation are different concepts. Mutations affect the single organisms. Variations happens between individuals, groups or populations of an organism.
- rolph 6y ago
  you dont seem to understand either concept. mutation is passed from individuals by vertical or horizontal transmission. variation of a gene [alleles] are mutations, mutations are the index variation. mutation is a change in the gene sequence, this is variation, this has created a mutant, also known as a variant. mutation is also a term loaded with connotations due to popular depictions. sexual reproduction is the mechanism of verticall transmission of variation of genetic sequence through a population. genetic drift is also a mechanism of variation of a population. the long and short of it is that mutation and variation, are tied together, they are the same thing. you also seem to have overlooked the abuse of the term mutation, by the original article title, the use of mutation is slicker, than the use of error prone generated variant. the use of the term strain is also erroneous in this context.

RcouF1uZ4gsC 6y ago

There are two important things to temper how worried you should be: 1. Many times there is an inverse relationship between ease of transmission, and severity of symptoms. There is a good chance that this new more transmissible mutant is likely to make people less sick. 2. So far all the available evidence seems to indicate that the vaccines will be effects against this strain as well.

saberdancer 6y ago
You shouldn't speculate about 1. especially as this is a virus that is new. It didn't have wave after wave where the "deadly" strains would lose out in evolution. Death rate in London and Kent didn't seem very different to other affected areas which would imply that the virus has same severity of symptoms but it is easier to transmit/contract.
- irq11 6y ago
  It’s not remotely clear that this strain is easier to transmit. It’s entirely hypothesis and speculation. We have seen strains quickly accelerate because of founder effect several times in 2020, and particular strains dominate in particular regions. The experimental studies that are needed to confirm a claim of evolutionary advantage have not been done, and the observational evidence is weak. Those who would panic about this should be just as circumspect in their their claims as those who would dismiss it.
  - jibbit 6y ago
    I'm guessing you're not living in Kent right now?
  - Jabbles 6y ago
    It is a hypothesis with a small prior, yes. But when considering the data - that the strain has grown faster than all others in the UK at the time - the likelihood becomes significant. Not certain, but not worthy of your casual dismissal. You dismiss their observational evidence as weak, but offer no further analysis. Please do so.

ethbr0 6y ago

> The people who tested positive with the new strain, which is said to spread more easily and was blamed for a recent spike in infections in the U.K., returned to Japan this month — two at Tokyo's Haneda airport and and three at Kansai International Airport in Osaka. This is talking about the SARS-CoV-2 VOC 202012/01 variant [0], aka B.1.1.7., aka carrying the N501Y mutation. No news here, other than confirmed spread to Japan. [0] https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-emerging-variant.html https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-br...

dnautics 6y ago
That's interesting that it's an N -> Y mutation, if it's a surface mutation, that AA shift is typically associated with tighter specificity in binding to it's target, e.g. and in antibody studies. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829252/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829252/
- ethbr0 6y ago
  I think this is a NextStrain link to it. There's probably more information, jumping off from there. https://nextstrain.org/groups/neherlab/ncov/S.N501?animate=2019-12-19,2020-12-23,0,0,30000&c=gt-S_501&f_region=Europe&s=Germany/BY-ChVir-1017/2020 https://nextstrain.org/groups/neherlab/ncov/S.N501?animate=2...
lbeltrame 6y ago
N501Y itself has already appeared around the world. By itself, it does look that it is not more transmissible (see Prof. Francois Balloux's Twitter for some explanations). The deletion, again by itself is not new, and also in this case it doesn't seem it has (on its own) increased fitness over the others. N50Y has also a similar antibody neutralization profile as the non-mutated version. Of course, these data refer to the mutations on their own, not together. More on the deletion (on its own, again): while it is supposedly tied to a faster entry into the cells (twice as efficient in experimental assays), it look like it has lower fitness in absence of an ongoing immune response (it would lower in presence - but not disappear - in the immunocompromised patient it was first found into between treatments with convalescent serum).

