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

japantimes.co.jp

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

#11

Post by rolph »

Volundr wrote: post #9
rolph wrote: post #2

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

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.

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.

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

#12

Post by rolph »

jonny_eh wrote: post #10
RcouF1uZ4gsC wrote: post #3

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.

Isn't this what happened with the 1918 flu? It mutated to be less deadly add became the seasonal flu. https://www.history.com/news/1918-flu-pandemic-never-ended

yes this is a property of influenza virus, however the influenza virus is very different from corona virus, in particular the cryptic incubation period of coronavirus that occurs before symptoms can alter the hosts ability to interact with other prospecific hosts.

it is worthy of note that one single point mutation in the influenza virus corresponded to high lethality.

https://journals.plos.org/plospathogens/article?id=10.1371/j...

>> The 1918 pandemic strain A/Brevig Mission/18 was reconstructed with a pathogenicity-reducing mutation in PB1-F2 (S66N). The resultant 1918 S66N virus was attenuated in mice having a 3-log lower 50% lethal dose and caused less morbidity and mortality in mice than the wild-type virus. Viral lung titers were also decreased in 1918 S66N–infected mice compared with wild-type 1918 virus–infected mice. In addition, both viruses with an S at position 66 (WH N66S and wt 1918) induced elevated levels of cytokines in the lungs of infected mice. Together, these data show that a single amino acid substitution in PB1-F2 can result in increased viral pathogenicity and could be one of the factors contributing to the high lethality seen with the 1918 pandemic virus.<<

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

#13

Post by trebligdivad »

sigil wrote: post #7

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/ 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 li…

[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+va...

and have a newer one where they're more confident: https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/...

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

#14

Post by jibbit »

irq11 wrote: post #8
saberdancer wrote: post #4

Earlier quoted context omitted.

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.

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 ab…

I'm guessing you're not living in Kent right now?

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

#15

Post by dnautics »

ethbr0 wrote: post #6

> 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…

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/

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

#16

Post by sigil »

trebligdivad wrote: post #13
sigil wrote: post #7

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/ 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 li…

[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+va... and have a newer one where they're more confident: https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/...

They discuss these in that TWiV episode as well!

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

#17

Post by randomsearch »

trebligdivad wrote: post #13
sigil wrote: post #7

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/ 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 li…

[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+va... and have a newer one where they're more confident: https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/file/...

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.

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

#18

Post by madhadron »

jonny_eh wrote: post #10
RcouF1uZ4gsC wrote: post #3

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.

Isn't this what happened with the 1918 flu? It mutated to be less deadly add became the seasonal flu. https://www.history.com/news/1918-flu-pandemic-never-ended

This is a very poor way of looking at it. H1N1 is considered a subtype rather than a strain, and there are many H1N1 strains around. It makes more sense to think of the 1918 strain going extinct and some of quasispecies descendants of it persisting.

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

#19

Post by UncleOxidant »

Volundr wrote: post #9
rolph wrote: post #2

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

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.

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?

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

#20

Post by jsnell »

sigil wrote: post #7

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/ 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 li…

TWIW has kind of painted themselves into the corner by insisting that anything except biological evidence is irrelevant. The evidence for B.1.1.7 being more transmissive is quite solid, and seems to be getting more so as time goes on. But no matter how strong the statistical data is, it could never be good enough for them. So their policy recommendation ends up as "do nothing at all until there is 100% certain non-circumstantial evidence".

The problem is that action now is way more valuable than action in 1-2 months. Mass vaccination is right around the corner, we just need to buy time to get there. If there is a substantially more transmissive variant around, that will make it much harder to buy that time. You need to be able to act on the balance of probabilities, not wait for perfect information.

(And their claim that there's nothing we can do differently is just total bunk.)

And because they run a popular podcast, their view gets massively amplified by being parroted in internet discussion.

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