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I have a question about numbers. Turkey's death figures have been consistently at 70 something for weeks. Yesterday that shifted up to 80 something, which I predict will be the case for a few weeks. What is the probability of those numbers actually being accurate?
 
I have a question about numbers. Turkey's death figures have been consistently at 70 something for weeks. Yesterday that shifted up to 80 something, which I predict will be the case for a few weeks. What is the probability of those numbers actually being accurate?

It's an impossible question to answer but if you look at cases and deaths weekly they kind of look flatish with maybe a little rise with natural variation.

6EA1B84B-1239-4AD5-A8A8-CAB28574C288.jpeg
 
I'd need to study their regional picture and have knowledge that I am unlikely to obtain before I could comment properly on Turkeys figures. Because, for example, some regions getting worse while some get better is one of the situations that could result in a fairly flat graph. I'd also want to look at the timing and scale of any restrictions they brought in, and also ideally hospital data.

If they have overall excess mortality statistics that are credible then those are what I would use in future years to judge how bad the pandemic got there.
 
N439K variant found to evade antibody immunity.

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity
Thomson et al

Abstract: SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics. Herein we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is the most divergent region of S, and provide epidemiological, clinical, and molecular characterization of a prevalent RBM variant, N439K. We demonstrate that N439K S protein has enhanced binding affinity to the hACE2 receptor, and that N439K virus has similar clinical outcomes and in vitro replication fitness as compared to wild-type. We observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, including one in clinical trials, as well as from polyclonal sera from a sizeable fraction of persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
doi: 10.1101/2020.11.04.355842

More details in thread here with commentary on DK variation in mink:
 
Certainly get the feeling it's out of control // and chances of a vaccine soon are getting slimmer

I entirely agree with you on the first bit (for now, at least!)

But as for the second, you'd need different reasons to be convincing with vaccine-pessimism, IMO :(

(Not that I'm all that optimistic about vaccine-timing myself :(, but make the right connections about why, I'd advocate ...... )

(..... apologies though if I've misunderstood your post above! :oops: )
 
Pfizer have just announced 90% effectiveness for their vaccine — better than expected
90% tantalisingly close to true herd immunity when factoring in refuseniks and the contraindicated. No information on immuno-effectivity wrt N439K.
 
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Pfizer have just announced 90% effectiveness for their vaccine — better than expected
Yup, big news.... here's hoping. I think the path to getting sufficient people vaccinated and seeing how it really, really works 'in the wild' is not going to be as quick as people hope.
 
90% tantalisingly close to true herd immunity when factoring in refuseniks and the contraindicated. No information on immuno-effectivity wrt N439K.

Assuming mass vaccination. I believe the idea here was to vaccinate only older people... I suppose it depends what the costs are.
 
Vaccines are less effective as we age. The elderly are protected by having younger generations vaccinated.

Maybe so, but that was still the plan. Kate Bingham quoted in the ft, 4th Oct:

https://www.ft.com/content/d2e00128-7889-4d5d-84a3-43e51355a751
“People keep talking about ‘time to vaccinate the whole population’, but that is misguided,” she said. “There’s going to be no vaccination of people under 18. It’s an adult-only vaccine, for people over 50, focusing on health workers and care home workers and the vulnerable.”

Article below unless the ft does it’s link fail thing.

 
Maybe so, but that was still the plan.
I wouldn't dispute that. But it remains a fact that duration of vaccine protection for the older cohorts is typically observed to be shorter and they gain a great degree of benefit from younger cohorts being vaccinated. The entire population can't be vaccinated overnight so there has to be a rolling plan. Roughly, vaccinate the elderly first then work your way down the age cohorts before returning to the elderly for boosters.
 
Can we keep the vaccine discussion to, err, the vaccine thread, to avoid duplicating everything? :)

 
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Vaccines are less effective as we age. The elderly are protected by having younger generations vaccinated.
That's really interesting, wonder how one then works out best cohorts to vaccinate. Face-to-
face NHS and care workers a priority perhaps?
 
Lack of action at the centre and in some states...

Pandemic on course to overwhelm U.S. health system before Biden takes office

The country’s health care system is already buckling under the load of the resurgent outbreak that’s approaching 10 million cases nationwide.

The University of Washington’s Institute for Health Metrics and Evaluation predicts 370,000 Americans will be dead by Inauguration Day, exactly one year after the first U.S. case of Covid-19 was reported. Nearly 238,000 have already died.

Some governors in the Northeast, which was hit hard early in the pandemic, are imposing new restrictions. In the last week, Connecticut, Massachusetts and Rhode Island activated nightly stay-at-home orders and ordered businesses to close by 10 p.m. And Maine Democratic Gov. Janet Mills on Thursday ordered everyone to wear a mask in public, even if they can maintain social distance.

But in the Dakotas and other states where the virus is raging, governors are resisting calls from health experts to mandate masks and restrict gatherings. On Sunday morning, South Dakota Republican Gov. Kristi Noem incorrectly attributed her state's huge surge in cases to an increase in testing and praised Trump's approach of giving her the "flexibility to do the right thing." The state has no mask mandate.

