[sigil]

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 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!

[jsnell]

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.

[tailspin2019]

> TWIW has kind of painted themselves into the corner by insisting that anything except biological evidence is irrelevant.

I definitely don't know enough about this topic to say you're right, but as an avid layman listener of TWIV for 8+ months now, I've recently started thinking along the same lines.

With the greatest of respect, Vincent Racaniello, while being clearly a true expert in the field, tends to take a very quick and polarised view to newly presented evidence, and can often sound like he's being overly dismissive to my layman's ears. To the degree where I end up thinking, "it can't be that black and white".

I get the sense that sometimes the co-hosts would likely go for a more nuanced perspective, and often they do try to soften the edges around some of his opinions, but the podcast is very much his domain.

By the same token, I've often heard him admit that he was wrong. The sign of a good scientist! So there's that.

Being in the UK, and having received head-on the full barrage of "communication" from our Government during COVID, I have learnt to be sceptical of the messages they put out, and defaulted to "cynical" when first hearing their report of the new variant at the end of a recent press conference. The more time goes on though, the evidence does seem to be mounting that we should be looking at this very closely and not dismissing it out of hand.

> The problem is that action now is way more valuable than action in 1-2 months.

Completely agree. We have to use a balance here of scientific evidence, but also strategic thinking - which may not be 100% scientific - and the strategy may be that it's safer to assume this variant is more easily transmissible, and act accordingly, rather than wait for the science to catch up and prove it 100%.

All of that said, re. TWIV - it has been a game-changer of a podcast for me during this pandemic. I thoroughly enjoy listening to the hosts, all of whom are generally good natured, clearly very experienced, and doing a good job overall of science communication. No view on COVID is going to be perfect, and in my view their output is a net positive (by far) even despite the above.

[InTheArena]

As a long term listener of TWIV (4 years, IIRC), I think the service they have done for the community is priceless, especially once Daniel Griffin started doing his clinical updates. That said, I remember when COVID first started hitting, and their reaction was initially "meh", then like everyone else, it started to dawn on them how bad this was going to be. So still take their voices with a grain of salt.

In the latest TWIV, their comment was that the things you would do to prevent COVID are the same no matter if it is a new Strain or not. That's true - but we also have to deal with a increasingly uncomfortable truth - in many places, the COVID incident and death rate are pretty much the same, despite dramatically different legal and social dictates around masking, etc. Italy, France, USA, UK, Spain, Belgium, etc are all within 10% of the total death per million population, for example.

There is a weird cycle around COVID. Everyone reports on how awful it is somewhere, people draw a over-broad conclusion about the moral or scientific failures of the continent / state / country / red state / blue state, then that wave of covid waxes in one place, and wanes is another, and the cycle repeats again.

This pattern continues despite different travel restrictions, different masking policies (way less then my state in the USA, for example), etc.

SO I think the answer is not - we couldn't change anything - but rather - what is really the science behind this - and do we truly understand what is going on? I get that Vincent is burned out and has a knee jerk reaction, if I had to deal with all the insanity around the Hydrochloroquine crap I would be too.

[m_mueller]

And then there are places like Taiwan that have kept themselves COVID free and report a grand total of 7 deaths on 22M inhabitants, without any lockdown needed and thus experiencing minimal economic impact. And yet no Western country seems to want to learn from that.

[dageshi]

What is there to learn?

1) Act immediately and aggressively at the first sign of potential virus.

2) Get your population used to wearing masks when ill with cold like viruses and thus ensure sufficient supplies and willingness to wear masks when the government mandates it.

3) Preferably be an island or have absolute control of your country (China)

There was a period when countries could've done what Taiwan did but once the virus got a hold in continental europe and usa it was over.

[m_mueller]

Taiwan had an emergency law in place thanks to lessons learned from SARS. Allowed government to track cell phones for quarantine and case tracking. This has turned out to be highly effective, without requiring a total authoritarian government. Even though I'm usually very much pro privacy, IMO with sufficient checks and limitations in place such a law is very effective - I'd gladly give up privacy in case I was tested positive or have traveled abroad in exchange of not needing any lockdowns and live normally otherwise.

