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Dec 30 2020 02:30pm
Quote (Bazi @ Dec 30 2020 02:19pm)
^thor123422
^black xistenz

I mean really the question is what are you going to do, genotype every covid case? How do you even properly isolate it to determine how community spread it is - similar to the March problem except a lot more difficult to genotype everyone vs just test everyone and we couldn’t even do the latter


Best to just assume it has community spread if you detect it at all. It's pretty unlikely you just happened to genotype an isolated case
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Dec 30 2020 03:01pm
Quote (Thor123422 @ Dec 30 2020 02:30pm)
Best to just assume it has community spread if you detect it at all. It's pretty unlikely you just happened to genotype an isolated case


I agree my point is what u gonna do differently with this assumption tho

the same mitigation measures apply, and every hospital in the country is bending dicks backwards trying to further increase capacity and staffing
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Dec 30 2020 03:03pm
I'm definitely in favor to slow down travels, or allowing it to vaccinated people.
Simple example: "Spanish Flu" when it mutated in US and started to kill young people and pregnant women. Exported by troops.
Scary.
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Dec 30 2020 04:20pm
Quote (Bazi @ Dec 30 2020 03:01pm)
I agree my point is what u gonna do differently with this assumption tho

the same mitigation measures apply, and every hospital in the country is bending dicks backwards trying to further increase capacity and staffing


Point is it changes nothing. All the same measures we haven't been willing to do are the things we should still be doing.

If there isn't a change to the spike protein the laymen can ignore it. It's only important to our sacrifices I mean heros like yourself
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Dec 30 2020 04:59pm
Quote (Thor123422 @ 30 Dec 2020 21:03)
I doubt there's "only a small fire". We haven't been sequencing every positive case of Covid, and if it really is spreading faster than previous strains it's almost certain that it's already spread.

I'm going off by the (limited) data we have from the UK. The new strain was already deteced back in September, it took until late November/early December until it really took off and replaced the older strains.

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Also, if you have 10k cases and you add another 5k, that doesn't actually change much. Exponential spread dosn't care much about doubling or halving the starting conditions. Remember that even if you start from 1/10th the initial value that's only about 3 doubling times, and that doubling time is only a few days. So by increasing it 50% you're only moving the timeline up like 36 hours.

You got your base variables wrong, leading you to vastly underestimate the difference this stuff makes.

The serial interval of covid is estimated based on observational data to be around 4-5 days. Since the generation time is unobservable for practical purposes, it's common practice in epidemiology to plug in the serial interval in its place. Furthermore, covid cases have, in practice, never doubled within just one generation except at the extreme onset when neither the people nor politics took any precautions. Data from March showed that people reduced their mobility and number of contacts voluntarily as soon as news about the epidemic situation broke into the mainstream; in Europe, it started about 2 weeks before lockdowns were being issued.

Data from this time, and also from the fall/winter wave in Europe, suggests that under practical conditions and the mildest of restrictions (no full sports stadiums, no live concerts, closed clubs and such), R_t never really exceeded a level of around 1.4, which, taken together with a serial interval of 4-5 days, produced a doubling time of 1 to 1.5 weeks at the point of peak growth. Accordingly, an increase in starting cases of 50% corresponds to moving the timeline up by something like 5 days, rather than just by 36 hours. And again, that's with the numbers from the point of peak growth; take any other point and the difference that 50% more starting cases make gets even larger than 5 days.

Allowing the number of "seed cases" of the new strain in the US to double or triple based on an influx from travellers from the UK would effectively get the country something like 2-4 weeks closer to the point of a collapsing healthcare system or, alternatively, far more restrictive and crushing lockdowns than the current ones. This difference is NOT negligible. Particularly when we keep in mind that hundreds of thousands of vaccinations are taking place every day and that we only need to get over the next 10-12 weeks until a change of seasons will bail us out. Every week we gain or lose counts right now.

This post was edited by Black XistenZ on Dec 30 2020 05:00pm
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Dec 30 2020 05:12pm
Quote (Bazi @ 30 Dec 2020 21:19)
I mean really the question is what are you going to do, genotype every covid case? Money isn’t infinite. How do you even properly isolate it to determine how community spread it is - similar to the March problem except a lot more difficult to genotype everyone vs just test everyone and we couldn’t even do the latter


My argument is quite simple:

  • The current measures which are limiting the pandemic to a United-States-wide R_t of around 1 to 1.1 would not be enough to prevent explosive exponential growth with an R_t of around 1.4 to 1.5 (assuming the same degree of countermeasures) once this new variant becomes dominant. The healthcare system is teetering on the brink of collapse as is, it cant withstand another significant surge of daily cases.
  • We can see the finish line on the horizon. Vaccinations are picking up pace, every single day, hundreds of thousands of vulnerable people leave the pool of susceptibles. Spring is only 8-12 more weeks away. Hence, it's a race against time between this new strain and the vaccination/seasons.
  • Since it would be an unmitigated disaster if the new strain becomes dominant before flu season ends/vaccinations have reached a meaningful share of the vulnerable groups, any low cost intervention to slow down the spread of this new variant should be used. Strict restrictions/quarantine rules for all arrivals from the UK are such a low cost intervention, and therefore very recommendable. Particularly since they can actually be enforced and do not depend on the compliance of the notoriously recalcitrant American people. ;)


This post was edited by Black XistenZ on Dec 30 2020 05:13pm
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Dec 30 2020 06:08pm
Quote (Thor123422 @ Dec 30 2020 04:20pm)
Point is it changes nothing. All the same measures we haven't been willing to do are the things we should still be doing.