Minnesota officials said last week that ICU beds in the Twin Cities metro area were 98 percent full, and in El Paso, Texas, the county morgue bought another refrigerated trailer to deal with the swelling body count.

 
Given the all consuming nature of the US election its hardly surprising that the pandemic has been pushed down the agenda. When that happens its only natural that people just revert to normal behaviour.

I'm glad we don't have a general election coming up though Brexit could easily do the same.
 
I dont see the current US viral surge as having much to do with recent events and mood music though, state inaction by certain governors has been one of the main dynamics in play there all the way through this pandemic.
 
I dont see the current US viral surge as having much to do with recent events and mood music though, state inaction by certain governors has been one of the main dynamics in play there all the way through this pandemic.


I doubt this planning meeting would have much effect, it looks like even this token effort was too much for Pence. Plus trump anti mask stuff, things are worse than they needed to be

Pence absent from Covid-19 planning calls for more than a month

 
I have a question about numbers. Turkey's death figures have been consistently at 70 something for weeks. Yesterday that shifted up to 80 something, which I predict will be the case for a few weeks. What is the probability of those numbers actually being accurate?

Although outbreaks rarely show an extended 'plateau' phase, it might be what you'd observe at a large scale if multiple smaller outbreaks were happening, each on a different time scale.
 
From November 23rd Spain will require a of covid test within 72hours of arriving for all passengers from high risk countries
 
JPMorgan have a take on the European situation. Worth a read, if you're interested in these things. I'll break it over two posts.

COVID-19: Will Europe reopen for Christmas?


By David Mackie

Click here for the full Note and disclaimers

  • Reproduction numbers lower than in first wave due to masks, increased hygiene, and test, trace, and isolate
  • Thus, decline in mobility needed to push reproduction numbers back below one is less than in the first wave
  • Many countries have already seen mobility fall enough
  • Economic and social activity to resume in December
Europe’s COVID-19 second wave has led to the re-imposition of broad-based restrictions across the region to limit the rapid increase in new infections and the steady buildup of pressure on healthcare systems. Most of these lockdowns are intended to be time-limited, although countries will likely keep some more modest restrictions in place for a while longer after the end of the broader-based lockdowns (Table 1). For example, in the UK, the second lockdown is scheduled to end on December 2, to be followed by regional measures if needed. If the lags are similar to the first wave, then new infections and hospitalizations should have clearly peaked across the region by early December (Table 2). Given the huge amount of economic and social activity that takes place in December, it is critical to know whether the current timetables will be kept to.

Table 1: Second wave lockdowns in Europe
Start date
Intended end date
Germany​
2-Nov-20​
30-Nov-20​
France​
30-Oct-20​
1-Dec-20​
Italy​
26-Oct-20​
22-Nov-20​
Spain​
26-Oct-20​
Not decided yet​
Netherlands​
23-Oct-20​
19-Nov-20​
Belgium​
2-Nov-20​
13-Dec-20​
Ireland​
20-Oct-20​
Not decided yet​
Slovakia​
15-Oct-20​
Not decided yet​
UK​
5-Nov-20​
2-Dec-20​
Source: J.P. Morgan
Table 2: Lags in the first infection wave
Date of lockdown
Days to peak in infections
Days to peak in hospitalizations
Days to peak in deaths
Germany​
13-Mar-2020​
21​
21​
40​
France​
17-Mar-2020​
16​
17​
30​
Italy​
11-Mar-2020​
10​
24​
16​
Spain​
14-Mar-2020​
11​
6​
20​
UK​
23-Mar-2020​
21​
17​
26​
Average​
16​
17​
26​
Source: J.P. Morgan All calculations are days from the date of lockdown.
Our judgement is that they will be. Mobility has already moved down a lot across Europe and new infections should peak in the next couple of weeks. Lockdowns should be eased by early December, which will allow a strong bounce in economic and social activity ahead of the holiday season. Whether or not there is another European lockdown during the early months of next year remains to be seen, and much depends on developments in the vaccine candidates. But, for now, enough has been done to turn infections around, in our view. However, in contrast to Europe, there has been very little decline in mobility in the US, despite a wave of infection that looks almost as severe as Europe’s (Figures 1 and 2).

1605175940065.png
 
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The key role of mobility
We know for sure that if the average number of daily contacts between individuals declines by enough, then new COVID-19 infections can be brought down to manageable levels. We saw this clearly in the first infection wave in the spring when government restrictions, and increased caution on the part of individuals, caused a sharp decline in daily contacts that turned the tide on new infections. The lag between the imposition of lockdowns and new infections averaged around 16 days.

The theory behind this is fairly straightforward. The reproduction number – which determines whether new infections are rising, stable, or falling – is driven by three things. First, the average number of daily contacts between individuals in the population. Second, the number of days during which infected individuals can infect others. And third, the probability of infection when in contact with an infectious individual. The critical role of daily contacts – which we proxy by Google mobility data – can be seen clearly in the first COVID-19 infection wave, when a very sharp decline in Google mobility corresponded with a very dramatic decline in reproduction numbers across countries. (We use the retail and recreation component of the Google data as our proxy for daily contacts.)