[lenkite]

4) Nod and smile but disregard everything the CCP says.

[tailspin2019]

> I get that Vincent is burned out and has a knee jerk reaction, if I had to deal with all the insanity around the Hydrochloroquine crap I would be too.

Totally agree on this.

[SomeoneFromCA]

I used to like TWIV, but once they aggresively and unprofessionally tried to "debunk" the lab origin hypothesis of the pandemic (which is still pretty much viable one) I kinda lost any respect to these people. I'd rather listen to UCSF podcast, way more professional.

[sigil]

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

[GregarianChild]

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

[GuB-42]

I often see "copy this country" but often, it is simply not possible, policies are usually a result of each country specificities more than the other way around. For Taiwan.

- It is an island

- It has an effective, well centralized surveillance network

- It has (presumably) an obedient population, or at least, one that don't think personal freedom includes the right to spread the disease

- They were well prepared thanks to the their experience with SARS

- A good enough welfare system to allow people to quarantine without starving or getting ruined

- A good enough police force to make sure they stay quarantined

- Enough masks and hand sanitizer, with domestic production

This is pretty much the opposite of the US. Which is highly connected, with a loosely connected government that has little control over the private sector that runs the country and a highly individualistic population.

Also, maybe there are some populations that just do better for a mix of reasons: climate, race (genetics), culture, average age, health and population density,...

Final note: closing borders is only effective if you contained the epidemic and others didn't.

[kinghtown]

I live in Taiwan.. I’m grateful to be living here during Covid.

Taiwanese people aren’t obedient. You should see how they drive.

They wear masks without flaking out about it as slavery or being against their will or whatever nonsense you guys are on about back home in the west.

Taiwanese people are couch potatoes and extremely reserved. They don’t really want to meet new people or hang out with strangers.

Also the government here didn’t play games in the early weeks. No wait and see business as usual lazy bullshit like in the US. They check tour temperature everywhere, mall entrances, restaurants, government buildings.

The us most certainly should copy Taiwan.

[hnlmorg]

> Taiwanese people aren’t obedient. You should see how they drive.

...

> They wear masks without flaking out about it as slavery or being against their will or whatever nonsense you guys are on about back home in the west.

The 2nd part is what the GP was talking about with regards to 'obedience'. In some western countries like the US and UK, even the simple request for individuals to wear a mask is seen by some as an infringement on their human rights. There are literally documents floating around social media in the UK citing the Magna Carta[1] as a legal document for why they are entitled not to have their temperature checked!

Granted these people are idiots. But unfortunately the UK and US has also fostered a culture where everyone's voice is deemed equal, even the idiots. A classic example of this was during the EU referendum with the oft quoted phrase "why should we trust those so call experts?" as a retort against financial analysts voicing their concerns.

The problem is when you have research demoted to the same level as hearsay, a general distrust of the government and mix in a large does of fear due to economical, political and/or social unrest, you end up in an environment where those aforementioned idiots end up recruiting more idiots into their cause.

[1] https://en.wikipedia.org/wiki/Magna_Carta

[lhl]

All of the things you've noted are true, but the flip side is that that there seems to be a "we've tried nothing and we're all out of ideas" (or worse, flat out pandemic denialism) mentality that takes hold instead of thinking about whether it would be possible to push for some of the most obvious policies that have been shown to be the most effective (eg, enforcing testing and quarantine for all travelers, improved science communication around a respiratory pandemic). Also, it's been 10+ months, so to the degree that developed countries like the US lack sufficient PPE manufacturing, it's certainly not down to resources or capabilities (or anything besides political will in the US considering the DPA could be invoked at any time).

Also, most countries still seem to be ignoring the best/cheapest way to control spread via rapid testing and isolation. This has been not only modeled extensively at this point [1][2], but also proven to be effective by sports leagues (NBA, MLB) and Universities (look at where UIUC has kept their numbers vs the state: https://go.illinois.edu/COVIDTestingData )

[1] Larremore, Daniel B, Bryan Wilder, Evan Lester, Soraya Shehata, James M Burke, James A Hay, Milind Tambe, Michael J Mina, and Roy Parker. “Test Sensitivity Is Secondary to Frequency and Turnaround Time for COVID-19 Surveillance.” Preprint. Infectious Diseases (except HIV/AIDS), June 25, 2020. https://doi.org/10.1101/2020.06.22.20136309.

