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Messages - gsgs

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181
genetics / RaTG13
« on: February 06, 2020, 04:07:32 am »
"RaTG13" is the closest known virus in animals. It is from a bat sampled in
a cave in Yunnan in 2013

it was transferred from GISAID to public genbank on 2020/02/06


the Wuhan virus compared with the RaTG13 virus has
one 3bp insertion at position 3316
one 12bp insertion at position 23586
one 3bp insertion at position 26517
one 1 bp-insertion at position 27371
one 1 bp-insertion at position 29820
29875 common nucleotides


http://magictour.free.fr/wuhrat1.GIF

{do the same with the Pangolin sequence and with ZC45 ... }

http://magictour.free.fr/wuhrat6.GIF

the claimed recombination is not so clear, IMO

well, how is it with these coronaviruses ? all these hills
shouldn't be there ... are they all recombinations  ?


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

 > TMRCA of the two sequences nCoV2019 and RaTG13 of 69.5 years ago –
 > roughly 1950 +/- 10 years or so.


182
studies,summaries / Zhou et.al. , Nature
« on: February 05, 2020, 11:51:53 pm »
A pneumonia outbreak associated with a
new coronavirus of probable bat origin
https://www.nature.com/articles/s41586-020-2012-7



183
nCoV - discussion / Re: disasters
« on: February 05, 2020, 11:45:10 pm »
I took the 20% from a CDC-estimate in Feb.2010, how many US-people had got
pandemic H1N1 by then.

When I first wrote this, I didn't realize that the CFR outside Wuhan is much lower

184
General Discussion / chatroom
« on: February 05, 2020, 06:25:25 am »
Thank you for your Chatroom system purchase.
This will soon be activated shortly on your account if not already.


185
financial / actual charts
« on: February 05, 2020, 05:58:58 am »
<A HREF="http://www.kitco.com/connectndx.html">
  <IMG SRC="http://www.weblinks247.com/indexes/idx24_russell_en_2.gif" BORDER="0" ALT="[Most Recent RUSSELL from www.kitco.com]">
</A>

http://www.kitconet.com/indexes.html

<A HREF="http://www.kitco.com/connectndx.html">
  <IMG SRC="http://www.weblinks247.com/indexes/idx24_usd_en_2.gif" BORDER="0" ALT="[Most Recent USD from www.kitco.com]">
</A>

<A HREF="http://www.kitco.com/connectndx.html">
  <IMG SRC="http://www.weblinks247.com/indexes/idx24_jse_en_2.gif" BORDER="0" ALT="[Most Recent JSE from www.kitco.com]">
</A>

<A HREF="http://www.kitco.com/connectfx.html">
  <IMG SRC="http://www.weblinks247.com/exrate/24hr-euro-small.gif" BORDER="0" ALT="[Most Recent Exchange Rate from www.kitco.com]">
</A>


186
actual epidemic charts / actual gold,$
« on: February 05, 2020, 05:35:50 am »
https://www.kitconet.com/charts/metals/gold/t24_au_en_usoz_2.gif
https://www.weblinks247.com/indexes/idx24_usd_en_2.gif
I'll try to include them in a thread in our forum





I'd also like :

dow jones
euro/$
oil
Chines Yuan
Chinese stock - index
VIX
credit default swaps

187
genetics / Re: origin
« on: February 04, 2020, 03:10:48 am »
mutation pictures of coronaviruses,
409 selected viruses from genbank,Dec.2019, close to SARS/nCoV

the ~30000 nucleotides were divided into areas of 3000
so they fit on one page

using my old program designed for influenza (which has segments of <2300 nucleotides)

each black pixel is a nucleotide different from the average at that position
each line is a virus, each column is a position
positions without mutation are left out
rows and columns are re-sorted for maximum connected areas of black pixels

the average = orange rows are mainly human SARS-viruses
(I should remove them and run it again ...)


http://magictour.free.fr/oro5f.GIF

189
vaccine / antivirals
« on: February 03, 2020, 03:34:07 am »
with fairly good inhibitory effects on the novel coronavirus (2019-nCoV) at the cellular level, a local newspaper has reported.

The three drugs are Remdesivir, Chloroquine and Ritonavir.

