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Discussion thread VI - COVID-19 (new coronavirus)

He proposes that host genetics played a part:

Studies have shown that more people in Asia have a defense enzyme called APOBEC3A that attacks RNA viruses, including the SARS-CoV-2 virus that causes COVID-19, when compared to people in Europe and Africa.
Click to expand...
 
There may well be genetic differences between populations but this is the same population that was running 23,000 cases a day three months ago and now has 150. If it did not protect them then why would it do so now?
 
JJackson, I misread the significance of the APOBEC3A enzyme. Inoue does not think that is the key to the mystery. Further down he says other Asian countries have similar expressions of the protein and vaccination rates, yet they have not done as well as Japan.
I see now he mentioned that because it provoked them to see how it affects the nsp14 protein. Then they found the haplotype network of the delta unexpectedly had lower genetic diversity than the alpha. But he doesn't seem to me to offer a mechanism as to why it happened yet.
I've read that Japan allowed doctors to prescribe Ivermectin even though it was not on the official guidelines. It binds to nsp14 with high affinity.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8203399/

Possibly it or some other antiviral they were using worked together with vaccines and other measures to break transmission.
 
it would be the first time that this effect were observed.
the old variants would still be there and competing, as jjackson wrote.
We saw unexplained declines (and surges) elsewhere.
E.g. the decline in April in Europe was unpredicted.
There could be some effects from weather (Storm Lupit ?)
other viruses, (seasonal) immunity cycles.
We saw small summer-delta-waves in Cyprus,Kosovo,Netherlands,Spain,France
Finland,Norway,Albania,Iceland
 
... well, maybe not the first time. Now I remember the A/Ck/Shanxi/2/2006(H5N1)
and another strain (Egypt ?) with an unusually high mutation rate in HA in response to
the vaccine. (or not ? see below)
--------------------------------------
https://www.sciencedirect.com/science/article/pii/S0042682209001810
clade 7
extensive genetic divergence at both the nucleotide and amino acid
https://journals.asm.org/doi/full/10.1128/JVI.00413-10
antigenically drifted H5N1 viruses, represented by A/chicken/Shanxi/2/06 (CK/SX/2/06), were
detected in chickens from several provinces in northern China.
The CK/SX/2/06-like viruses are reassortants with newly emerged HA, NA, and PB1 genes that
could not be protected against by the GS/GD/1/96-based vaccines.
CK/SX/2/06-like viruses caused mild disease in mice and could not replicate in ducks.

We documented the emergence of the latest variant of H5N1 (A/chicken/Shanxi/2/06 [CK/SX/2/06])
that broke through existing poultry vaccines. We show that this variant is less pathogenic in mice
and ducks than the earlier strains and propose that the variant was not selected by the use of
vaccines.
 
> The funniest part is that, the Japanese prof who claimed Delta's over its error
> catastrophe threshold, was referring to a particular mutation: NSP14:A394V
> Which actually is one of defining mutations of all Deltas, has >92% prevalence
> now (100% in Japan), and still growingClown face
 
https://twitter.com/i/status/1463275901718876160


Dr. Eli David
@DrEliDavid

Dutch police beating a man unconscious to fight Covid. Notice how even the dog refuses to take part in this barbaric act.

Video at link is graphic - E.

https://twitter.com/i/status/1463275901718876160
752.4K views
0:02 / 0:26
From zwinki_zwonki





Tamsanqa
@Tamsanq29395794

Replying to@DrEliDavid

Exactly how Dutch Police used to beat Africans here in South Africa, only difference being their dogs also took part in those barbaric acts. Does it mean Covid has been in existence here is SA long before it was detected in Wuhan???