sigil 6y ago

As discussed on TWiV yesterday, B.1.1.7 isn't a "strain," which has demonstrably different biological properties, but is still considered a "variant." https://www.microbe.tv/twiv/twiv-697/ https://www.microbe.tv/twiv/twiv-697/ Any biological differences are theorized solely from the genome at this point. In the episode, Racaniello is at pains to point out that genomic differences alone don't imply biological differences in say transmission, and things like founder effects might also explain the variant's prevalance. We simply don't know yet. There's a neat cautionary example at 35:10 which I'll try to summarize here. Polio was endemic, with low incidence, for thousands of years. Around 1900 it went from endemic to epidemic. Why? Did it suddenly mutate into a deadlier or more transmissable strain? While we don't have polio sequences from before and after 1900 to compare, we do know that rapid improvements in sanitation delayed exposure to the polio virus. Babies were now encountering the virus after maternal antibodies to it had waned! And it turns out this adequately explains the spike in polio a century ago. Goes to show how complex the dynamics of these systems can be!

trebligdivad 6y ago
[edited to add newer doc] The UK NERVTAG had other measures of transmissability that got them to the conclusion it did have higher transmissability; https://khub.net/documents/135939561/338928724/SARS-CoV-2+variant+under+investigation%2C+meeting+minutes.pdf/962e866b-161f-2fd5-1030-32b6ab467896?t=1608470511452 https://khub.net/documents/135939561/338928724/SARS-CoV-2+va... and have a newer one where they're more confident: https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/756964987830 https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/...
- sigil 6y ago
  They discuss these in that TWiV episode as well!
- randomsearch 6y ago
  Worth noting that you can’t test a hypothesis from the data you used to formulate it. I haven’t seen any work on this variant that doesn’t fall into that trap.

Lin99 6y ago

I can see very easily how Japan could be the first epicenter of this new Covid-19 mutation.

laydn 6y ago

People appear to be expecting there will be "weaker" variant/strains/mutations of this virus as time goes on. I am not sure why this is the mainstream thought. Shouldn't these viruses get selectively better at fighting human immune systems? And we're throwing 750.000 new hosts to this virus worldwide every day.

pakeha 6y ago
What is the evolutionary value of killing the host (potentially) before transmission can occur? I’d have thought the sweet spot is weak enough to minimise fatality/maximise accidental transmission while strong enough to ensure minimal symptoms that result in increased transmission vectors (eg coughing) But. I have no training.
smichel17 6y ago
I am not an expert and have no special knowledge of this particular situation. In general, a "weaker" virus has an evolutionary advantage. Killing or disabling the host means fewer opportunities to spread.
rq1 6y ago
They shouldn’t as they have no will whatsoever, nor it is “fighting” our immune system. If any (will), it shouldn’t be killing its host. These are anthropomorphic reasoning and antagonisms.
- throwaway2245 6y ago
  I know that some people consider it poor practice to anthropomorphise virus particles, but isn't this just an abstraction - a reasonable illustration - of what is happening? What would you say instead, to capture these ideas, that are equally clear to everyone?
guscost 6y ago
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/ > Trade-offs between different components of parasite fitness provide the dominant conceptual framework for understanding the adaptive evolution of virulence (Alizon et al. 2009). ... > By far, the most widely studied trade-off involves transmission and virulence (Anderson and May, 1982; Frank, 1996; Alizon et al. 2009).

Threeve303 6y ago

What happens if the world gets into a situation where the virus mutates rapidly and we find the vaccines becoming less effective? We assume the drug companies will be able to adapt the vaccine quickly to the new variants. If this happens then it creates a few problems.. One problem is having to continuously distribute a new vaccine to people indefinitely. Another problem is only certain countries are capable of manufacturing the vaccine. So you have a kind of supply chain scarcity develop where only certain people in certain countries will be able to get one. I've seen mixed reports about whether the current vaccine will hold up as variants appear.

