Credible Covid 19 Sources in SA

Geoff.D

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One of the issues we have about Covid 19 in SA has been to try and find sources of information that are not influenced by all sorts of Agendas and political interference.
One such site is the NICD site:


Here at least, the facts are presented clinically and objectively.

The first Weekly summary report on Covid 19 can be found here: https://www.nicd.ac.za/wp-content/u...on-TB-testing-in-South-Africa-10-May-2020.pdf

There are also daily reports available and reports of how Covid 19 is impacting on other disease management such as TB

The Conclusions in this report are disturbing:

The COVID-19 level 5 restrictions has resulted in a ~ 48% average weekly decrease in TB Xpert testing volumes while, the number of TB positive declined by 33%. The relative difference resulted in a higher weekly positivity rate during the lockdown period. These unintended consequences will have a negative impact on efforts to control TB which remains the leading infectious disease cause of death in South Africa currently[7].
The dramatic declines in tests conducted for TB investigations are not explained by reduced testing capacity nor health service availability for TB as these were available and operational during the intervention period. The primary factor is restrictions introduced limiting movement and thereby access to services. During the lockdown period availability of public transport was
severely limited. Individual motivation to seek care is another factor in the face of the restrictions and it is possible that only those more with advanced TB would seek care. This may explain the increase in positivity during the lockdown period.
The implications of undiagnosed TB are serious and will compromise past successes in reducing the burden and mortality associated with TB and DR-TB. As both TB and COVID-19 share similar clinical presentation (cough, fever, shortness of breath etc.) and are transmitted through respiratory droplets and aerosols, a combined strategy needs to be applied. This would utilise resources effectively while providing both short term and long term benefits.

Another is a link to the Modelling Consortium released last night:


Now, IF the NCCC was focussed on fighting this "war" then they would be taking far more cognisance of things like this than worrying about the sale of underpants and flip flops.
 
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Gordon_R

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Thanks. I wanted to start a thread like this a month ago, but the data were simply not available.

Caveat: All the NCID data are subject to the same uncertainties and testing delays.

Edit: Interesting profile of the experts behind that model:
 
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Oghmazan

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It seems to me that this news is already boring, so people do not take it as much as they did just a few weeks ago.
Honestly, I think that everything already wants peace and just to go back to normal life.
 

Geoff.D

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More Presentations have been added to the NICD site after this mornings round of televised presentations. Links are not available to all the presentations delivered this morning, or, I have not been able to find them. The really good ones are not available but the extreme fear-mongering ones are.

See these links for the details:


 

Geoff.D

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While this link is NOT to a data source, it is absolutely essential reading for anyone really interested in understanding what is going on with Covid-19.

Some will say it is all fake news because it takes on the hype generators and their way out theories but so be it.



The whole article is important. It is very difficult to try summarise it. Below is the extract and one paragraph that says it all for me.

Is it possible that governments have shut down countries, effectively pushing nations into economic crisis, on the basis of flawed Covid-19 data analysis? This concern is growing. And, as more data becomes available, the statistics are pointing to the possibility that lockdowns have been, at best, misguided.
Isaac Ben-Israel, a prominent mathematician, chairman of Israel’s Space Agency, and a former general, caused controversy when he publicised his theory that Covid-19 peaks after about 40 days and declines to almost zero after 70 days. The “hysteria” he sees around him is “as contagious as biological diseases”, he told The Times of Israel. Ben-Israel’s ideas find resonance in a South African group that has been established to look at the human and economic costs of Covid-19 in South Africa.
Called PANDA, short for Pandemics Data & Analysis, this group is a collective of leading actuaries, economists, mathematicians, medical professionals, lawyers and businesspeople working to bring more data and analytics to the decision-making table. In this fascinating article, they highlight why they are “left wondering why anybody in their right minds would be talking up a story that involves anything more than 10,000 deaths for South Africa”. Let’s hope government policymakers here, and elsewhere, are paying attention. – Jackie Cameron
The projections entailed by the SEIR models seem to us to be cases of outlandish academic scientism, devoid of satisfactory explanation and transparency. They are causing fear and driving policymakers to implement measures that we have shown are hugely damaging to South African lives and our social fabric. Their acolytes need to explain how their models account for these observations. If they cannot, then our policymakers owe it to the nation to recruit new advisors.
 

Gordon_R

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While this link is NOT to a data source, it is absolutely essential reading for anyone really interested in understanding what is going on with Covid-19.

Some will say it is all fake news because it takes on the hype generators and their way out theories but so be it.



