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Cont: 2019-nCoV / Corona virus Pt 3

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NYC added 3 thousand something New deaths from corona virus previously unreported.

CDC recently changed reporting criteria. Additionally, up to now COVID-19 cases were not required to be reported nationally but are generally publicly reporting though each state/locality may have different criteria.

From the CDC:

*As of April 14, 2020, CDC case counts and death counts include both confirmed and probable cases and deaths. This change was made to reflect an interim COVID-19 position statement issued by the Council for State and Territorial Epidemiologists on April 5, 2020. The position statement included a case definition and made COVID-19 a nationally notifiable disease.
....
State and local public health departments are now testing and publicly reporting their cases. In the event of a discrepancy between CDC cases and cases reported by state and local public health officials, data reported by states should be considered the most up to date.
 
Yes, and this has been happening in the UK as well, with people who die at home or in care homes not being registered as having died of COVID-19.

This has shown up on the "excess deaths" of this and last month.

This thing is killing far more people than the official figures state.

It is slightly more complex. The UK policy is that all suspected covid cases in a nursing home are tested. Once more than 3? (it may be 5) persons test positive in a nursing / care home further persons with the same symptoms are assumed to have covid and do not need testing. There has never been a requirement to test positive to diagnose covid nor to put covid on a death certificate. There is a clinical case definition that can be used. There is a two week delay in these cases coming through on national statistics but they are recorded.

The excess deaths are what is called excess attributable deaths. This is well described in flu. Following on flu and other pneumonias for a few weeks there is an increased rate of death from stroke and heart attack. Indeed the main cause of death from pneumonia is not the infection but the increased risk of heart attack or stroke in the next month. This does not mean that these deaths would ever have been attributed to covid even if tested. They would occur after apparent recovery from the initial infection and would be registered as stroke or heart attack.
 
The idea that Nadine Dorries is a minister still fills me with both wonder and dread. That said, it makes complete sense that if the lockdown is effective (and it appears to be starting to have an effect) then the best way to stop the NHS being overwhelmed is to keep measures in place until a vaccine is available.

It could be 18 months or more before that happens. That can't possibly be sustainable.

ETA: I see this has been addressed already. Ignore.
 
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It seems to me that the most effective, least onerous measures that will have to remain in place involve all of the following:
- widespread testing (with rapid turn-around times and full disclosure of results)
- vigorous contact tracing
- strict isolation of those found infected
- (maybe) isolation of all contacts (irrespective of test results, until we know a lot more about this devil).

I, for one, hope no one, anywhere, returns to the old normal. The only way we will drive SARS-COV-2 (and future nasties like it) to extinction includes a new normal that accepts mandatory strict isolation of those infected (to take one example).


There can be no maybe of isolation of all contacts. I think that and the testing was the main reason SK has been so successful.

I think the changes in the UK for the return to normality has to have a 100% commitment to testing with the will to enforce very good contact tracing and quarantining. And that’s where the state support still needs to be in place for employers and employees. Automatic same salary payment if you are forced to quarantine.

Personally I’d like to go a stage further if we find recovering does give you immunity and/or we get a vaccine. People can then be forced to confirm they are immune before they are allowed to buy tickets for the likes of football matches and concerts etc. Whilst those that aren’t aren’t allowed to. It means we slowly build back up to “life as normal” while keeping the risk to the health service and to individuals as low as possible.
 
crescent's and lomiller' tables merged



I don't see these as actually having any predictive value, but I find them useful as frames of reference. What happens if we keep up the growth rate we saw earlier? What happens if it drops a bit. Drops a lot?

None of that tells us which table columns are more or less likely, but coupled with news of actions being taken, we get an idea of how different courses of action can lead to very different death tolls, even if the change is not immediately apparent.


Updated again:

date|20% daily|15% daily|decreasing|actual
31-Mar| 1.2 4053| | | 4053
1-Apr| 1.2 4863 | | | 5102
2-Apr| 1.2 5836 | | | 6076
3-Apr| 1.2.... 7003 | | |7121
4-Apr| 1.2.... 8404| | |8451
RESET
5-Apr| 1.2.... 9616| 1.15.... 9616| 1.15.... 9616|9616
6-Apr| 1.2.... 11539| 1.15.... 11058| 1.15.... 11058|10871
7-Apr| 1.2.... 13847| 1.15.... 12717| 1.15.... 12717|12841
8-Apr| 1.2.... 16616| 1.15.... 14624| 1.15.... 14624|14811
9-Apr| 1.2.... 19939| 1.15.... 16818| 1.15.... 16818|16712
10-Apr| 1.2.... 23927| 1.15.... 19341| 1.1..... 18500|18747
11-Apr| 1.2.... 28713| 1.15.... 22242| 1.1..... 20350|20577
12-Apr| 1.2.... 34456| 1.15.... 25578| 1.1..... 22385|22105
13-Apr| 1.2.... 41347| 1.15.... 29415| 1.1..... 24623|23640
14-Apr| 1.2.... 49616| 1.15.... 33827| 1.1..... 27086|29825
15-Apr| 1.2.... 59639| 1.15.... 38902| 1.05.... 29794|32588
16-Apr| 1.2.... 71447| 1.15.... 44737| 1.05.... 31284|
17-Apr| 1.2.... 85737| 1.15.... 51448| 1.05.... 32848|
18-Apr| 1.2.... 102884| 1.15.... 59165| 1.05.... 34491|
19-Apr| 1.2.... 123462| 1.15.... 68039| 1.05.... 36215|
20-Apr| 1.2.... 148153| 1.15.... 78245| 1.05.... 38026|
21-Apr| 1.2.... 177785| 1.15.... 89982| 1.05.... 39928|

From a previous post:
Last year about 34,000 Americans died from the flu. If the current rate of growth keeps up with what we've had over the past two weeks, then we'll hit the 34,000 mark at about April 12.

The 2009 H1N1 pandemic is also often mentioned in comparison. That killed about 12,000 people in America. Again, if the current trajectory holds, we'll hit that around April 6.

To me, at least, hitting 34,000 would tell us that the current pandemic is much worse than the flu, because we've taken an "all hands on deck" approach, albeit later than many would have preferred. If we hit the same level of fatalities as influenza despite all that effort, that tells us something.

So we are close to matching last year's flu mortality, but in far less time than it took for the flu to get there. At least it was slower than what would have happened if the earlier growth rates held. This is despite of the social distancing and other actions being taken to slow or reduce the severity of the outbreak.

Yet an earlier post:

...The worst in the past 10 years was about 60,000 deaths during the 2017-2018 flu season. That might happen by the end of April.

Next is to argue that corona virus mostly only kills people who would have died anyway. There is some truth to that, but we won't really know those numbers until some time after this is over. Plus, that same argument also applies to most deaths from the flu.

We just might hit 60k mark by the end of the month, but I doubt it. I think we are in for a stretch of 1000+ deaths per day, but I think most days we'll be below 2000 per day.

Pretty hard to generalize even over just the U.S. due to variance between states - the actions they take and the ways they report. Running this out internationally would be much less precise. And time consuming...
 
The mystery to me is Japan and to a lesser degree South Korea.


Why SK? They immediately started rigorous testing and extensive contact tracing with then enforced quarantine as soon as they had any confirmed cases. They had the likes of drive thru’ testing stations before the rest of us and so on. They really do seem to have known what to do and when to do it.

I do wonder if it is because they have war gamed a lot of attacks by NK, such as a biological weapon attack so had plans they could immediately pull off the shelf.
 
I've been using the Worldmeters site. It is more of a live update total right now showing 33,931.

The Johns Hopkins site only updates once a day at 24:00 GMT. It does not yet seem to have taken yesterday's updated numbers from NY into the total.

Thanks.

I've been mostly using this NYT site which is also giving lower numbers and says it was updated recently. It also shows a lower number for "total cases".
 
How can I calculate R0 or R whatever, is it doable from the 1.3acres data?

https://coronavirus.1point3acres.com/en
marting described how in the following three posts:
#1912: definition
#1960: worked example
#1989: clarification

Ignoring the smoothing (marting used a sorta 7-day moving window), you need two data points; let's call them "today" and "change from yesterday".

So, from the 1.3acres site, for deaths "today" is +936. I can't immediately see how to find historical data (in this example, the number of deaths yesterday), but let's suppose it was +852.

R is then (936/852)^6 ≈1.78*.

Except, of course, this is deaths, so it's an estimate of R for ~three weeks ago.

You can do the same calculation, using changes in number of cases, to get an estimate for R for today.

Hope this helps.

*the number 6 is an estimate of the delay (in days) between initial infection and infection of others
 
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There can be no maybe of isolation of all contacts. I think that and the testing was the main reason SK has been so successful.

I think the changes in the UK for the return to normality has to have a 100% commitment to testing with the will to enforce very good contact tracing and quarantining. And that’s where the state support still needs to be in place for employers and employees. Automatic same salary payment if you are forced to quarantine.