Back in the spring, the initial decline in reproduction numbers was caused by the collapse in mobility. As time has passed, other developments have also weighed on reproduction numbers, such as mask wearing, increased hygiene, and test, trace, and isolate regimes. These developments allowed mobility to gradually recover over the late spring and early summer. Without these other developments, infection control would have required mobility to remain at the very depressed levels seen in the spring. Instead, there is an equilibrium level of mobility that, given all the other influences on the reproduction number, would keep the reproduction number at one or below. Clearly, European mobility exceeded that equilibrium during the summer, setting the scene for the second wave of infection.

Given this framework, the key question to be answered is how far mobility needs to decline to push the reproduction numbers across Europe back below one. Table 3 provides a way of answering that question for some of the Western European countries and the US. Due to the massive increase in testing in the first infection wave, we use hospitalizations to estimate the reproduction numbers rather than new infections. Unfortunately, this excludes France and Italy from the analysis due to insufficient data.

Table 3: Mobility and Reproduction numbers
Decline in mobility in first wave (%-pt)
Decline in R in first wave
Impact on R of a 10%-pt decline in mobility
Latest peak in R
Recent decline in mobility (%-pt)
Implied latest reading for R
Germany​
-63​
-2.2​
-0.35​
1.49​
-27​
0.55​
Spain​
-92​
-2.9​
-0.32​
1.15​
-25​
0.35​
UK​
-81​
-3.4​
-0.42​
1.36​
-20​
0.52​
US​
-49​
-1.7​
-0.35​
1.30​
-4​
1.16​
Source: J.P. Morgan. 'R' refers to the reproduction number and is based on hospitalization data.
The first three columns assess the impact on the reproduction numbers of the moves in Google mobility in the first infection wave. On average in the first wave, a 10%-pt move down in the Google mobility data depressed the reproduction number by 0.36pt. Meanwhile, the final three columns assess how much mobility needs to decline in the current infection wave to get the reproduction numbers back below one. It is important to recognize that reproduction numbers at the start of the second wave were lower than at the start of the first, due to a combination of mask wearing, increased hygiene, test, trace, and isolate regimes, increased self-shielding by the elderly, and some buildup of immunity in the population, so that mobility doesn’t have to fall as much as it did in the spring to gain control over the virus.

Our calculations suggest that mobility has already fallen enough in Germany, Spain, and the UK to get the reproduction numbers back below one. Interestingly all three countries have seen similar-sized declines in mobility. Given that the Google mobility data do not yet fully reflect the impact of the latest restrictions (they go through November 6), further falls in mobility are likely, which will put even more downward pressure on the reproduction numbers. Due to lags in the publication of the Google mobility data, it will take another week or so to see the full impact of the current measures. With reproduction numbers back below one, new infections across Europe should peak very soon.

In contrast to Western Europe, the reproduction number in the US appears still to be above one, and mobility has hardly declined at all in recent weeks. This suggests that new infections will continue to climb, with hospitalization pressure increasing and deaths rising further. It looks like a decline in mobility in the US is needed, which would have to come from either government restrictions or a shift in individual behavior. On the basis of our analysis, US mobility needs to fall by a further 10%-pts to push the reproduction number down to just below one. This cumulative move of 14%-pts would be around 29% of the decline seen in the spring. By comparison, the falls in mobility already seen as a proportion of the first wave move are 43% in Germany, 27% in Spain and 25% in the UK.

Evidence from the early movers
Our confidence in the view that Europe will ease lockdowns by early December rests partly on the theoretical framework outlined above, and partly on the experience of the early movers. Not everyone introduced restrictions at the same time and it is evident that some of the countries and regions that moved first have already seen a turn in new infections. On a regional basis, early moves were made in Liverpool and Manchester (UK), in Marseilles and Paris (France), and in Madrid (Spain). Among these, infections have already turned down in Liverpool, Manchester, and Madrid. In terms of countries, early movers such as Ireland, the Netherlands, and Slovakia have also seen new infections turn lower (Figure 3).

View attachment 238503

These experiences suggest that the restrictions put in place across Europe in recent weeks will be sufficient to reassert control over the virus, at least for now. Unless a vaccine is rolled out relatively quickly, further lockdowns may be needed next spring. In contrast to developments in Europe, it does not look like mobility has fallen by enough in the US to regain control of the epidemic. We are very much in an exponential phase in the US: daily new COVID-19 hospitalizations are already at 59% of the spring peak and the number of new hospitalizations is doubling every two to three weeks.
 
New regulations in Turkey. Over 65s are on curfew in major cities (4pm to 8am although this varies by region). Smoking in public completely banned. Step by step edging back to more restrictions. Poor over 65s. Funny thing is, they don't ban visiting each other in homes...
 
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