[2] Atkeson, Andrew, Michael C. Droste, Michael Mina, and James H. Stock. “Economic Benefits of COVID-19 Screening Tests.” National Bureau of Economic Research, November 2, 2020. https://doi.org/10.3386/w28031.

[incrudible]

Consider the countries like Japan that do not actually have excess mortality despite COVID-19. Suppose they just stopped testing for it. You would not be able to tell the difference. You could then come up with any reason for this “huge success”.

[dragonwriter]

> Consider the countries like Japan that do not actually have excess mortality despite COVID-19. Suppose they just stopped testing for it. You would not be able to tell the difference.

That assumes that testing-dependent interventions (whether contact tracing and quarantines of the exposed, appropriate treatment of systematic infections, etc.) have nothing to do with the absence of excess deaths.

Which seems improbable.

[anonymoushn]

Sure, then copy Vietnam or Australia.

[dageshi]

How do you copy being an Island?

How do you go back in time and get your population used to wearing masks (and having supply) at the beginning of the pandemic when it really matters?

[xg15]

This probably would have been good advice in late summer or early fall when contact tracing was still possible.

However now there seem to be so many diffuse infection events and undetected chains that the question is more about how to regain control. I'm not sure how this is achievable without contact restrictions.

[m_mueller]

One way to regain control is to mass produce cheap rapid test kits, do a couple of mass testing events where significant percentage of population is tested to identify all clusters, isolate and trace from there. See Slovakia as an example.

[turing_complete]

It's just insane how incompetent European and American governments have been in this pandemic compared to East-Asian countries. We are lucky to have some functional private institutions that bailed us out -- kept the countries running and developed a highly effective vaccine super fast.

[tchalla]

Moderna has received a lot of government funding despite not ever making a profit as a private institution.

[ethbr0]

https://www.axios.com/moderna-barda-coronavirus-funding-disc...

[starkd]

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.

[scarmig]

I find this argument unconvincing. The UK is an island, and it's doing badly. "But it's highly connected with the rest of the world, so it makes it honorarily a non-island!" Okay, sure. How about South Korea? It isn't an island, and it's doing pretty well. "But it's de facto an island, it's not getting cases from North Korea!" Okay, sure. But by that standard the US is an island: it didn't get its cases from Mexico or Canada.

And, of course, China has more land borders than any other country in the world, and it's managed to engineer the most drastic turnaround of any country in the world.

Having a small number of entry points is useful to limit initial inoculations, but internal policy and cultural cohesion are key for preventing the explosion of any successful inoculation into national disaster, regardless of a polity's geography.

[fomine3]

You can't say that US is virtually island same as South Korea because US isn't on war with Canada or Mexico.

[irq11]

> How about South Korea? It isn’t an island, and it’s doing pretty well.

Cases are at all-time highs, and have pretty much escalated out of control:

https://www.google.com/amp/s/www.aljazeera.com/amp/news/2020...

[howlgarnish]

Sigh, this old canard again. Vietnam, Thailand, Laos, Cambodia, Singapore are all doing fine without "locking people into their homes" and they're not islands.

(Ok, Singapore technically is an island but it's connected to Malaysia by the world's busiest border crossing; and Thailand's grappling with a new outbreak now but it seems to be improving.)

[jandrewrogers]

Viet Nam is not doing fine. I have a lot of contact there, there is an outbreak of “severe pneumonia” for which no one is being tested for COVID despite being pretty obviously COVID. To make matters worse, in addition to not testing anybody with symptoms, the government hospitals have been turning people with these symptoms away so they are going to their family homes to be taken care of.

I would take the stories of Viet Nam’s “success” with a very large grain of salt. It should be impossible for me to know so many people with odd “severe pneumonia” there given that the entire country has nominally only had a thousand cases or so.

[refurb]

I have a friend in Vietnam. They were effectively locking people in their homes. If a Covid case was found in an apartment, the entire floor was locked down. If you didn't stay in your home, you were brought to a facility where you didn't have a choice in the matter.