IAmGraydon 6y ago
The vaccine creates broad protection against the virus’s spike protein structure. If the virus mutated enough to evade this protection, it would have to develop a structure so radically different that it would likely no longer be able to attach to the ACE2 receptor. What is going on right now is mass anxiety. The vaccine is out, so humanity is imagining how things could still go wrong. The easiest thing to imagine is a version of the virus that doesn’t respond to antibodies. Luckily, they imagine this because they don’t understand how the vaccine works. It’s fantasy, and it is highly unlikely that any of this would play out.
- enraged_camel 6y ago
  >> What is going on right now is mass anxiety. The vaccine is out, so humanity is imagining how things could still go wrong. Not enough anxiety, in my opinion. Tons and tons of people are still behaving as if everything is normal, or that they are somehow special.
  - nradov 6y ago
    So you think we need more irrational anxiety to control behavior? Mental health is just as important as physical health.
    - throwaway2245 6y ago

napier 6y ago

B.1.1.7 bodes stealthily and percussively enough, but I propose it be re-designated the Great Barrington Variant.

throwaway2245 6y ago
Regarding Great Barrington: I wonder if we'll ever see people apologise for their contribution towards this mess.
- bluescrn 6y ago
  The cost/benefit of lockdowns will be argued about for decades. Assuming we ever get out of them...

DebtDeflation 6y ago

Has there ever been any genomic sequencing done to pinpoint what made SARS and especially MERS so much more deadly than SARS-CoV-2?

AdrianB1 6y ago
I don't know if we are that advanced in medicine to figure out from the genome of the virus what will be the impact on a human being.
klondike_ 6y ago
The lethality of a virus is inversely proportional to its transmissibility. In other words, a virus won't spread very far if it kills its host.
- jliptzin 6y ago
  I don’t really understand why this is a “rule.” Say there’s two viruses and it takes both 3 weeks to run their course. They are both equally contagious during the 3 weeks, however the first virus results in death for 50% of those infected (50% recover after 3 weeks and are no longer contagious), and in the second the death rate is only 1% (99% recover after 3 weeks). Is such a virus not possible to exist?
  - rolph 6y ago
    the rule being discussed doesnt apply to a virus that reproduces and transmits to another host before causing illness. the basis of the lethality and transmissibility are inversely related is dependent upon dead or ill hosts having down time and not interacting with other hosts. thus if you are sick and febrile, you contact fewer individuals thus less opportunity for virus transmission between individuals. in the case of the coronavirus the dynamic is different. you contact the virus, virus replicates, and becomes transmissible, you still feel fine and behave as always transmitting the virus to other individuals, Then you begin to feel ill and bedridden. the virus has reproduced, transmitted and even if it kills you, it has escaped the selection pressure of the first case, where lethality or morbidity must be decreased for maximization of transmission. here is a slightly difficult read but is is a classic example of the rule you are asking about. https://en.wikipedia.org/wiki/Myxomatosis https://en.wikipedia.org/wiki/Myxomatosis

CWuestefeld 6y ago

How is this news at all? The virus has been mutating and throwing off different strains all along. There are entire websites devoted to tracking these, e.g., [1] Perhaps this is just the normal operation of American media to exaggerate the negative side of the situation? [2] [1] https://nextstrain.org/sars-cov-2/ https://nextstrain.org/sars-cov-2/ [2] PDF link: https://www.nber.org/system/files/working_papers/w28110/w28110.pdf https://www.nber.org/system/files/working_papers/w28110/w281...

totaldex 6y ago
The title requires context - although given recent events we can infer that it is referring to the specific mutation seen in the UK. This particular mutation is of note since it has postulated as being more transmissible than other variants.
ethbr0 6y ago
Not sure Japan Times [0] qualifies as "American media." [0] https://www.japantimes.co.jp/about-us/ https://www.japantimes.co.jp/about-us/
jackmodern 6y ago
Bingo, media overhyping this thing at every turn.
orblivion 6y ago
It's news if there's anything notable about the strain. More deadly, faster spreading, potentialy resistant to the vaccines. So far UK and South Africa have two strains that are faster spreading (and hopefully that's the only difference). If there's nothing special about the one from Japan, I bet that this is just getting attention because the other two are in the news. Either news orgs jumping on a bandwagon or HN readers expecting that it's similar when it's not. But maybe this one actually is notable too, I don't know.
- jsnell 6y ago
  This is not a report about a new variant, but that they found 5 cases of B.1.1.7 (the UK one) in Japan.

