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Messages - gsgs

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166
actual epidemic charts / Re: hubei vs. rest of China
« on: February 10, 2020, 10:26:52 pm »

In order to resolutely implement the decision-making and deployment of the Party Central Committee and the State Council, to fully support Hubei Province in the prevention and control of new-type coronavirus pneumonia, and to resolutely win the fight against epidemic prevention and control, the National Health and Health Commission has made a national effort to gather high-quality resources and establish interprovincial counterparts to support Hubei Provincial mechanism of medical treatment of new coronavirus pneumonia in cities other than Wuhan.
The National Health and Health Commission fully considers the current situation of the epidemic situation, human resource reserves, and medical resource gaps in the aided cities. Based on the support of the original medical team from other provinces, the overall arrangement is based on the principle of unchanged relations and supplementary needs. 19 Each province supports 16 cities, counties, and counties in Hubei except Wuhan. The following support relationships are identified: Chongqing, Heilongjiang, Xiaogan, Shandong, Hunan, Huanggang, Jiangxi, Suizhou, and Guangdong. 3. Hainan Province supports Jingzhou City, Liaoning Province, Ningxia Hui Autonomous Region supports Xiangyang City, Jiangsu Province supports Huangshi City, Fujian Province supports Yichang City, Inner Mongolia Autonomous Region, Zhejiang Province supports Jingmen City, Shanxi Province supports Xiantao, Tianmen, Qianjiang 3 counties Level cities, Guizhou Province supports Ezhou City, Yunnan Province supports Xianning City, Guangxi Zhuang Autonomous Region supports Shiyan City, Tianjin City supports Enshi Tujia and Miao Autonomous Prefecture, and Hebei Province supports Shennongjia Forest District.
The National Health and Health Commission requires all supporting provinces to effectively improve their political positions, and to negotiate with the aided cities to determine support arrangements. Based on solving the local medical and health resource gap, a support team composed of medical, management, and disease control professionals is formed The combination of on-site support and telemedicine services, and multiple countermeasures to carry out counterpart support work. At the same time, we must take into account the needs of epidemic prevention and control in the region, work together to improve medical treatment, and strive to improve the rate of treatment, cure, reduce infection and mortality .

(Source: National Health and Health Commission website)
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167
actual epidemic charts / Re: hubei vs. rest of China
« on: February 10, 2020, 09:35:44 am »
most were visiting family for new yesr.
I don't think it was school closures, workplaces, public transport,
That was tried earlier with not much effect.

More likely the massive screening of contacts.

168
nCoV - discussion / Re: Scenarios for the coming months
« on: February 10, 2020, 07:21:42 am »
thanks a lot.
You know, I'd been asking for such probability estimates since
2006-H5N1 birdflu !?!
But experts were very reluctant to give some.

Where do I stand currently ...A:50 B:20 C:30  (2020/02/10)

why do you think it's likely mild , after correcting the CFR to 1.7 in the other post
(3 weeks lag until death)

I mean, it could become mild, killing the host is ineffective, well,
but no recombination in sight and coronavirus does proofreading as I recently learned.

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

we may find/develope some efficient drugs
it may go down in warm weather
it may take some months until it is in Europe,USA
we may have vaccine (I know, it takes a year because of the testing
but maybe the testing can/will be reduced if it's severe.

how likely is each of these ... I should think about it and try to give estimates.

when you hear the news in Germany you must think that they
have some secret recipe how to handle it, that it won't do much bad.
That seems to be what government, reporters, normal people think.

169
nCoV - discussion / Re: estimating the cfr
« on: February 10, 2020, 07:12:45 am »
10 February 2020 - Imperial College London‌
Report 4: Severity of 2019-novel coronavirus (nCoV)
(Download Report 4)‌

https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-2019-nCoV-severity-10-02-2020.pdf
this assumes a time-lag of 22.2 days from "confirmed" to "death"
and it assumes that all cases are confirmed ; CFR=deaths/(confirmed cases)