And they are controlling it now by effectively locking down the country to the rest of the world. Even if you're a Vietnamese citizen you can't get back into the country without permission. And the gov't is denying permission in all but the most extreme circumstances.

[ValentineC]

> Vietnam, Thailand, Laos, Cambodia, Singapore are all doing fine without "locking people into their homes" and they're not islands.

Malaysia shut its border with Singapore in mid-March [1], and Singapore had what I'd consider a lockdown (most businesses closed, no social gatherings allowed) between 7 April to 19 June [2].

[1] https://www.todayonline.com/8days/eatanddrink/newsandopening...

[2] https://www.gov.sg/article/ending-circuit-breaker-phased-app...

[paganel]

Maybe there's a genetic component to this virus? Which is "verboten" to be discussed and analysed because of various reasons ("race is a social construct" and all that), but at some point one has to take this into consideration too. All due respect to Laos, but I don't see it as having the needed expert infrastructure in order to keep this virus under control as well as they have. Similar discussion for Thailand.

[harimau777]

Is it possible that they are all effectively islands? For example, it appears that Vietnam has miles of jungle between its major cities and neighboring countries. The same cannot be said for the US and Europe.

[thomasz]

Look at the demographics of these countries and compare them to the United States and Europe. Throw in less detailed reporting and less transparency. We’re dealing with a virus that overwhelmingly affects old, obese people. A country like Vietnam probably wouldn't even notice the pandemic wave that currently affects Europe and the United States.

[Izkata]

Thailand was doing fine, but as of this past week it broke past their quarantine.

[jdminhbg]

> Vietnam, Thailand, Laos, Cambodia

I guess perfect covid policy is contagious!

[GregarianChild]

The UK is no island?

[rualca]

> 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.

[ALittleLight]

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?

[Aeolun]

If the new strain is showing up in the UK now, and you haven’t had the borders closed for the past 2-4 weeks, there is little point to starting now (in terms of stopping it from getting to the US entirely anyway).

[disgruntledphd2]

And the new strain was first recorded on September 16th. It's laughable to think it hasn't spread further (although hopefully I'm wrong on this).

[SomeoneFromCA]

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?

[grey-area]

This variant is already widespread. It is very unlikely that it is not already spreading in the US.

[SomeoneFromCA]

It is very likely it is not spreading in US at all, otherwise it would have long been found. US also does fair amount of genomic surveillance, a new strain would not be unnoticed. Anyway, there must be proof that it is already spreading in US before, before keeping the borders open.

[matwood]

What I’ve seen discussed is that closing borders only works if it’s done totally and immediately. Otherwise, it just slows response and causes super spreader events like we saw early this year in the US.

[dehrmann]

The UK also teed-up a super spreader event with its rushed lockdown last week. India did the same thing back in ~April, and it ended up encouraging traveling and dispersed people across the country.

[bestnameever]

How does closing a border cause super spreader events?

[jtxx]

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?

[vixen99]

Britain has closed one trade door but opened a new one with the EU. Specifically they have reached a “zero tariff-zero quota deal”. Not ratified by the British Parliament but no one supposes this won't be done in the next few days before the final break with the EU on the 31st December.

[Izkata]

Yeah, from a bit over a year ago: https://www.businessinsider.com/trump-boris-johnson-brexit-t...

Though AFAIK it's kinda up in the air if Biden would go for the same thing.

[nostrademons]

Makes it harder for doctors to get supplies if all the borders are closed.

The UK has an upcoming COVID vaccine (the Astra-Zeneca/Oxford one) that may prove useful in the near future. Cut off the UK from the rest of the world and the rest of the world can't benefit from it.

Also, it's almost certain that the UK strain is in the US already, and the US is shit at dealing with pandemics once they're on our soil. Border closures only work if your test/trace/isolate institutions and compliance with social distancing is good enough to eradicate the virus from within your borders; they prevent reinfection in that case. The US has shown we're completely incapable of that, so it really doesn't matter.

[khuey]

Nobody is talking about closing borders to cargo.

[maxerickson]

Don't people and goods mostly travel separately?