If there isn't a change to the spike protein the laymen can ignore it


Ah we agree

Quote (Black XistenZ @ Dec 30 2020 05:12pm)
My argument is quite simple:

  • The current measures which are limiting the pandemic to a United-States-wide R_t of around 1 to 1.1 would not be enough to prevent explosive exponential growth with an R_t of around 1.4 to 1.5 (assuming the same degree of countermeasures) once this new variant becomes dominant. The healthcare system is teetering on the brink of collapse as is, it cant withstand another significant surge of daily cases.
  • We can see the finish line on the horizon. Vaccinations are picking up pace, every single day, hundreds of thousands of vulnerable people leave the pool of susceptibles. Spring is only 8-12 more weeks away. Hence, it's a race against time between this new strain and the vaccination/seasons.
  • Since it would be an unmitigated disaster if the new strain becomes dominant before flu season ends/vaccinations have reached a meaningful share of the vulnerable groups, any low cost intervention to slow down the spread of this new variant should be used. Strict restrictions/quarantine rules for all arrivals from the UK are such a low cost intervention, and therefore very recommendable. Particularly since they can actually be enforced and do not depend on the compliance of the notoriously recalcitrant American people. ;)


I think it’s already in the community so restricting European flights at this time is of minimal use. Unless the cases they have found in the states can be contact traced to UK contacts or exposure, I think Thor is right. The genotyping is very expensive and can’t be done in every positive case

Unfortunately I don’t see vaccinations being rolled out as fast as we would like. My grandparents are considered high risk for example and I’ve been having them call their PCP office weekly for vaccine updates. They have been told March -April.

This post was edited by Bazi on Dec 30 2020 06:11pm
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Dec 30 2020 06:54pm
Quote (Black XistenZ @ Dec 30 2020 04:59pm)
I'm going off by the (limited) data we have from the UK. The new strain was already deteced back in September, it took until late November/early December until it really took off and replaced the older strains.


You got your base variables wrong, leading you to vastly underestimate the difference this stuff makes.

The serial interval of covid is estimated based on observational data to be around 4-5 days. Since the generation time is unobservable for practical purposes, it's common practice in epidemiology to plug in the serial interval in its place. Furthermore, covid cases have, in practice, never doubled within just one generation except at the extreme onset when neither the people nor politics took any precautions. Data from March showed that people reduced their mobility and number of contacts voluntarily as soon as news about the epidemic situation broke into the mainstream; in Europe, it started about 2 weeks before lockdowns were being issued.

Data from this time, and also from the fall/winter wave in Europe, suggests that under practical conditions and the mildest of restrictions (no full sports stadiums, no live concerts, closed clubs and such), R_t never really exceeded a level of around 1.4, which, taken together with a serial interval of 4-5 days, produced a doubling time of 1 to 1.5 weeks at the point of peak growth. Accordingly, an increase in starting cases of 50% corresponds to moving the timeline up by something like 5 days, rather than just by 36 hours. And again, that's with the numbers from the point of peak growth; take any other point and the difference that 50% more starting cases make gets even larger than 5 days.

Allowing the number of "seed cases" of the new strain in the US to double or triple based on an influx from travellers from the UK would effectively get the country something like 2-4 weeks closer to the point of a collapsing healthcare system or, alternatively, far more restrictive and crushing lockdowns than the current ones. This difference is NOT negligible. Particularly when we keep in mind that hundreds of thousands of vaccinations are taking place every day and that we only need to get over the next 10-12 weeks until a change of seasons will bail us out. Every week we gain or lose counts right now.


I didn't mix up any variables. I was using crude estimates. Even so, your math says it buys us a week. It's a ridiculous assumption to make that you would double the seed cases when the strain has been around for months with international travel. It's been found as far away as Japan. Sorry bro, it's already prolific worldwide.

Also, we're already at hospital capacity here in the states a ton of places already. Basically making the point moot for this country at least.
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Dec 30 2020 10:44pm
Quote (Bazi @ 31 Dec 2020 01:08)
I think it’s already in the community so restricting European flights at this time is of minimal use. Unless the cases they have found in the states can be contact traced to UK contacts or exposure, I think Thor is right. The genotyping is very expensive and can’t be done in every positive case

To the best of my knowledge, virtually all international cases of the UK variant which were found in recent days were travellers who had recently entered NA/EU/AUS/JAP from the UK.

Quote (Thor123422 @ 31 Dec 2020 01:54)
It's a ridiculous assumption to make that you would double the seed cases when the strain has been around for months with international travel. It's been found as far away as Japan. Sorry bro, it's already prolific worldwide.

The UK variant did not become the predominant strain in London/SE England until late November/early December, so it hasnt been highly prevalent for thaaaat long. Since most international cases of this variant could (so far) be traced to recent travel from the UK, we cannot rule out that it is not super prolific yet and that imposing strict testing and quarantining protocols on travelers from the UK could make a significant difference.

For the record: I dont think this scenario is particularly likely, I also consider it more likely that the mutation is already more widespread. Nonetheless, the huge potential benefit of travel restrictions for the UK and their super low (social and economic) cost still make it a recommendable approach. If a public health measure creates costs of X (with X being comparatively low), has say a probability of 90% of providing no benefit, and a 10% probability of preventing 200*X of damage (in lives and economic activity), then that's a worthwhile strategy.

This post was edited by Black XistenZ on Dec 30 2020 10:45pm
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