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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

#41

Post by rolph »

laydn wrote: post #32

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.

the incubation and transmission of the corona virus is not tightly coupled to morbidity, this virus moves to another individual before debilitating symptoms occur.

the virus will not become weaker as time goes on, it will have less variation to call upon for evasion of host defenses.

the major selective pressure on this virus appears to be exhaustion of variant production bringing the cat and mouse game of new viral antigen sequence vs antibody respecification to a stalemate, and the virus must move on [spillover] to a new host species. The ability to occur in many novel variations, and eventually spillover from a host species to a conspecific host is how this virus persists.

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

#42

Post by m-ee »

SomeoneFromCA wrote: post #30
m-ee wrote: post #25

Earlier quoted context omitted.

What evidence are you saying is “quite solid”. So far everything has just a been inferred from the epidemiology and the error bars are extremely wide. I wouldn’t call that solid at all.

What you consider a solid evidence?

Some actual lab work? I’m not a biologist so I can’t give you specific assays. The TWiV team might, I’ll submit a question. If you look at the data behind the NERVTAG report it’s extremely noisy, and is circumstantial. Nothing in there directly measures the viruses ability to spread.

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

#43

Post by fpgaminer »

laydn wrote: post #32

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.

IANAV: So, when someone gets visibly sick, they tend to get isolated from other people. That makes it more difficult for the virus to spread. So over time there's a slight advantage to variations of a virus that don't make as many people sick.

I'm sure there are other factors, but that's a big one. So most viruses tend to harm the host less over time.

We saw the opposite effect during the Spanish Flu. As I recall at least one theory: because there was a war on, only severely sick soldiers would get sent away from the front lines, where they could come into contact with the general population. Less severe cases were kept on the front lines. This behavior created an inverse effect, applying selective pressure on more _severe_ strains of the virus. Hence, the second more deadly wave.

Once the Spanish Flu pandemic was "over" and the war was over, that pressure wore off and the Spanish Flu slowly evolved into various common cold strains that we still see today (AFAIK).

My guess is that it's hard to speculate what will happen with COVID-19. Several common cold viruses are coronaviruses, so from that one might conclude that COVID-19 will follow the same path of becoming less severe over time. But COVID-19 also has a _very_ large incidence of asymptomatic transmission. So isolating people who are very sick is unlikely to provide much selective pressure to this virus.

If COVID-19 _does_ become less severe over time, it will occur only because of different selective pressures or for different reasons. For example, maybe the mutations that result in higher transmission also, by some genetic necessity, lower severity.

The asymptomatic nature of COVID-19 gives it a big question mark, and we should _not_ assume anything about it becoming less severe over time. We should keep up aggressive measures to control its spread and lean on our vaccines to squash it before it has a chance to get worse. The quicker we get the vaccine out, and the more aggressive we are about controlling the virus's spread, the higher our chance of getting out of this mess.

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

#44

Post by jsnell »

m-ee wrote: post #25
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…

What evidence are you saying is “quite solid”. So far everything has just a been inferred from the epidemiology and the error bars are extremely wide. I wouldn’t call that solid at all.

So, when the news broke a week ago, I was wearing my skeptic hat just like for the handful of previous announcements about "new strains". And some initial reading suggested that there was nothing to worry about. But the one data point that was so eye-popping that I thought it had to be a misprint was that 60% of the cases in London were for the new variant. It wasn't a misprint, and it wasn't isolated to London.

That is the single strongest set of data here. In the areas where both the new variant and the older ones can be distinguished (via sequencing or via the fortuitous FN from the commonly used PCR test), the new one is spreading substantially faster. This measurement is not sensitive to confounding factors such as environmental or behavioral changes, because those would affect all variants equally.

The thing that the TWIV guys seem to love repeating is that this is just a founder effect. I just don't understand where they're getting that idea from. Yes, that's almost certainly been the explanation in the earlier cases we had where one variant become predominant. But that happened in low prevalence environments. It's basically inevitable that if there are few cases, one variant or the other will become predominant just by random chance. That was not the case in the UK. In mid-October, when this variant was still basically non-existent, they were at 15k confirmed cases / day. This variant is not a founder, it was a very successful invader.

The other evidence is weaker, because it's less direct and the data is noisier. (Increased viral loads, many of the changes happening in parts of the genome that were already expected to be of biological interest, correlation studies showing that areas where the new variant is predominant have higher growth rates when controlling for other factors). That data would not be conclusive by itself. But all of it is directionally consistent with the main data point of concern, and strengthens the case.

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

#45

Post by mns »

anonymouse008 wrote: post #35
SomeoneFromCA wrote: post #30

Earlier quoted context omitted.

What you consider a solid evidence?

30% of people infected not able to walk a block without losing breath and being exhausted for a day — that’s enough evidence to say the risk profile has changed. Infection rate does not change outcome of recovery (unless it’s resource constrained like vents or meds) and to that point — we’ve walked back the immediacy of vents because they were actually harmful to recovery. So technically the resource management argum…

Where is that 30% coming from?

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

#46

Post by Threeve303 »

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.

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

#47

Post by jtxx »

SomeoneFromCA wrote: post #29
ALittleLight wrote: post #27

Earlier quoted context omitted.

I feel we (US) should absolutely be closing the border to the UK, Japan, Italy and whoever else has the new strain/variant. Why would we wait on this when the evidence suggests the new version is more infectious?

There must be some very special political reason for keeping borders with UK open, so even Fauci seem to approve it. I wonder what is it?

I’ve been thinking about this as well, they also kept their borders open to US citizens despite most countries closing them.

Perhaps Brexit closing trade doors with the EU could be resulting in a stronger relationship between the US & UK?

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

#48

Post by endgame »

SomeoneFromCA wrote: post #26
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…

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...

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

#49

Post by GregarianChild »

sigil wrote: post #22
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…

What could we be doing differently beyond what we already should be doing? Are you referring to things like border closing?

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, decisively and rationally Taiwan reacted, and compare it with other countries. It probably helped having had an epidemiologist as vice-president [3].

[1] https://www.theguardian.com/world/2020/oct/29/taiwan-domesti...

[2] C. Y. Wang, C. Y. Ng, R. H. Brook, Response to COVID-19 in Taiwan: Big Data Analytics, New Technology, and Proactive Testing, https://jamanetwork.com/journals/jama/fullarticle/2762689

[3] https://en.wikipedia.org/wiki/Chen_Chien-jen

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

#50

Post by lozenge »

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…

The study says that model doesn't fit as well as other ones. The model isn't an assumption, it's testing possibilities. The same as any use of statistics involves testing a model.
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