[bredren]

Any new precedent for completely closing borders between developed nations for any reason is bad. Because it creates a “we did this before.”

Even if the scale or details of circumstance are different—such as Clinton’s pardoning of his brother in minimizing Trump’s choices.

Another reason is exceptions cause outrage. And there may be many instances of diplomatic or other government travel that needs to happen or happen in the slipstream of limited public travel.

[GregarianChild]

Could you elaborate by which moral principle you come to the conclusion that a vague slippery slope and even more vague outrage is more important than stopping a pandemic with hundreds of thousands of preventable deaths?

Most moral systems of my acquantance are based on a hierachy of values that puts saving human lives over just about anything.

[SomeoneFromCA]

Yea, slippery slope works both way, "we did not do this before", do not you think so? Remember that phrase about "the came after Jews, commies then after me"?

[soared]

FWIW, the US is now requiring negative covid tests from UK travelers - announced <24 hours after this comment was posted.

[jsnell]

Concentrating contact tracing resources on cases of the new variant, where they'll do more good than applied randomly on all Covid cases. Targeted local shutdowns in locales where the new variant appears to have gotten a foothold. Enhanced screening of people with recent ties to the high risk areas. All the stuff we did, or should have done, for Covid itself when that pandemic was in its early stages, but with focus on the new variant.

And sure, border closures too. They're late in that the new variant is probably present at some level in most of Europe. But the fewer cases you have to start with, the longer it'll stay contained at low levels. You might even be able to contain it entirely for a while. All the cases of B.1.1.7 in Denmark (0.4% of their sequencing) appear to be part of the same cluster. They should be able to manage that much better than if the variant was being constantly reintroduced by travelers.

For the UK specifically, they're doing a bunch of things differently for their Tier 4 level vs. Tier 3, which was introduced specifically in response to B.1.1.7. Are you suggesting that all of those measures should have been done everywhere anyway?

[m-ee]

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.

[jsnell]

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.

[bjornsing]

Agree 100%. I can’t see any alternative hypothesis that explains the UK sequencing data. Here’s a good graph from a seemingly reliable source: https://twitter.com/mugecevik/status/1341094871822680067?s=2...

What could explain that data other than increased transmissibility...?

[SomeoneFromCA]

What you consider a solid evidence?

[m-ee]

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.

[bjornsing]

The UK is a giant lab right now and the results of the experiment are in: https://twitter.com/mugecevik/status/1341094871822680067?s=2...

What could explain that data other than increased transmissibility?

[m-ee]

We’ll have to wait for actual science to come in to answer that. They’re just making inferences from epidemiology and gene sequences. None of this actually does anything to confirm their hypothesis.

[anonymouse008]

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 argument should be reduced in weight by some factor.

[mns]

Where is that 30% coming from?

[anonymouse008]

(Sorry GP) asked a personal opinion question and I offered one —

My gut feeling tells me this pandemic is suffering from a similar phenomenon in user interface latency. The research shows that if the latency is under a few hundred milliseconds, we believe that we are in control of the device and our cause and effect matters. However, if the latency is longer than some hundred millisecond mark, we think the device is under someone else’s control and that our cause has no effect on the system — though in fact, it is the direct cause.

To me, a pandemic kinda follows the same thought — if the disease isn’t having a direct, somewhat immediate effect (intuition says a couple days) to our actions, then it’s hard to issue broad, population level behavioral change that comes with direct costs to life and property - it’s just beyond the timeline for us to accept our actions (not wearing a mask or not distancing) as meaningful inputs to the pandemic system.

Personal opinion: I have no trouble wearing a mask even after having covid, but the current gov’t approach is 100% not the way I’d approach this issue. I would approach the mask mandates and business shutdowns this way only if the disease symptoms were severely impacting (so that’s my symptom description with walking a block) a large set of the population (so that’s the 30%, no age brackets needed) — and to me, that number is about 1 in 3. Now the counterpoint to this, is that if there is a tipping point in the proposed pandemic that once it gets to a certain spread, it becomes that 1 in 3 statistic - but I digress, you get the point I believe.

Edit: to tie this all together — there’s a lot of talk about increased sanctions from this new variant — but if the severity of symptoms do not change, only the transmissibility - it is a dangerous seed to sow amongst an already incredulous population.

