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Discussion thread V - COVID-19 (new coronavirus)

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it becomes clearer and clearer that hospitalisations and deaths are much (<30%) lower in Europe in wave 2.
http://magictour.free.fr/continen.GIF
http://magictour.free.fr/e-0909.GIF
This was also the case in USA, although maybe not as much.
http://magictour.free.fr/us-us.GIF
Drosten,Lauterbach,Althoff still doubt it, pointing to Florida, where deaths came later but still came.although
_somehow lower.
http://magictour.free.fr/us-fl.GIF
Anyway, we'll know it in a few weeks when Spain and France peak.
We have the reverse effect in Australia (winter) , where deaths are higher in this wave.
There is also the mysterium why some places were hit so hard in wave 1
http://magictour.free.fr/dea2.GIF
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if true, what could be the reasons ?

A) vitamin D builds up in summer
B) warmer weather
C) different immunity in winter
D) other cirulating microorganisms
E) masks
F) increased testing and contect-tracing
G) immunity from wave 1

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this looks important to me. What would be the implications ?
catch it now as long as it's milder ?
lockdown in winter until vaccine comes ?
give vit.D supplements ?
fight other viruses ?
 
From what I have learnt I would guess.

A) vitamin D builds up in summer - I do not think vitamins help, unless you were deficient.
B) warmer weather - lower chance of catching it but negligible effect on severity.
C) different immunity in winter - can not think of a mechanism
D) other circulating microorganisms - no clinical evidence
E) masks - again reduced chance of infection but not severity
F) increased testing and contact-tracing - again chance of catching it but not severity
G) immunity from wave 1 - not enough reinfections to account for previous exposure/ partial immunity
H) Different age groups are getting infected - major factor
I) Improved usage of available treatments/ non-usage of damaging treatments - major factor

Re. A) There have been a number of papers which show vitamin deficiency is a problem but supplements above normal levels did not help.

Re. B, E, F) Lots of evidence that low viral loads decrease the chance of the infection for all viruses (ID50) but not that it has any noticeable impact on morbidity or mortality.

Re. G) Possible if there have been many more viral challenges than we are aware of which have been dealt with by an innate immune response/T-Cells without producing detectable levels of anti-bodies. This would prime the immune system leading to lower morbidity on re-challenge. Possible mechanism but I do not think it likely to be significant.
 
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H) but why would more younger infected reduce the probability of olders infected ?
A) yes, many are D-deficient especially in S-Europe
B) temperature could influence why it worsens after 1-2 weeks in some
C) metabolism changes with temp.-change. See also deaths increase with lower temp.
("seasonality" of deaths, only partially explained by pathogens)
D) could be mild ones, common cold
E) (masks) also severety, recent podcasts, initial load
G) waves look like normal epidemic waves , immunity of superspreaders
H) infecting children magically protects old people ? Or the whole wave is so mild
and it only shows up because of many younger ones are now tested ?
I) improved treatment explains not why hospitalisations are equally low
 
H) but why would more younger infected reduce the probability of olders infected ?
A) yes, many are D-deficient especially in S-Europe
B) temperature could influence why it worsens after 1-2 weeks in some
C) metabolism changes with temp.-change. See also deaths increase with lower temp.
("seasonality" of deaths, only partially explained by pathogens)
D) could be mild ones, common cold
E) (masks) also severety, recent podcasts, initial load
G) waves look like normal epidemic waves , immunity of super-spreaders
H) infecting children magically protects old people ? Or the whole wave is so mild
and it only shows up because of many younger ones are now tested ?
I) improved treatment explains not why hospitalisations are equally low

