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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

#81

Post by rualca »

mns wrote: post #31
jsnell wrote: post #20

Earlier quoted context omitted.

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-ci…

Well, the preprint ( https://cmmid.github.io/topics/covid19/reports/uk-novel-vari... ) from the UK has this: >Third, we modelled increased susceptibility among children (aged 0-19) by assuming they could be as susceptible as adults (aged 20+) to infection by VOC 202012/01 given exposure. Basically they applied their own model on a lot of noise and data and assumed certain things. It's wild were we are at this point a…

You're showing a fundamental misconception and outright ignorance of what research papers are, and more importantly what science is. For example, you're somehow assuming that academic papers about to be subjected to peer review are somehow milestones which write in stone the truth instead of what they actually are and always have been: a way to share data, observations, theories, hypothesis, and even assumptions on research topics. Researchers share their work not because it's bullet-proof but because it's food for thought that can be used to drive our understanding a bit further.

And a paper is retracted only in extreme cases such as gross scientific malpractice such as fraud. Unless you have some info that you refused to share, I see no coherent and rational reason to indicate any of these papers should be retracted. Having strong emotionally-driven positions on a subject is not a reason to demand a paper should be retracted.

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

#82

Post by ethbr0 »

dnautics wrote: post #15
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/

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=2...

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

#83

Post by GregarianChild »

starkd wrote: post #78
GregarianChild wrote: post #49

Earlier quoted context omitted.

Copy Taiwan. No country has been dealing better with Covid than Taiwan. No lockdown, and > 200 days without new Covid case [1]. Taipei had daily direct flights from Wuhan, and the Diamond Princess mooring near Taipei. They told the world early on [2] how they did it. Summary: Border closure, contract tracing, testing and controlled quarantine for those testing positive . It's worth reading [2] to realise how swiftly,…

that's because it's an island. All the islands are doing better than whole continents. You can't contain it unless you go full bore like the chinese - locking people into their homes.

The UK is no island?

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

#85

Post by [deleted] »

jpster wrote: post #60
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…

I’m a big fan of TWiV podcast (This Week in Virology) and I understand Racaniello’s point of view. However, this thread and other info I’ve read lead me to believe that this is an important new development. https://twitter.com/billhanage/status/1341857733633581063?s=...

[deleted]

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

#86

Post by rualca »

GregarianChild wrote: post #83
starkd wrote: post #78

Earlier quoted context omitted.

that's because it's an island. All the islands are doing better than whole continents. You can't contain it unless you go full bore like the chinese - locking people into their homes.

The UK is no island?

> The UK is no island?

An island that has high-speed railway connections to Europe is not exactly isolated from the world, not to mention it's ferry connections with multiple neighboring countries in mainland Europe.

Additionally, Great Britain has about 3 times the population of Taiwan, and it's urban centers have between 5 and 7x the population of Taiwan's largest urban centers.

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

#87

Post by didibus »

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…

Okay, but from your own explanation, this is only a hypothesis and it's possible that sanitation had nothing to do with it either. So I'm not sure what this really shows us except that we can make up any justification for anything after the fact. Correlation is easy to show, causation is hard.

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

#88

Post by SomeoneFromCA »

endgame wrote: post #48
SomeoneFromCA wrote: post #26

Earlier quoted context omitted.

There is some other point I heard recently on Twitter - the appearance of new variants with increasingly faster speed of spread (BTW, if anyone remembers, there was a mutation in Australia, which had shorter incubation - 8 HOURS), may quite soon cause rise of true strains, and, it might potentially lead to the ADE, when suboptimal vaccines will make disease much worth instead of easing it.

You're not thinking of the pizza worker in SA who told porkies, are you? https://www.theguardian.com/world/2020/nov/21/south-australi...

Not sure, just read about it somewhere.

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

#89

Post by jsnell »

tomxor wrote: post #79
jsnell wrote: post #20

Earlier quoted context omitted.

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-ci…

> The problem is that action now is way more valuable than action in 1-2 months [...] If there is a substantially more transmissive variant around, that will make it much harder to buy that time. But which action? I can see two class of possible cause that do not entirely overlap in response: A singular cause such as a strain; or fluctuations as the emergent behavior of a complex dynamic system. If incorrectly attrib…

That seems like just a fancier way of expressing TWIV's "we can't possibly know anything without lab experiments that establish the exact mechanisms, so we should do nothing" philosophy.

The undeniable fact is that this variant has successfully replaced other already highly prevalent variants. That needs to be explained somehow.

Could it be a founder effect? No.

Could it be random chance? No. Of course a stochastic process could converge like this even with no selective advantage eventually. But the change has been too fast and too consistent in this case.

Could it be a super-spreading event? No. The change has been continuous, and a single event would cause just a step-change in relative prevalance.

Could it be the new variant being more transmissive, or having another similar selective advantage? Yes.

Could it be an unspecified emergent behavior? I guess it could. But how are we supposed to reason about something that vague? We have a simple explanation that's consistent with the known facts, I feel that anyone proposing that it's just emergent behavior should be at least a little bit more specific.

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

#90

Post by carlmr »

bumbada wrote: post #71
Threeve303 wrote: post #46

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 manuf…

We have over 80 different COVID vaccines today if you look at the COVID vaccine tracker. Next year it will be at least 120. In Spain alone they have 3 different vaccines that are not even in phase 1, but will be next year. There will be at least 5 totally different technologies against it. There are "slower to market" technologies than RNA but stronger and proven. Also the weather is going to get better in the North…

>Also the weather is going to get better in the North Hemisphere soon

January is colder than December usually. We're not even over the peak. February should be roughly similar to December, March is when it gets better again usually. But that's still 2 months of people staying indoors a lot.

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