[_cs2017_]

Much as I like TWiV, they often present incorrect viewpoints.

What you describe is one such example. TWiV suggests that anything short of convincing proof should be ignored. However, every bit of evidence updates our individual confidence to some extent. It's quite silly to draw an arbitrary line at a certain "quality" of evidence, and treat anything below that line as useless.

I suspect that in an effort to debunk unreasonable and sensational stories in the media, TWiV got carried away, and started to sweep the subtleties under the carpet.

It seems these days, it's really hard to find highly nuanced, carefully balanced, sources of information.

[SomeoneFromCA]

They are doing this not the first time. They are extremely aggressive against any hypothesis about the lab origin of the pandemic - and yet it is increasingly becomes acceptable by the mainstream media (BBC News tried independently verify some claims, but had literaly obstacles (physical) on their way,set by Chinese government). Racaniello (?) was big defender of GoF experimentaion on flu during 2012-2015 moratorium on this research; Osterholm AFAIR was against. TWIV are strange people, it turns out. UCSF podcasts are way more professional.

[yurlungur]

Yeah it really depends on how the numbers match up and how much risks you are willing to take given the degree of confidence in those numbers.

By current accounts the vaccines will still work against this variant. So the last thing you want to happen is for the virus to catch the vulnerables in the last moment before they are vaccinated and essentially renders the whole vaccination program ineffective.

Of course there's the debate of this whole pandemic about the harm to economy and people's lives etc. To me the majority of the damage has already been done and can't be undone. So I'd like the measures to be taken to end this ASAP, even if they are even stricter, and to mitigate the harm as much as possible. But I highly doubt that's what's going to happen. The actual policy effects may be neither here nor there.

[dehrmann]

> By current accounts the vaccines will still work against this variant

This isn't surprising because the variant hasn't really encountered the vaccines yet, so it's not an adaptation to them.

[tomxor]

> 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 attributed to a localised strain, efforts may be ineffectively focused on creating division between larger populations while removing the public's focus on the more evenly distributed measures we are already employing.

> You need to be able to act on the balance of probabilities, not wait for perfect information.

How about the probabilities between the two class of above cause? We seem to have an innate bias towards inferring 1:1 causal relationships which makes a strain feel like a simple and attractive explanation. This bias fails miserably in the face of dynamic systems where behavior cannot usually be attributed to a single variable... IANAV, but the spread of infectious disease is without a doubt a complex dynamic system from which a significant degree of unpredictable behavior must emerge.

To be honest this problem is not even particularly unique to this situation... The world is vast and complex, yet people usually want simple explanations - particularly for undesirable situations, something tangible to blame, a villain... The media continually exploit this desire and I cannot help but feel this is another example. A strain (real or not) makes for an excellent villain and story VS "chaos" which is extremely difficult for any reporter to spin an accessible narrative into.

[jsnell]

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.

[tomxor]

> how are we supposed to reason about something that vague? [...] I feel that anyone proposing that it's just emergent behavior should be at least a little bit more specific.

Sometimes it rains when we predicted it wouldn't, sometimes we get a full blown storm we didn't see coming... And that's using advanced techniques developed over decades on a continually available complex system for which there is demand to be able to predict on a daily basis. The very nature of these things is to have unpredictable behavior... That does not mean we necessarily do not understand the governing rules, but that the emergent behavior is not reducible into a simplified description.

> We have a simple explanation that's consistent with the known facts

It's simple and correlated, but highly suspect when a significant degree of chaos adds massive error bars to the significance of that correlation.

[rimliu]

Do you have any arguments behind your "No."s?

[jsnell]

I think I gave arguments for all of the "No"s except for the founder effect, which I'd just discussed in another message of this thread so it seemed redundant to do that again.

Just how much detail were you hoping for?

[tailspin2019]

> But which action?

In the UK, my view is the action to take was very clearly to dial back the public's expectations of having a 5 day "free for all" period of relaxation of our restrictions over Christmas.

This 5 day period, as originally planned, was going to lead to massive cross-country travel, plenty of it being completely unnecessary, with no doubt a lot of risk taking in the spirit of "it's Christmas" and an inevitable huge spike of cases and deaths in the weeks that followed.