H) It wouldn't but despite ample warning from China Europe and N. America did not protect their care homes adequately initially. Belatedly they did and after the lockdowns were eased younger age groups went back to work or play, the more aged stayed insulated.
A) I did not know that, is it due to a faulty allele prevalent in that population? . It seems odd that S. Europe would be the problem not dark skins nearer the poles.
B) I think that has more to do with the immune inflammatory response kicking in causing the symptoms if the virus is getting the upper hand a week or so post infection.
C) I do not think ambient temperature has much to do with it. Most patients who go on to die are going to be in hospital, and largely climate controlled for most of their illness, so there would not be much variation post infection.
D) Almost all of the population have antibodies to one, or more, of the seasonal human CoVs year-round although they probably fall a little in the summer. Recent papers have show that there lots of cross reacting epitopes (40%ish) but there is no evidence that any of them will impact SARS-CoV-2 disease progression and if they did it would probably boost immunity. For things to get worse in winter they would need to enhancing the immune reaction - possible but again no evidence. My guess negligible effect in either direction.
E) There are lots of claims initial viral load is important and correlates to pathogenicity but I have not seen any convincing evidence. It can do, from memory, experimentally but they were using unrealistic viral loads (this is normal in lab experiments to make sure the test animal gets infected). I suspect in humans variations in individual immune response swamps any effect in initial load. Location of the point of infection does have a significant effect. If there is a component of more aerosol transmission that could play a part in how quickly the virus got established and the course of clinical illness.
G) They do look like normal epidemic waves but I do not think they are. There has been an novel introduction messing with the wave form - us. The lock downs, mask wearing, physical distancing etc. etc. Nothing about this is normal. I think it has more to do with us spotting things are getting dangerous in our area and either reacting, of being forced to react, which depress R[SUB]t[/SUB] for a while - then we relax and we yo-yo like that.
H) infecting children magically protects old people ? No. Or the whole wave is so mild
and it only shows up because of many younger ones are now tested ? Testing has definitely spread to more of the population than at the peak of initial infections, less cases & more test capacity, but the virus has not changed. Outcomes are better IMO because the patient cohort is younger and their treatment is better focused.
I) True the better treatment will not cut in until you are hospitalised. Only causes of lower hospitalisations I can think of are less circulating virus in the community due to public health measures but if you are catching asymptomatic or pre-symtomatic cases this will effect the % hospitalisation and insure earlier treatment with, hopefully, better outcomes.
 
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Je me pose une question: a-t-on essay? la contamination digestive d'animaux sensibles ?
On ne semble parler que du syst?me respiratoire, alors que ces virus vont en bien des lieux, donc, quid en fonction du mode de contamination et en particulier digestive ?
 
As sewage is being tested, as a proxy for infections in the population, they are finding plenty of viral RNA by PCR. No body has cultured live virus from excreta, that I know of. I do not know hard they have looked but part of the problem is SARS-CoV-2's designation as a BSL3 pathogen. Plaque assays need to be done in BSL2 labs as getting BSL3 time at the moment is neigh on impossible. It is not logical to maintain that this is a virus that needs to be contained at all cost from escaping the lab and becoming a menace to the public - that ship has sailed. An EUA allowing some procedures in BSL2 now would let us find out how much infectious virus, if any, is in sewage, breast milk & anything else in the queue. It has the added benefit of letting the BSL3 labs get on with the work that requires their extreme containment measures.
 
sharon sanders said:
Hi Everyone!

I have an idea for a change to our format as we go into the 2020-2021 cold and flu season. I propose we stop updating country/province/state threads on September 30 as Wave One is over. What we are looking for now is how things will progress as we move into the future. Next is cold and flu season in the northern hemisphere.

For instance, I will bunch together all of the European countries under one main heading called - Europe: Wave 1 of COVID-19 Pandemic, January - September 2020. All of these threads are basically becoming an open archive while we focus on current outbreaks. The new sub-forum will read, for instance, Europe: Wave 2 of COVID-19 Pandemic, September - May 2021.

This way the focus will be on the countries that have new problems while the beginnings of the pandemic are still available so people can see how the situation developed. The new threads will start with the existing case and deaths counts and will be added to if the situations get out of control.

Sadly, the fact is that COVID-19 is now endemic to the world. It is not news when a case is diagnosed. Most sadly, deaths are not unusual. Therefore, we are going to switch to reporting by exception which is our normal method. This is..what is unusual? Out of the norm for that country/state/province?