Personally I’d like to go a stage further if we find recovering does give you immunity and/or we get a vaccine. People can then be forced to confirm they are immune before they are allowed to buy tickets for the likes of football matches and concerts etc. Whilst those that aren’t aren’t allowed to. It means we slowly build back up to “life as normal” while keeping the risk to the health service and to individuals as low as possible.

I don't argue that SK was not successful in controlling covid-19. However the initial UK government policy was the same as SK, though the technology to deliver the policy was different. Many people posting here seem to be under the misapprehension that the UK never attempted the same policy as SK, the UK did but it failed. Initially the UK attempted case finding (identifying any cases of covid-19), isolation of identified cases, and contact tracing. This was the containment phase.
https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(20)30128-4/fulltext
It was only later in early / mid March the UK stopped contact tracing as it was not effective in the UK and moved into the mitigation phase which is where we are now.

I do not know whether the policy was more effective in SK than UK because of technology used or because SK has a more homogenous and compliant population, or for other reasons. Those are all important questions, but we have to be careful in jumping to the conclusion that a policy that previously failed in the UK will work when it is repeated because it worked in another country.
 
UK lockdown extended for 'at least' three weeks

Lockdown restrictions in the UK will continue for "at least" another three weeks as it tackles the coronavirus outbreak, Dominic Raab has said.

The foreign secretary told the daily No 10 briefing that a review had concluded relaxing the measures now would risk harming public health and the economy.

"We still don't have the infection rate down as far as we need to," he said.

It comes as the UK recorded another 861 coronavirus deaths in hospital, taking the total to 13,729.
 
I'm a bit disappointed at death reports in Italy, UK, Germany and many others in Europe. Declines have been paltry and in some cases recent increases in consecutive days.

Not looking good when U of W puts out the next revision of their models including the USA model since they are basing it in significant part on Italy's results. How well the USA tracks these models won't be really known for at least another week and probably two.
 
There's hundreds of strains. Basically every sample is different. And they are mixed quite well, basically every country has infections from several different distant countries. There is nothing like 'this country has this strain', that is simply nonsense.

Your link doesn't really support the idea of it being nonsense at all - in fact, it looks suspiciously to me that what I said is dead right - the different strains have different results. The fact there are multiple strains isn't the point.

Playing the video seems to indicate different concentrations of the strains, and a lot of them match the more severe outbreaks.

This thing is killing far more people than the official figures state.

It's not just UK - how about this, from NJ?

https://www.nbcwashington.com/news/...sey-nursing-home-after-anonymous-tip/2275586/

The mystery to me is Japan and to a lesser degree South Korea.

Japan might be about to catch up, and SK is all about being prepared and hitting the sweet spot in response. Very smart.

I'm a bit disappointed at death reports in Italy, UK, Germany and many others in Europe. Declines have been paltry and in some cases recent increases in consecutive days.

Yeah, I've been watching and waiting for a decent reduction in numbers out of Europe and it's just not happening. I don't know whether their lockdowns aren't working, or if it's a time lag thing, but even the Euros will run out of Euros if it goes on for much longer.
 
Some interesting pieces overnight:

A Dutch study found that 3% of all people have developed Covid-19 antibodies: https://www.cnbc.com/2020/04/16/coronavirus-latest-update.html

That being the case, if we presume Netherlands' real case total is 510,000 as of right now, their mortality rate becomes 0.6%, but that's with 1200 people in serious or critical condition, so it will increase.

That looks like the benchmark at this stage, and matches reasonably well with South Korea's current 2% mortality rate, where they have only 50 in serious/critical.
_____________________________

A study from Harvard is emphasising the pollution factor, showing that a 1 millionth of a gram per cubic metre increase in PM2.5 causes a 15% increase in mortality: https://projects.iq.harvard.edu/covid-pm/home
_____________________________

Bangladesh looks like being another country where the disease is about to explode - a perfect storm of slums, poverty & pollution. With swathes of Africa looking to do much the same, we're about to find out how the disease impacts developing countries.
 
I've added the number of test results reported per day, and the percent positive of those test results, to the table. (Also added today's figures.)

The columns are:
date
total confirmed cases to that date
increase factor of total confirmed cases for the day (rounded to two decimal places)
new confirmed cases for the day
number of test results for the day
percentage of test results positive

"S" indicates Saturdays and Sundays, which might affect the timing of reporting and thus shift the numbers of cases between days.

