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Discussion thread VI - COVID-19 (new coronavirus)

Emily the numbers have gone down over the last week in each of the WHO regions and the deaths went down in all but SE Asia, but they only rose 1% and the region only accounts for 1% of cases. If you look at the daily case count maps for the world it has gone up and down a number of times. By country, region or or any defined area it peaks and falls but not in unison so the some areas are going down while others have a resurgence.
I have not seen any convincing evidence that any of the new variants are either more contagious or more pathogenic. What they are showing is a selective advantage over the wild types in a mixed population of seropositive and naive hosts.
 
That sounds hopeful, JJackson, thanks! I probably saw some fearful hype in an article. I do actually agree with you and Sharon about fluctuations and waves. My last sentence meant to express that, but I see it was rather ambiguous.
 
deux questions:

- la premi?re , vu ceci : https://www.epi-phare.fr/app/upload...s_hospitalisations_deces_covid19_20210209.pdf
comment d?finir la cause de mortalit? en cas de facteurs de risques av?r?s :

dit de fa?on simple : il y a un code cim covid unique, ou l'on accepte et ou doit de faire cohabiter les x codes CIM av?r?s ?

Ceci implique que l'O.M.S parle de synd?mie et non d'?pi et ou de pand?mie ...



- la deuxi?me ( je ne peut l'?crire qu'en langue de Moli?re , d?sol? )

allo Docteur ,

comme il n'y a pas de m?dicament, vous acceptez de me traiter ?

et ou de me prescrire un ou des traitements ?

ou je dois aller voir un traiteur ?

https://artflsrv03.uchicago.edu/philologic4/publicdicos/query?report=bibliography&head=traitement
 
Emily I do not know what you mean by a variant clash, a clash between what and what? He does not seem to have had any virus in him and it was weeks since he had been vaccinated.
 
I'm trying to find out how they would differentiate between natural and vaccine antibody profiles.

https://www.fda.gov/media/144325/download
Pfizer:
Two doses of BNT162b2 induce: • SARS-CoV-2 neutralization antibodies • GMTs comparable to or higher than GMT of a human convalescent serum panel from individuals who recovered from COVID-19 -GMTs highest with 30-μg dosage • S1-binding IgG antibodies • S-specific CD4+ and CD8+ T cells with Th-1-skewed secretion of IFNγ or IL-2, or both

https://www.fda.gov/media/144585/download
Moderna:
Immunogenicity:
•Two doses induced SARS-CoV-2 binding and neutralizing antibodies
•Th1-biased CD4+ T-cell response elicited

So how do they tell the difference? And then how accurate is the estimation of when someone was infected or vaccinated? If the metric is the numbers of antibodies, I think new research is showing this could be unreliable when a previously infected person is vaccinated.

https://www.medrxiv.org/content/10.1101/2021.02.07.21251311v1
Poor antigen-specific responses to the second BNT162b2 mRNA vaccine dose in SARS-CoV-2-experienced individuals
...
'In individuals naive to SARS-CoV-2, we observed robust increases in humoral and antigen-specific antibody-secreting cell (ASC) responses following each dose of vaccine, whereas individuals with prior exposure to SARS-CoV-2 demonstrated strong humoral and antigen-specific ASC responses to the first dose but muted responses to the second dose of the vaccine for the time points studied. These data highlight an important gap in our knowledge and may have major implications for how these vaccines should be used to prevent COVID-19."
 
Emily Merci,
Cela parle de l'int?grit? des d?marches de l'O.N.U .
https://www.youtube.com/watch?v=Gz8QeqOi-sg&t=7s

J'avais dit que cette crise ?tait due ? des probl?mes de management. Je connais les avantages et inconv?nients de la hi?archie militaire. Elle est pire que la hi?archie politique, scientifique ou des normes ?

En ce moment, ils souhaitent faire des enqu?tes, en Mozelle, qui doivent aborder le comportement des adultes le 1er janvier: ce sera du mensonge en bande organis?e ou des causes de bien des meurtres...


Avec ces envois, que j'ai d?gust?, je me sens moins seul . Mes cheveux sont encore sur ma t?te et continuent de pousser. Le temps, ou certaines communaut?s pourraient donner le ton, me semble, peut ?tre, advenu.


Vive la diversit? ...
 
all these waves going up and down just like normal epidemic waves - is there immunity involved ?
Despite only 10% or such infected in a wave.
It looks unlikely that this is just driven by stricter avoidance of risks, of contacts as the wave proceeds.
We see it in 3rd world countries as well.
And with seasonal flu - there are usually also only 10%-20% infected.
In the severe fall-wave in 2009 just 30M were infected in USA
https://www.cdc.gov/H1N1flu/estimates/April_February_13.htm

OTOH in Manaos,Bergamo >50% were infected, 30% in NYC in spring

http://magictour.free.fr/e-0212.GIF
 
au fait maintenant que l'on sait qu'au d?but il n'y avait pas une , mais : "elon Embarek, l'?quipe a ?galement ?tabli qu'il y avait d?j? plus d'une douzaine de souches du nouveau coronavirus, SARS-CoV-2, en circulation en d?cembre"

https://www.hindustantimes.com/worl...-outbreak-in-2019-report-101613315826615.html

les tests PCR fonctionnaient pour les douze souches ou ?

La sous question pourrait ?tre: se lancer dans un vaccin sans savoir de quoi il retourne c'est sympa ...
 