Ansgar John
@ansgarjohn
·
8h

Replying to@DrEliDavid

This was a while ago. The police is generally pretty good now (in Amsterdam). Thanks, I believe to @PolForFreedom
ex-Army veterans and conscripts like myself standing up. #IHGVV etc, etc. We have a 24/7 freedom fire on Dam Square. #vlamopdedam "Freedom in the opposite of fear."

 
https://twitter.com/leucasch/status/1372180860288573441

ᗰiᑕK ᒪEᑌᑕᗩSᑕᕼ @leucasch

"This is apparently the photographer who was beaten up by the Mobile Unit on Sunday [in the Hague]. He is a nature photographer. But now he has seen real animals. Still in uniform."




qDbl_ig0_mini.jpg


Jan B. Hommel - alias @the_stinging
@hommel_b
Mar 17

https://trouw.nl/ts-b6f8dddf via @trouw Dit is blijkbaar de fotograaf die zondag werd afgetuigd door de Mobiele Eenheid. Hij is natuurfotograaf. Maar nu heeft ie echte beesten gezien. In uniform nog wel. #coronavirus #Malieveld #verkiezingen

8:39 AM · Mar 17, 2021·Twitter Web App
 
Experimentally you can create mutations in the ribosome which increase fidelity but when introduced back into a wild type population they are out performed. Each virus maintains a fine balance between the amount of genetic diversity derived during duplication and its ratio of replication competent to non-replication competent particles it produces. Variations in this genetic strategy vary enormously between viruses from ratios of 1:1 up to 1:10,000.

Regarding the peaks and troughs in SARS's waves - which I do not understand - I do not see anything particularly odd in the Japanese data but the current low could just be a lull before the next storm. The UK daily case graph is more interesting as this wave structure seems to have broken down and we now have small ripples from a constantly high base which I assume is due to a change in host behaviour as vaccination has changed the perceived personal risk. The CFR has dropped to 1 in 300, from 1 in 48 a year ago and in the first wave 1 in 5.
 
Last edited:
35 amino-acid mutations in the spike protein alone !?!
incredible 9alpha had 7, delta 6)
68 nonsynonymous changes
plus the synonymous ones, which I don't have
(I don't know, what PL below means , from a tweet od @Tuliodna )

spike:
A67V
del 69-70
T95I
G142D
del 143-145
N211I
L212V_RE
V213P
R214E
G339D
S371L
S373P
S375F
K417N
N440K
G446S
S477N
T478K
E484A
Q493R
G496S
Q498R
N501Y
Y505H
T547K
D614G
H655Y
N679K
P681H
N764K
D796Y
N856K
Q954H
N969K
L981F


E:T9I
M:D3G
M:Q19E
M:A63T
N:P13L
N:del 31-33
N:R203K
N:G204R

orf1ab :
PL:K38R
PL:L862LF
PL:V1069I
PL:del 1265
PL:L1266I
PL:A1892T
nsp4:T492I
3CL:P132H
nsp6:F34FL
nsp6:F35FILV
nsp6:del 105-107
nsp6:I189V
RdRP:P323L
nsp14:I42V
nsp15:F122FILV
 
Cases increased rapidly in Gauteng in November, particularly in schools and
among young people, according to Lessells.
------------------------------------
2 weeks until BNT knows whether it's a vaccine escape.
Then 100 days until they can deliver the first charges of an adapted vaccine.
Too late for a possible spring-wave in March-April
 
Dr. Angelique Coetzee, chair of the South African Medical
Association and a practising GP based in Pretoria, said it
was "premature" to make predictions of a health crisis.
"It's all speculation at this stage. It may be it's highly
transmissable but so far the cases we are seeing are
extremely mild," she said.
"Maybe two weeks from now I will have a different opinion
but this is what we are seeing. So are we seriously worried ?
No. We are concerned and we watch what's happening.
But for now we're saying "OK; there's a whole hype out there,
[We're] not sure why."
 
it redoubles in 3 days !
https://www.nicd.ac.za/latest-confirmed-cases-of-covid-19-in-south-africa-26-november-2021/
It started 10 days ago in Gauteng province and in the last
4 days there was an increase also in neighboring provinces.

unless there was some -still unrecognised- superspreading
this is almost like pandemic influenza.
2009 H1N1 reached its peak in just 3 weeks from zero in NY

expect a wave starting in Jan.
in 2 weeks we'll know how much the vaccines may help and how virulent it is ...
 
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