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Cont: 2019-nCoV / Corona virus Pt 3

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Fast Eddie B said:
After several days of zero new daily deaths, I noticed that China is showing 1,290 new deaths today. Probably an anomaly due to less than daily reporting of their numbers, but still an interesting data point.
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These are older deaths not previously attributed to COVID-19 that were reclassified. This doesn't reflect people who have died in the last day.
 
As to the German numbers - everybody know how good we are at following orders, and everybody who met us knows how much social distancing we practice voluntarily compared to Spain, Italy and France... ;)
 
Fast Eddie B said:
After several days of zero new daily deaths, I noticed that China is showing 1,290 new deaths today. Probably an anomaly due to less than daily reporting of their numbers, but still an interesting data point.
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So the China claims is from correcting presumably overwhelmed data from months ago when they were in the thick of things. Sure.

More likely they have known about this for quite a while but now it's politically acceptable to reveal it as the US has recently been saying that deaths in nursing homes, a pretty big part of COVID deaths, weren't counted in some places as a matter of policy. Also NY didn't report suspected COVID deaths when some 200/day were dying at home and never hospitalized.

Not surprising given that the disease often causes a person to descend rapidly in a few hours.

I wonder if some of this is why Italy hasn't been seeing the decrease in daily deaths that were projected over the last week.
 
Apologies if this has already been posted, I have been following the Covid 19 politics rather than medical thread;

http://inproportion2.talkigy.com/indoor_transmission.html

"Sharing indoor space is a major SARS-CoV-2 infection risk. All identified outbreaks of three or more cases occurred in an indoor environment

By early April 2020, the COVID-19 pandemic had infected nearly one million people and had spread to nearly all countries worldwide. It is essential to understand where and how SARS-CoV-2 is transmitted.

Case reports from 320 municipalities in China were studied, not including Hubei province, between 4 January and 11 February 2020. All outbreaks involving three or more cases were studied

Three hundred and eighteen outbreaks with three or more cases were identified,involving 1245 confirmed cases in 120 prefectural cities."
 
Maybe I won't get ninja'd this time ...

Myriad said:
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.
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The % of tests which came back +ve is a good addition to the data.

However, there may still be a strong selection effect here ... I read somewhere that you need ~20% (or fewer) of your tests to be +ve before you can say you're likely sampling the population well enough.

I think it likely that there are considerable selection effects showing in the data. For example, the incidence of covid-19 is surely not random throughout all who are (or were) in MA at the time; the population is not homogeneous. There are likely several kinds of inhomogeneity, not only geographic. So as the testing samples more or less from one or another sub-population, so the changes in numbers of confirmed cases changes too.

The pattern you're seeing in the data may be only indirectly related to changes happening the spread of covid-19.

Another factor that may be at play: test sensitivity. No test is perfect, there will always be false positives and false negatives. It seems very unlikely that the %-ages of each, for each of the (many?) types of tests used over this period are the same*. Hence the patterns in the data may, to some extent, reflect differences in the distributions of test sensitivity throughout the period.

*while strange patterns may emerge even if they are, the fact that the reported %-age of +ves is ~flat suggests this effect would be minimal
 
Most of the top runners now seem to have hit a plateau in daily cases, rather than peaking. The length of the plateaux is the next big question. What was that popular article a few years back about if you don't know where you are in a process you're probably in the middle?
 
sphenisc said:
Most of the top runners now seem to have hit a plateau in daily cases, rather than peaking. The length of the plateaux is the next big question. What was that popular article a few years back about if you don't know where you are in a process you're probably in the middle?
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One other (at least for the US): are there any "late comer" states which will put on a burst of speed and overtake the current front runners?

Or: will Texas become the new New York (and if so, when)?
 
Darat said:
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.
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No, it is from previous experience with SARS and MERS
 
angrysoba said:
I’m guessing your theory that we will be talking about this as much as we talk about finger spinners in six months is looking on shaky ground right now.
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No, I still think it's likely that it will be very largely under control in the US by then. I also think there will be much fewer deaths than have been predicted by many. Of course it's now apparent we'll be talking about it for a long time, but i think it will be talking about the economic fallout, the response, future possible pandemics, etc.

Now, any answer to the question you quoted? The Johns Hopkins site still doesn't seem to be showing 30K deaths in the US. Am I looking in the wrong place?
 