Emily I am still not quite clear what you are asking but a natural infection will produce antibodies to any viral peptide that the immune system encounters. The vaccine only produces one protein, Spike, so you are only get antibodies to Spike after vaccination. If you find antibodies to M (or anything other than S) then the person has had a natural infection. I am not sure about a 'clash' as if the variant has changes on the spike one or two antibodies may not bind as well but all the others should give good protection and the B-cells will create new antibodies to accommodate the changes.
There is now good data on the immune response in both infected and vaccinate individuals and they are remarkably similar both in Spike antibody abundance and distribution, B and T cell responses.
The pre-print you linked to gives 3 possible reasons for a poor response after a 3rd. challenge, infection being the first and vaccine being 2 & 3. After looking at the data my guess would be the depletion of the naive B cell pool that are ready for activation due to the short time in which they have been depleted 3 times.
 
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Thanks for your response on this again, JJackson. By 'clash', I was thinking of ADE/original antigenic sin. But I put that to rest since when you mentioned the negative virus testing, I read up on that again and it seems there would be virus found during the illness in an ADE case.
Your explanation of the antibody profiles for natural vs vaccine is great. It agrees with an MD article I saw but yours has more detail. I'm still unclear on how they could tell from his blood work that he had both the vaccine and the natural infection This Memphis news article says:
https://www.localmemphis.com/articl...rome/522-7bb29487-c330-4de4-b1b0-188fe3865e35
"Threlkeld added, Williams also had been vaccinated for COVID about a month ago and that testing found the two types of antibodies in his system - one type of antibody that results from a natural COVID infection, and a second type of antibody from the vaccine."

That must be a mistake because from what you say and the FDA docs relate, the spike antibodies are indistinguishable between the vaccine and the natural infection. All I can guess is that the spike antibody count is higher relative to the other antibodies in a person who was naturally infected and also vaccinated versus a person who was only naturally infected.

Do you think that could be correct?
 
Emily I have been writing a series of posts in the immunity thread in my workshop which are getting into this area in more detail.
If you keep an eye on this thread https://flutrackers.com/forum/forum.../jjackson-s-workshop/895212-covid-19-immunity I plan to add more posts. In the next I aim to write about B cell maturation in the germinal centers and the role of somatic hypermutation in the refinement of IgG affinity but the first 3 posts have been laying the necessary ground work.
As these posts explain there have been some engineered changes in the S gene but they relate to the Spike's cleavage and will have little impact on antibodies produced. The only change that would have an effect you may be able to detect in the blood work relates a change in the ratio of antibodies produced to a slight conformational change across the RBD that occurs post cleavage of the s1/s2 loop. I very much doubt this is what they are observing as it requires ELISA assays very few labs could do. A more likely explanation is they found the usual panel of non spike antibodies had declined over time but the Spike antibodies were disproportionally higher due to these being the only ones that got a boost from a spike only vaccine.

ADE and OAS are different. In ADE you are getting an adverse reaction at infection from an earlier vaccination. There are a number of different mechanisms relating to the different vaccines that have induced it but I do not think it is a concern in these COVID vaccines as none of the known mechanisms are applicable. OAS is when the immune system is reactivating a response to a previous infection that is not quite the same and a poor match. As it has these 'not quite right' antibodies it persists in trying to use them where as if they had not had the previous infection it would be making a better matched antibody but would take longer to get them into mass production. Each Effector B cells (AKA Plasma Cells) can produce IgG at a rate of 1 per millisecond and you have a lot of them. The promised post, I have not written yet, will explain how the maturation of B cells is designed to correct the OAS problem and deals with the variants in SARS-CoV-2 as they arise.
 
GS - Looking around at people in my own personal life - I can see colleagues in different businesses and families who are not concerned by the pandemic becoming ill. The people who are careful and wear masks tend not to. This is just from my own observation. I think it comes in waves partly because people become scared, take precautions - and then some of them - choose not to take precautions. Most maskless companies we deal with have had a complete surge and the entire company has become infected. I drove past a large company that makes PPE this morning - and there were a dozen ladies gathered around a canteen table having a cup of tea/coffee... They wear masks on the floor - but not in the canteen. No windows open either. It is just a matter of time before someone who is ill sits down at that table. It is just a numbers game.
 
We know that humidity has an effect on Covid transmission - probably due to precipitation of aerosols from the atmosphere along with small droplets. Temperature appears to have less of an effect, although virus is longer lived in very cold conditions, which are prevalent across large swathes of the N. Hemisphere at the moment. UV radiation levels also would appear to have a damping down effect, which may account for the late spring / summer lull we saw last year, but it is far too early in the season for raised UV radiation levels. One of the other biggest transmission factors is human behaviour, and tendency to gather in crowds indoors in poorly ventilated spaces increases transmission.. so could recent significant falls in case numbers be due to cold weather and people staying indoors with family more, i.e staying more isolated perhaps?

However, even with all those factors considered, the case loads have also been falling hard across the N. Hemisphere where current environmental conditions might suggest that transmission should be increased, and we are also seeing falls in areas where lockdown measures have not been very severe, and overall seroprevalence is low. So why is this happening?

Whilst searching for an answer, I wondered if space weather could have anything to do with it (its the only thing that could have influenced the whole N. Hemisphere at the same time that I can think of) but data is sketchy, and it is quite a bit of a 'reach'. https://www.spaceweatherlive.com/en/...gion-2797.html.

It is too soon for vaccines to have had such a marked effect across such a large geographical area also.

Any ideas anyone? It certainly is a puzzle...
 
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