If people want a daily case by case count there are numerous free services doing a fairly decent job. I like Johns Hopkins. Various moderators may choose to update some states/countries/provinces on a daily basis, but for the entire world - we will not be doing that.

I also want to thank everyone for participating. This year has been very tough. I know everyone is struggling to maintain some type of normal life.
Click to expand...

Hey everyone! I am going to make the change on September 12.

Thanks!
 
changed nutrition in winter

this process, how we adapt to temperature-changes, how is it called ?
After some days/weeks you become comfortable with the new temperature
This may also change immunity.


H) maybe I can check later, many countries give the numbers, who died in care homes
but it's so uniform in all EU-countries, I don't consider this to be a major effect
A) (vit.D) I haven't seen major genetic reasons. I speculate it's adaptation to cold weather
B) I've read after 1week it may enter other organs, i.e. lungs - or not
C) how is it called : when we adapt to temp.changes and after some days/weeks we are
comfortable with the new temp. ? That process might be connected to seasonal
mortality {remembering my old 19th century charts}
[other points maybe later...]


Code: 
              all ages                      >=70
Spain   case  hosp  ICU death      case  hosp  ICU death
---------------------------------------------------------
wave1,250273,92113,7695,20534  ,  92367,45794,2576,17724      37%,22% ; 50%,39%
wave2,253557,12109, 878, 1140  ,  24483, 4795, 244,  925      27%,10%,09%,05%
----------------------------------------------------------
        101%,  13%, 11%,   6%  ,    27%,  10%,  9%,   5%  


Aragon,1.3M
xx,May21,5588,2442,256,848
42,Sep03,21506,1808,110,302
         385%, 74%, 43%, 36%

Madrid,6.5M
xx,May21,67049,42497,3617,8931
42,Sep03,65228,3256,163,297
           97%, 8%, 5% , 3%

Cataluna,7.5M
xx,May21,55888,29497,2969,6021
42,Sep03,57149,1255,85,130
          102%,  4%, 3%, 2%
 
New Study Finds Vitamin D Can Eliminate Coronavirus Hospitalizations

https://www.ibtimes.sg/new-study-fin...izations-51349

Journal of Steroid Biochemistry and Molecular Biology

https://www.sciencedirect.com/scienc...764?via%3Dihub


76 consecutive patients hospitalized in Spain with COVID-19 infection
50 got oral calcifediol (0.532 mg), at admission and 0.266 mg on day 3 and 7,

Results: Of 50 patients treated with calcifediol, one required admission to the ICU (2%),
while of 26 untreated patients, 13 required admission (50%) p value X2 Fischer test
p<0.001. Univariate Risk Estimate Odds Ratio for ICU in patients with Calcifediol
treatment versus without Calcifediol treatment: 0.02 (95%CI 0.002-0.17). Multivariate
Risk Estimate Odds Ratio for ICU in patients with Calcifediol treatment vs Without
Calcifediol treatment ICU (adjusting by Hypertension and T2DM): 0.03 (95%CI: 0.003-
0.25). Of the patients treated with calcifediol, none died, and all were discharged, without
complications. The 13 patients not treated with calcifediol, who were not admitted to the
ICU, were discharged. Of the 13 patients admitted to the ICU, two died and the remaining
11 were discharged.


owest Calcidiol in Feb+Mar , highest in Aug,Sep

https://www.iofbonehealth.org/sites/...n_D_Europe.pdf

mean serum 25(OH)D levels of
20-30 S-European centres
40-50 N-Europe [3].

the high consumption of fatty fish and cod liver oil in N-Europe

43 in N-France
94 in SW-France

<25 in 8% of men in NL and 14% of women
similar in Switzerland

45 Italian women
<25 in 30% of Italian women

Very low levels in Spanish elderly and institutionalised persons

<25 in 47% in Greece in winter

<25 in 40% of non-western immgrants in NL

<30 in 1.7% in Brazil mean age =63 { but still the high COVID in Brazil ! }

below the detection limit in 22% of Turkish women

<50 in 40% in Germany 33% in summer
 
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gs
I had a look at the linked paper and some additional links re Vitamin D.
The p value (p < 0.001) in the paper is impressive but there are a few problems. The population in the area is know to have low levels of D, the small sample size (n=76) caused their randomisation to leave some troubling variations in possible confounding factors between the groups (Age - >60 control group 19%, < 60 treated 28% & Previous Diabetes mellitus - control 6%, treated 19%), they did not test baseline Vit D levels before treatment and both groups were also on HCQ and azithromycin. They noted that there are lower levels of D in late winter early spring, this study ran over May, June and July.