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Darat said:
Policy is not the same as doing.

SK: we plan on doing a,b,c to get to X
SK: did a,b,c
SK: got to X

UK: we plan on doing a,b,c to get to X
UK: did a,c
UK: didn’t get to X

You can’t say the plan didn’t work in the UK because the plan wasn’t followed.
So again what I said is correct regardless of the inability of our government to carry it out.
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Sorry you are wrong.

That you want it so does not make it so. You are expected to provide evidence to support your case please provide evidence that the UK did not follow a policy of contact tracing.

This is an example of trans-national contact tracing during the containment phase in Europe of the covid-19 pandemic.
https://www.bbc.co.uk/news/uk-51442314

The UK (and other European countries) did follow the plan. The plan is set out in ECDC pandemic plan*, at scenario 1 and 2 containment is the main plank of the policy with contact tracing and isolation. Scenario 3 which the UK entered mid March is the mitigation phase when contact tracing ceases as it has been ineffective. Arguably it may have worked better for Germany than the rest of Europe, but it was not a success. This was not a unique failure to the UK but all European countries. When a policy failed in many countries and was a success in only one before repeating the previously failed policy it is sensible to enquire why it worked in one place and failed in many.

*https://www.ecdc.europa.eu/sites/de...9-increase-transmission-globally-COVID-19.pdf
https://www.gov.scot/publications/coronavirus-how-contact-tracing-works/
https://publichealthmatters.blog.gov.uk/2020/02/13/expert-interview-what-is-contact-tracing/
 
Dr.Sid said:
Big difference is also when those policies start. What's easy with 10 people per day, cannot be possible with 1000 people per day.
I don't know specific timeline in UK, but in local news UK was reported from the start as 'let it run wild' country, and only later they were supposed to make their mind.
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This is absolutely untrue. Up until mid March every identified case in the UK was contact traced. E.g. a report of contact tracing from 12/03/20
https://www.shb.scot.nhs.uk/board/news/documents/20200312-ConfirmedCases.pdf
 
JeanTate said:
The % of tests which came back +ve is a good addition to the data.
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This statistic can give a clue as to which countries are trying to get ahead of the spread (unless a country is testing randomly or trying to test everyone as Iceland is). Countries in which less than 10 percent of tests are positive tend to have the lowest fatality rates. Raw counts of people tested can be misleading; for example, South Korea does not have an especially high percentage of people tested because the spread there is slow enough that they haven't had to test a lot of people for the past few weeks. Unfortunately, it means that the US has to double its testing capacity before anyone can think about lessening restrictions.
 
Planigale said:
Sorry you are wrong.

That you want it so does not make it so. You are expected to provide evidence to support your case please provide evidence that the UK did not follow a policy of contact tracing.

This is an example of trans-national contact tracing during the containment phase in Europe of the covid-19 pandemic.
https://www.bbc.co.uk/news/uk-51442314

The UK (and other European countries) did follow the plan. The plan is set out in ECDC pandemic plan*, at scenario 1 and 2 containment is the main plank of the policy with contact tracing and isolation. Scenario 3 which the UK entered mid March is the mitigation phase when contact tracing ceases as it has been ineffective. Arguably it may have worked better for Germany than the rest of Europe, but it was not a success. This was not a unique failure to the UK but all European countries. When a policy failed in many countries and was a success in only one before repeating the previously failed policy it is sensible to enquire why it worked in one place and failed in many.

*https://www.ecdc.europa.eu/sites/de...9-increase-transmission-globally-COVID-19.pdf
https://www.gov.scot/publications/coronavirus-how-contact-tracing-works/
https://publichealthmatters.blog.gov.uk/2020/02/13/expert-interview-what-is-contact-tracing/
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The article I linked to provides the details of the failings of the government not to follow an effective plan.

You need to keep your partisan political views out of these discussions.
 
Darat said:
The article I linked to provides the details of the failings of the government not to follow an effective plan.

You need to keep your partisan political views out of these discussions.
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What political views? I have stuck strictly to the facts and evidenced the facts. I have made no political points. Disagreeing with you is not political. I think you are projecting; you clearly do have a political agenda, when someone disagrees with you, you consider that to be political. It may simply be because you are wrong.

ETA To be helpful could you quote the bit in the article or clearly point to the bit in the article so I can address the issue, or admit being wrong.
 
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