My data starts Jan.25, before that there were 572 confirmed cases in Wuhan,
157 in Hubei ex Wuhan, 558 in China ex Hubei.
Currently there are ~70 daily deaths in Wuhan, 18 in Hubei ex Wuhan, 7 in China ex Hubei.
If those cases pre-Jan.25 were all attributed to Jan.18 , then with the 22-day-lag
I get CFR=12.2 in Wuhan, CFR=11.5 in Hubei ex Wuhan, 1.3% in China ex Hubei.
Obviously many cases were unconfirmed, especially in Wuhan. There were those 5M people
leaving the city at that time.It is likely that severe cases had a greater probability
of being confirmed.
You would expect deaths climbing sharply after 10-20 days already - even if 22 were the average.
I do not see this. Deaths in Hubei ex Wuhan (where I'd assume not much underreporting)
were 2,6,12,12,12,13,15,16,16,18,5,14,18,18

And we clearly have no exponential increase in confirmed cases as they assume
--------------------------------------------
I'm unsure, that all doesn't make so much sense to me.
The CFR might be changing. The CFR might be different in Wuhan.
The 22-day-lag might be too long.
(CFR=deaths per all infections).
------------------------------------------------------
and then we have "severe cases" . These counts were up quite a lot since Feb.03,
but now they somehow have redefined "severe":
daily reported new severe cases in Hunan Jan.26-Feb.09 : 109,400,189,89,106,200,268,139,442,377,564,918,119 3,52,258
daily reported new severe cases in China ex Hunan , Jan.26-Feb.09 :
28,115,74,42,51,68,47,47,50,54,96,44,87,135,38 (212)

170
actual epidemic charts / Re: hubei vs. rest of China
« on: February 10, 2020, 01:17:23 am »
---------------------------------------------------

did they well because they were better preparing or just because they were
not being overwhelmed ?

With Wuhan's CFR 2.2 times higher than in the rest of Hubei
(since weeks now) I'd assume 2.2 times more cases in Wuhan,
silent, unconfirmed  which would have been confirmed ones in other cities.

Deaths in China outside Hubei are increasing now in the last days


----------------------
oops, I accidently had edited the post above instead of replying.
Good that I still had the original , I hope it's correctly restored now

172
nCoV - discussion / Re: Tracking coronavirus: Map, data and timeline
« on: February 08, 2020, 09:59:09 pm »
numbers are going down, right ?

173
nCoV - discussion / Re: estimating the cfr
« on: February 08, 2020, 09:57:40 pm »
thanks for the cfr-updates.
Yes, 1.7% is still pretty bad .

however the case numbers are going down !

175
nCoV - discussion / Re: estimating the cfr
« on: February 08, 2020, 02:30:48 am »
take cases outside Wuhan or outside Hubei , that gives much more cases
and still relatively few deaths.

deaths in Hubei outside Wuhan started to climb on Jan29, since then ~12 deaths per day
=1% of cases.
deaths in Wuhan started ~Jan 25
deaths outside Hubei may be starting now slowly, 3,4,5 the last days
 
--------------------------------

yes, I should have considered that time lag. I thought it were just a few days

176
genetics / Coronaviruses
« on: February 07, 2020, 10:21:07 pm »
“There is some evidence that people can be reinfected with the four coronaviruses
and that there is no long-lasting immunity,”

 SARS has a molecular proofreading system that reduces its mutation rate, and the
 new coronavirus’s similarity to SARS at the genomic level suggests it does, too.
“That makes the mutation rate much, much lower than for flu or HIV,” Farzan said.

https://www.statnews.com/2020/02/04/two-scenarios-if-new-coronavirus-isnt-contained/

------------------------------------------------------
Thus nsp14-ExoN is essential for replication fidelity, and likely serves either as a direct
mediator or regulator of a more complex RNA proofreading machine, a process previously
unprecedented in RNA virus biology. E
The discovery of a protein distinct from a viral RdRp that regulates replication fidelity also
raises the possibility that RNA genome replication fidelity may be adaptable to differing
replication environments and selective pressures, rather than being a fixed determinant.


 Proofreading Exoribonuclease.

Coronaviruses genome also encodes a protein called a replicase which allows
the RNA viral genome to be transcribed into new RNA copies
using the host cell's machinery.
The replicase is the first protein to be made; once the gene encoding the replicase
is translated, translation is stopped by a stop codon.
This is known as a nested transcript. When the mRNA transcript only encodes
one gene, it is monocistronic.

A coronavirus non-structural protein provides extra fidelity to replication because it
confers a proofreading function,[9] which is lacking in RNA-dependent RNA
polymerase enzymes alone.