I mean I love Christmas, but I can cope with not having 5 days of partying for just one year... *

As it happens, the government did take action to dial this back at the very last minute to allow just 1 day of relaxed rules (Christmas Day) rather than the week that was originally on the table. In my view they should have been planning for this right from the start and they unnecessarily screwed up a lot of people's Christmas plans by leaving it until the very last minute to make this change.

Now even if the variant turns out to be a "non issue" (and we still have rising numbers anyway), I think it's better that they took this action to further limit Christmas (as tough as it is for everyone) rather than take the "wait and see" or "hope for the best" approach, both of which seem to have been UK govnt strategies at one time or another during 2020.

* I'm being slightly flippant here. This is clearly a tough time for a lot of people, and many families will be spending Christmas apart and will find this very hard for all sorts of reasons.

[Ntrails]

> This is clearly a tough time for a lot of people, and many families will be spending Christmas apart and will find this very hard for all sorts of reasons.

Honestly, I think people are being incredibly relaxed about the fact that lockdown restrictions are incredibly expensive to the mental health of swathes of the population. I am not claiming that letting covid kill more people would be better - but I wish there was more acknowledgement of the fact that it is a trade off, and that the goal is getting society in the best shape out the other side of this. Not just the largest one.

[tailspin2019]

Good point. It's a really difficult balance to strike.

[wokwokwok]

Don’t you think this reflects a bias in the opposite direction?

Systems are dynamic and complex, but that doesn’t make them unknowable. If complex systems were impossible to model science wouldn’t be a thing.

Sure, the “new variant” narrative is an easy one to pick up because it’s superficially understandable; but what other complex interactions are resulting in a new strain becoming dominant over an existing one?

Do we just sit on our hands and go, well gee, better do nothing? Guess it’s just too hard to know what to do at this point...

There is a typical government fallacy that to be seen doing something is better than nothing, even when it’s the wrong thing... I get it, that’s bad.

...but this is a case where doing nothing has been a colossal disaster so far; and it’s extremely clear what the result of doing nothing different will be if the new variant hypothesis is correct.

So it’s a risk game. Is the cost * probability of A vs B a better choice?

You’re saying the probability is not known at this point because systems are complicated.

So what? It’s still clear to me that it’s very likely that something is happening, even if exactly what it is, is unclear.

You can still build a risk matrix taking that into account.

[tomxor]

> Systems are dynamic and complex, but that doesn’t make them unknowable. If complex systems were impossible to model science wouldn’t be a thing.

Not quite. It can makes them unpredictable, not unknowable... more specifically it can make them computationally irreducible which means we cannot find a simplified description of their behavior without having to compute every step, even when we understand the underlying rules that govern them. In fact we often cannot model them very well, an easy every day example is the weather, which we desperately want to know, but our methods are a significant compromise - that may seem like an unfair analogy but it really isn't, the atoms of society may be fewer but they have far more dimensions and more complex individual interactions.

It doesn't always apply, even within the same medium, it depends on the context e.g predicting weather requires some kind of simulation of fluid and pressure, yet in a different, more narrow context it's not necessary to attempt simulating the underlying mechanisms in any way or form, instead the overall behavior can be simplified to a set of descriptive equations (Bernoulli's).

It's funny because this does touch on a core issue for science - we still mostly hold this traditional view of it based on a history of going after the more easily obtainable nuggets of behavior with nice manageable reducible descriptions, but we have been unwittingly selective.

> what other complex interactions are resulting in a new strain becoming dominant over an existing one?

It does not need to result in a new _variant_, this right here is the misunderstanding. These two things can happen and not be related.

[wokwokwok]

There is a logical fallacy referred to as the “red herring”; you do not fool me, or anyone, by using it.

The side points you make are irrelevant to the point at hand; rather than hand waving address the point at hand:

Why is this an excuse to do nothing?

If not, what action do you propose instead?

How do you justify it?

Be specific.

[tomxor]

I did not suggest doing nothing, please see my original comment.