A better powered paper (n=10,933) in the BMJ https://www.bmj.com/content/356/bmj....apid-responses shows that at a population level vitamin D levels varied from 40 to 80nmol/l but that significant patient benefit occurred in those with < 25nmol/l baseline (used due to UK definition of being vitamin D deficient).
Subgroup analysis revealed a strong protective effect of vitamin D supplementation among those with baseline circulating 25-hydroxyvitamin D levels less than 25 nmol/L (adjusted odds ratio 0.58, 0.40 to 0.82, NNT=8, 5 to 21; 538 participants in 14 studies; within subgroup P=0.002; see Cates plot, supplementary figure S1) and no statistically significant effect among those with baseline levels of 25 or more nmol/L (adjusted odds ratio 0.89, 0.77 to 1.04; 3634 participants in 19 studies; within subgroup P=0.15; P for interaction 0.01)
Click to expand...

Based on this data it seems that testing baseline D levels on hospital admission would be worth doing with supplements given as needed to bring levels to >40nmol/l.
 
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I was wondering if anyone has seen any roll up of data or a tracking source that monitors the CT values for the PCR tests being done. There is a lot of questioning happening now in trying to understand why some labs are running CT values >35 and driving community responses, etc. It would be nice if all labs used a standard value but it seems they do not. Any data you could send my way would be great.
 
I have started to make the forum changes. I have started with the United States forum. I am going slowly because so much data is being moved. Please excuse the dust! Everything will be done by the end of this weekend.

You will find the new, current COVID-19 information easier to find as we move forward. Only the problems areas in the world will be highlighted as they occur. I like the Johns Hopkins map for daily totals link.

Please remember all numbers are now suspect. They are large enough to be some level of erroneous. There are many different methods of government reporting being utilized and many citizens in the world are not being tested.

Please use all counts for trends only. We will not know the real totals until retrospective studies are done in future years.

Stay safe.

Thanks!
 
I am not sure you will find much outside of a research setting. The problem seems to relate to legislation - as far as the US is concerned. Not all RT PCR testing machines produce a CT value, q RT PCR machines (the q is for quantitative) does but individual labs, running non-identical hardware, may not give directly comparable scores. I have heard that diagnosticians requesting this data are told they are not permitted to supply CT values for this reason. From a clinical stand point approximate values, even varying by an order of magnitude (a little over +/- 3CTs), would be fine. They need to know if the score is around 20 or over 30 (the former having about 1000 times as much viral load as the latter). Big hospitals have their own q PCR and can see the values which, all coming from the same kit, are comparable.
 
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FluTrackers.com
@FluTrackers
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Hey everyone!

We are re-modeling the forum this weekend. Unfortunately COVID-19 is a world endemic situation. We will be keeping track by looking for unusual upsurges, etc.

We are primarily an early warning site & everyone knows about #coronavirus now.

Please stay tuned..


-------------------------------------------------------------


FluTrackers.com
@FluTrackers
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2h
We understand there is a lot of controversy about #coronavirus in the northern hemisphere for the fall and winter.

No one knows what will happen.

Think about what you know about cold & flu season.

Be prepared just-in-case.

Re-visit your econ situation too.


--------------------------------------------------------


FluTrackers.com
@FluTrackers
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2h
We are not going to debate #coronavirus numbers.

Actually - all of the numbers are inaccurate now. Look for major trends only.

Many people do not bother to get tested and many "natural" deaths are still not diagnosed with COVID-19 as being a major contributing factor.
 
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