Sexton NR, Smith EC, Blanc H, Vignuzzi M, Peersen OB, Denison MR (August 2016).
"Homology-Based Identification of a Mutation in the Coronavirus RNA-Dependent RNA
Polymerase That Confers Resistance to Multiple Mutagens".
Journal of Virology. 90 (16): 7415–7428. doi:10.1128/JVI.00080-16. PMC 4984655. PMID 27279608.

CoVs encode a proofreading exonuclease in nonstructural protein 14(nsp14-ExoN),
which confers a greater-than-10
fold increase in fidelity compared to other RNA viruses. It is unknown to what extent the CoV
polymerase (nsp12-RdRp) participates in replication fidelity

multiproteinreplicase-proofreadingcomplex.

Proofreading-deficient coronaviruses adapt for increased fitness over long-term passage
without reversion of exoribonuclease-inactivating mutations


Alanine replacement of the motif I residues (AA-E-D; four nucleotide substitutions) in
murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV yields
viable mutants with impaired replication and fitness, increased mutation rates, and attenuated
virulence in vivo. Despite these impairments, MHV- and SARS-CoV ExoN motif I AA mutants
(ExoN-AA) have not reverted at motif I in diverse in vitro and in vivo environments, suggesting
that profound fitness barriers prevent motif I reversion

The Amazing Diversity of Nidoviruses


177
genetics / Re: origin
« on: February 07, 2020, 10:52:11 am »
I'll check this later. I have no experience with coronaviruses, but mainly influenza.
I already noticed, how close the envelope protein is and how distant
the spike protein. But is it unusual ?

South China Agricultural University claimed today they have a 99% matching pangolin sequence
to be published soon


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

OK, I selected 65 Wuhan-close coronaviruses, spike=protein-area and made my mutation-picture:
http://magictour.free.fr/spike6j.GIF
http://magictour.free.fr/spike6j.l2

the ones close to each other in other areas are closer in the spike-area too -
that looks to me as if it were just mutating much more in that area -
rather than recombination.

-----------------------------------------------
Pangolin paper from Sept.2019 : https://www.mdpi.com/1999-4915/11/11/979/htm

178
studies,summaries / masks
« on: February 07, 2020, 10:35:46 am »
protective effect of masks and respirators against clinical respiratory illness (CRI)
(risk ratio [RR] = 0.59; 95% confidence interval [CI]:0.46–0.77) and influenza-like
illness (ILI) (RR = 0.34; 95% CI:0.14–0.82). Compared to masks, N95 respirators
conferred superior protection against CRI (RR = 0.47; 95% CI: 0.36–0.62) and
laboratory-confirmed bacterial (RR = 0.46; 95% CI: 0.34–0.62), but not viral infections
or ILI. Meta-analysis of observational studies provided evidence of a protective effect
of masks (OR = 0.13; 95% CI: 0.03–0.62) and respirators (OR = 0.12; 95% CI: 0.06–0.26)
 against severe acute respiratory syndrome (SARS).

https://academic.oup.com/cid/article/65/11/1934/4068747

179
genetics / Re: origin
« on: February 07, 2020, 03:49:35 am »
South China Agricultural University finds pangolin as a potential intermediate host
 for a new coronavirus

Review and release: Chen Chenchen, the propaganda department Source unit and
reviewer: Yang Zhiqun, propaganda department Time: 2020-02-07 Views: 5114

The latest research conducted by South China Agricultural University, Lingnan Modern
Agricultural Science and Technology Guangdong Provincial Laboratory,
Professor Shen Yongyi, and Professor Xiao Lihua, together with Researcher Yang Ruiyu
from the Military Medical Research Institute of the Chinese Academy of Military Sciences
and Chen Wu Senior Veterinarian of the Guangzhou Zoo Research Department, shows
Pangolin is a potential intermediate host for a new coronavirus. This latest discovery
will have great significance for the prevention and control of the origin of the new coronavirus.

https://www.scau.edu.cn/2020/0207/c1300a219015/page.htm


180
all of China, left and right , but right is logarithmic.
Hubei is only in the other thread.
I may add a new thread with Wuhan vs. rest of Hubei.

In this thread maybe I should omit the left side altogether and only take the logarithmical one.

There are frequent changes currently, in what form China offers the data



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