[ianai]

Personally I’ve taken it to changing optimization tactics. I’m going to use pseudo-statistical language to illustrate my point so please try to be charitable. In a usual model I’d base my actions on the mean outcome for a given set of choices. For covid, I think it’s smarter to choose to minimize the maximum, worst outcome. Ie assume the absolute worst and react in the harshest way. This new strain may prove to be nothing major, but personally I’ve decided it’s wise to be even more distanced from possible disease vectors. I suspect this may be a good strategy in a universe in which an already rare occurrence has been observed, in a larger sense.

[GavinMcG]

> removing the public's focus on the more evenly distributed measures we are already employing

How is this focus "removed" and why is there any reason to think that evenly distributed measures along with targeted ones would be a problem for the public?

[xg15]

What would be your advice we should do in the face of a system so complex it's impossible to understand or predict?

[SomeoneFromCA]

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.

[endgame]

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...

[SomeoneFromCA]

Not sure, just read about it somewhere.

[bonzini]

> 8 hours

That seems weird, to be kind. Source?

[SomeoneFromCA]

Appears to be unreliable info. Anyway, this not my point. My point is ADE, which make vaccination a terrible disaster. ADE is known to happen in some diseases , including SARS-1.

[m_mueller]

A lot of COVID discussions remind me of the history of Beri-Beri in Japan. Recommend everyone to read up on that one. Clinical purists who deny any validity to field data have cost many lifes going back longer than you think.

[inglor_cz]

Hi, can you recommend me a good book on that?

[m_mueller]

Good rundown: https://www.atlasobscura.com/articles/rice-disease-mystery-e...

"Takaki became navy surgeon general in 1885, yet other doctors attacked his theories and questioned his results. The sad result was that while the navy ate barley, the army ate only rice. According to Bay, the use of barley smacked of discredited traditional Japanese medicine to many Western-trained doctors. Plus, recruits were enticed into the army by promises of as much white rice as they could eat."

27 thousand deaths and a decree by the emperor later, and army doctors finally yielded to the evidence.

[inglor_cz]

Thank you!

This is actually not-too-dissimilar to the story of scurvy in European navies in a more distant time. It took a lot of lives and most attempts to alleviate it were based on the totally false theory of humors.

Doctors can be very resistant to change of paradigma. I wonder what is our scurvy or beri-beri; given how fat and diabetic the developed world has grown, maybe nutrition.

[mssundaram]

> 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!

What is the source for this? I've read another explanation: the overuse of pesticides like Paris Green, DDT (see pictures of kids literally sprayed with it on their clothing), and the use of "medical metals" to treat any kinds of diseases - giving mercury, arsenic etc. All of these (pesticides, metals) can weaken the bowels and allow the polio virus (which resides in the bowels) to enter into the spine where it then causes paralysis.

Maternal transfer of antibodies is one of my favorite immunity topics - it is far overlooked in usefulness lately, largely seen as impractical due to changes in lifestyle (not many mothers breastfeed)

Dear downvoters: what do you find does not contribute to conversation about sharing this theory?

[jpster]

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=...

[tailspin2019]

Thanks for this link, a lot of valuable insight in those 17 tweets!

I share your opinion.

[trebligdivad]

[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/...

[randomsearch]

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.

[disgruntledphd2]

I would really, really hope that they are using a good cross-validation strategy (as they'll definitely need it).

[randomsearch]

cross validation won't save you in this situation. it's a subtle point, but you can't say "omg this strain is increasing and it must therefore be more contagious" and then show that it is more contagious by showing it is increasing... this is counter-intuitive even to most scientists, in my experience. I remember when I learnt this during my PhD. I suspect many people high up in academia don't understand this point.

[randomsearch]

an observation that may help: as your stats at time t+1 are dependent on stats at time t, you cannot separate your validation set from the set you used to perform exploratory data analysis - they are highly interdependent.

[sigil]

They discuss these in that TWiV episode as well!

[skybrian]

It would be more accurate to say that we don't know yet whether it should be considered a new strain or not.

Any adjective like "strain" implies a binary distinction, but that doesn't mean you should round off "don't know" to false.

[didibus]

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.

[suifbwish]

Well if it isn’t a different strain then the vaccine should still work on it.