The whole article is important. It is very difficult to try summarise it. Below is the extract and one paragraph that says it all for me.
The PANDA hypothesis is unproven, but the article has a lengthy table of the things that the SIR models get wrong, that need alternative explanations. Sorry for formatting:
Conventional model prediction Outcome to date PANDA hypothesis prediction Outcome to date
Deaths exponentiate for months Not observed anywhere Deaths exponentiate only for days Observed everywhere
Daily deaths decline as herd immunity of ~60% approach Decline much earlier Daily deaths decline when prevalence rates much <40% Observed everywhere
Daily deaths exponentiate even under lockdown, though at a slower rate Not observed anywhere Lockdown may have a small effect (a few days) on the timing of the peak Not yet falsified
Ending lockdown causes daily deaths to exponentiate at higher rate Not observed anywhere Ending lockdown will have negligible effect on rate of decline from peak Not yet falsified
Not having a lockdown causes daily deaths to exponentiate until herd immunity of ~60% approached Not observed anywhere Broad pattern of daily deaths substantively unaffected by lockdown Not yet falsified
Cumulative deaths in Africa as bad as in Europe Not observed anywhere Cumulative deaths negligible in Africa Observed everywhere to date
Positive testing rate should rise as epidemic progresses Contradicted—stable positive test rate. Positive testing rate should be quite stable Observed in many countries
 

Geoff.D

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Here is the link to the PANDA model for those interested.
In that article, there is a further link:


There is a paragraph in the main article of interest.:

We should wear masks, we should cocoon our old and infirm, and we should be cautious in our interactions. We should not incarcerate the masses in their homes, limiting their hard-earned freedoms and decimating the economic system that furnishes their livelihoods. We should be doing everything we possibly can to allow businesses to operate,” they say.
 
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Brian_G

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Thanks, that's some very detailed insight! Will be treating the thread as my forum "cake".
 

Geoff.D

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The next data source that is relevant to the debate on the effects on SA of Covid 19 is this one:

And the weekly report:


In the context of the emerging COVID-19 pandemic, it has become essential to track the weekly number of deaths that occur. Deaths recorded on the National Population Register are provided to the SAMRC on a weekly basis and are compared with the number that would be expected based on the historical data from 2018 and 2019. The number of deaths of persons 1-year and older are reported because birth registration was put on hold during lockdown stage 5 affecting the number of infant deaths recorded on this system. The start date of each week is represented on the graph.
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Geoff.D

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The next very interesting development about the SA data, which sort of proves that the government, despite plenty of pressure is STILL hiding the real picture from the public is this one, which has now been table on the media hack site.

Makes for good reading.

In the supporting document link here:

or this one for the background to R(t):


There is this interesting pearl of information:

To obtain an onset distribution we need case data that gives reporting time and estimated contraction time for each case. In South Africa, we are unable to obtain such data because the government won't release it.
See this site for the latest estimates of R(t).
[What is R(t)? I suggest you read the linked above pdf document.]

1590614488451.png
 
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Gordon_R

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The next very interesting development about the SA data, which sort of proves that the government, despite plenty of pressure is STILL hiding the real picture from the public is this one, which has now been table on the media hack site.

Makes for good reading.

In the supporting document link here:

or this one for the background to R(t):


There is this interesting pearl of information:



See this site for the latest estimates of R(t).
[What is R(t)? I suggest you read the linked above pdf document.]

View attachment 847217
Thanks for the very interesting links and charts. I know just enough statistics to make the following observations:
1. R(t) is always a lagging indicator, particularly when there is a testing backlog. It is best looked at on a weekly basis.
2. The fact that asymptomatic infections are ignored introduces systematic biases, though these average out over long time periods.

The chart of R(t) is mostly as expected, high before lockdown, largely flat thereafter. The one outlier which nobody explained, is the very sharp drop in the first week in April.

This was hinted at by Prof Karim, who suggested it was a time period between travel related and community transmission. The unstated factor is that R(t) varies by demographic, which is a political hot potato in SA.

A lot more research could be done on regional variations, and occupational links such as essential services. However the dataset is already being stretched thin. Trying to to this by district, to monitor hot-spots (as the Minister suggested), is ridiculous.

P.S. I don't think its a case of the government not wanting to release the test data, its just that nobody captured the date of the tests and results, only the total numbers.
 

Lupus

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P.S. I don't think its a case of the government not wanting to release the test data, its just that nobody captured the date of the tests and results, only the total numbers.
This, the testing just seems to be there to scare people, instead of doing proper checking and such they just focus on the total numbers. They don't seem to even really focus on the recoveries, and also wasting 2 tests on recovering people as well.
 
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