"*" and "+" indicate a new all-time high for new confirmed cases on that day.

Code:
3/21     525   1.27    112   S
3/22     646   1.23    121   S
3/23     777   1.20    131
3/24    1159   1.49    382   4827    8% +  <--- business closures / lockdown
3/25    1838   1.59    679   6045   11% +
[COLOR="SeaGreen"]3/26    2417   1.32    579   3827   15%
3/27    3240   1.34    823   5750   14% +
3/28    4257   1.31   1017   5678   18% * S[/COLOR]
[COLOR="RoyalBlue"]3/29    4955   1.16    698   4017   17%   S
3/30    5752   1.16    797   3727   21%
3/31    6620   1.15    868   4142   21%
4/01    7738   1.17   1118   4803   23% +
4/02    8966   1.16   1228   4870   25% +
4/03   10402   1.16   1436   6354   23% *[/COLOR]
4/04   11736   1.13   1334   5838   23%   S
4/05   12500   1.07    764   3137   24%   S
[COLOR="DarkRed"]4/06   13837   1.11   1337   4992   27%
4/07   15202   1.10   1365   4915   28%
4/08   16790   1.10   1588   6167   26% +
4/09   18941   1.13   2151   7447   29% *
4/10   20974   1.11   2033   7414   27%	
4/11   22860   1.09   1886   6404   29%   S
4/12   25475   1.11   2615   7954   33% * S[/COLOR]
[COLOR="SeaGreen"]4/13   26867   1.05   1392   5319   26%  <--- 1.5 hr. change in data closeout time
4/14   28163   1.04   1296   4502   29%
4/15   29918   1.06   1755   5472   32%
4/16   32181   1.08   2263   8750   26%[/COLOR]

It's pretty clear that day to day differences in the timing of test result completion (or reporting) cause day to day variations in the numbers. For instance, it's pretty obvious that the anomalously low figure on 4/5 is the result of fewer test cycles completed that day. However, such delays can only shift "new" cases by a day or two. Longer-term trends such as the drop in rate from the "blue" period to the "red" period can't just be an artifact of such anomalies.

It also appears the figures from 4/14 and 4/15 were artificially low due to fewer (relative to prior days) test cycles being completed on those days, pushing those results forward to today's all time high number of test results and today's higher (but not all-time high) number of new cases. A similar weekday effect (with fewer results reported earlier in the week and more on Thursday and Friday) might have happened last week as well, but no such pattern extends to previous weeks.

On 3/24, the first date on which I could derive exact figures for new test results that day from the data available, testing in Massachusetts had just ramped up to an effective level, with over a dozen different labs reporting results, versus three labs two days earlier. (The 4,827 tests completed on the 24th were over 35% of the total number of MA tests completed, as of that date, since testing began.)

It's hard to pin down a reason for the low early percentage of positive tests, but the percentage itself speaks against there being a large backlog of symptomatic patients who hadn't yet been tested, thus artificially lowering the early case figures. The percent positive trended upward over time, but settled in the range of about one fourth to one third of all test results after the first week. More precautionary (as opposed to diagnostic) testing would tend to decrease the positive rate, while a dramatic proliferation of asymptomatic cases would tend to increase it. Different effects of that nature can't be separated out. But the lack of large (let alone sudden) changes in either of those stats in the past 3 weeks does not support any hypothesis that the apparent case rate is being artificially boosted by increased testing capturing a higher percentage of the actual cases, nor artificially suppressed by any drop-off in testing.
 
I don't argue that SK was not successful in controlling covid-19. However the initial UK government policy was the same as SK, though the technology to deliver the policy was different. Many people posting here seem to be under the misapprehension that the UK never attempted the same policy as SK, the UK did but it failed. Initially the UK attempted case finding (identifying any cases of covid-19), isolation of identified cases, and contact tracing. This was the containment phase.
https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(20)30128-4/fulltext
It was only later in early / mid March the UK stopped contact tracing as it was not effective in the UK and moved into the mitigation phase which is where we are now.

I do not know whether the policy was more effective in SK than UK because of technology used or because SK has a more homogenous and compliant population, or for other reasons. Those are all important questions, but we have to be careful in jumping to the conclusion that a policy that previously failed in the UK will work when it is repeated because it worked in another country.


You yourself have just posted the difference between the UK and SK and it’s even implied in the article you linked to but then you say there was no difference!

SK implemented a rigorous test, contact tracing and quarantine, the UK didn’t.
 
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