sjg007 6y ago

Just wait until it mutates and starts killing kids. Kids are currently the last to be vaccinated. I know this is morbid but this does not bode well but there is precedent. Spanish flu first only killed the elderly and then on its return killed young adults and kids disproportionately. Now the Spanish flu was influenza and this is coronavirus but this specific coronavirus should not be underestimated. I’ve said this from the beginning and I hope I’m wrong.

ketamine__ 6y ago
> I’ve said this from the beginning Is that relevant and who are you?
- breitling 6y ago
  It's just a figure of speech
- hombre_fatal 6y ago
  It's just a low effort rhetorical device where the speaker hopes to boost their signal. Much like "I don't normally say this but."
jMyles 6y ago
I have found myself concerned about this as well (and thinking about what decision-making for parents must have been like in late summer when this characteristic started to become evident). Ask yourself: if you're that parent, do you wish that your kid had already been exposed and run a complete course of the virus prior to this mutation? It seems obvious that the answer is 'yes', and, at least to my way of thinking, is an indictment of the purely horizontal approach to pandemic control so far displayed by states.
capkutay 6y ago
There’s no evidence that it’s more deadly at this time. In the words of Derek Lowe... “Many infectious pathogens, in fact, gradually evolve versus a given animal host to be more infectious and less virulent over time. Remember, it’s not the job of a virus to make people deathly ill: it’s the job of a virus to make more virus.”

mancerayder 6y ago

It's not too surprising to anyone following the events. Retroactive blood testing of donated blood should the original strain (the phrase original variant sounds like an oxymoron) having reached places like France and NY months earlier than we realized, certainly November if not September of 2018. The magic of the virus is its ability to travel and spread undetected due to asymptomatic carriers. At least now widespread testing is available and we're able to track new variants in geography and time. Looks like the mutated one mentioned just hit France a couple of days ago.

sokoloff 6y ago
> November if not September of 2018 Presumably you mean 2019?
- mancerayder 6y ago
  Yup :-)

ehnto 6y ago

Would a tally not necessarily be at record highs after any additional cases?

landemva 6y ago

It is difficult to know what sources of information to trust. I already have antibodies, and thought I would be ok for a while. If this is a new strain, how would they know to make a vaccine for it, and how many vaccines will I need each year? Also, the article here says "case count". I'm really interested in the count of "excess deaths".

space_fountain 6y ago
I'm also a lay person so take this with a grain of salt. There isn't evidence that this new variant can reinfect people who previously had covid and all the expert speculation I've heard is that it probably won't break out of immunity. It's better to be cautious, but also no need to think the worst
GoldenStake 6y ago
The current vaccine is a new technology, which codifies the spike protein in mRNA. SAR-COV-2 works by using their spike protein to attach to your body's ACE2 receptors, This new vaccine time is targeting something that is invariant and integral to SAR-COV viruses (the spike protein which gives it entrance) and almost certainly covers the new variant
- landemva 6y ago
  I already have the antibodies (from June), so it seems I won't need that vaccine. Right? Or in other words, my antibodies would almost certainly cover the new variant.

Animats 6y ago

New paper on transmissiblity in the UK: [1] NYT article on paper: [2] [1] https://cmmid.github.io/topics/covid19/reports/uk-novel-variant/2020_12_23_Transmissibility_and_severity_of_VOC_202012_01_in_England.pdf https://cmmid.github.io/topics/covid19/reports/uk-novel-vari... [2] https://www.nytimes.com/2020/12/23/health/coronavirus-uk-variant.html https://www.nytimes.com/2020/12/23/health/coronavirus-uk-var...

lumberingjack 6y ago

I traveled to Florida for the holidays nobody wears masks here nobody's sick. Back in California in the office retarded people were scared out of their minds on lockdown wondering if their mask their glove and the new plexiglass over their desk is enough precaution. Land of the free home of the brave only in Florida now I guess. This whole thing is just red pilling people by the millions creating a massive amount of anti-vaxxers.