190
links / TWiV
« on: February 02, 2020, 09:31:15 pm »

191
genetics / Re: origin
« on: February 02, 2020, 07:42:45 pm »
Coronavirus conspiracy debunked by Wuhan researcher
By Zhang Zhihao | chinadaily.com.cn | Updated: 2020-02-02 19:29
A scientist from the Wuhan Institute of Virology of the Chinese Academy of Sciences has
debunked a recent conspiracy which claimed the novel coronavirus was manufactured and
escaped from the institute’s most advanced biocontainment facility.
Shi Zhengli, a researcher from the institute, said on her social media on Sunday the virus
was the result of "nature punishing the uncivilized habits and customs of humans",
and she is willing to "bet my life that [the outbreak] has nothing to do with the lab."
Shi was the leading scientist who made the discovery the novel coronavirus can enter
cells through ACE2 receptors and may have originated from bats.
Her comments came after Indian scientists recently published a non-peer reviewed
paper suggesting scientists had artificially inserted genes from the HIV virus into the
coronavirus, thus making it susceptible to anti-HIV treatments.
The paper was immediately panned by experts around the world and retracted from
biology journal server bioRxiv on Sunday.
...
http://global.chinadaily.com.cn/a/202002/02/WS5e36b2b7a31012821727432e.ht

----------------------------------------
ahh, "nature punishing the uncivilized habits and customs of humans"
doesn't sound like a scientific, rational, logical arguing to me ...
BTW. the lab was not level IV before 2015
https://en.wikipedia.org/wiki/Wuhan_Institute_of_Virology

192
expert opinions / Feb.2020
« on: February 02, 2020, 07:35:35 pm »
Fauci, 2020/02/01, NY-Times
“It’s very, very transmissible, and it almost certainly is going to be a pandemic,”
“But will it be catastrophic? I don’t know.”
In the early days of the 2009 flu pandemic, “they were talking about Armageddon in Mexico,”
But it turned out to not be that severe.”
Still, asymptomatic carriers “are not normally major drivers of epidemics,”
------------------------------------------------------------------------
2020/02/01, Dr.Thomas Frieden ,former CDC director
It is “increasingly unlikely that the virus can be contained,"
“It is therefore likely that it will spread, as flu and other organisms do, but we still
don’t know how far, wide or deadly it will be.”
-------------------------------------------------------------------------------
2020/02/01  Dr.Peter Piot ,London school of Hygiene and Tropical Medicine
“This looks far more like H1N1’s spread than SARS, and I am increasingly alarmed,”
 “Even 1 percent mortality would mean 10,000 deaths in each million people.”
----------------------------------------------------------
2020/02/01 , Dr. W. Ian Lipkin, Columbia Univ.
although the virus is clearly being transmitted through casual contact, labs are still
behind in processing samples.
But life in China has radically changed in the last two weeks. Streets are deserted, public
events are canceled, and citizens are wearing masks and washing their hands, 
All of that may have slowed down what lab testing indicated was exponential growth
in the infection.
I know of one lab running 5,000 samples a day, which might produce some false-positive results,
inflating the count. “You can’t possibly do quality control at that rate,”
-----------------------------------------------
2020/02/01 , Schaffner
At the moment, it seems unlikely that the virus will spread widely in countries with vigorous,
alert public health systems,
“Every doctor in the U.S. has this top of mind,” Any patient with fever or respiratory problems
will get two questions. ‘Have you been to China? Have you had contact with anyone who has?’
If the answer is yes, they’ll be put in isolation right away.”
“In God we trust,” Dr. Schaffner said. “All others must provide data.”
---------------------------------------------------------------------------------------------------------
2012/02/01 , Dr.Mike Ryan, WHO
There is still reason to believe the growing coronavirus outbreak in China can be contained,
some evidence that the disease may not be spreading as rapidly as is feared.
[downplayed reports that people infected with the virus may be contagious before
they show symptoms]
“Until [containment] is impossible, we should keep trying,”
The gargantuan efforts China is making to try to halt the spread of the virus is buying the
rest of the world “precious lead time” to prepare for the possibility they might have to cope
with it as well, We need to thank China for that opportunity.”
“That is not to say that the disease won’t get ahead of the Chinese authorities completely
or get ahead of the other countries that are containing it,” But there’s enough evidence to
suggest that this virus can still be contained.”
For instance, data from some studies in China looking at how much transmission occurs
when the virus gets introduced into a household suggests the secondary attack rate —
the number of people the first case infects — isn’t that high. “But that’s obviously a few
studies across a very large event,”
There haven’t been many reports of health worker infections, a feature that fueled the
earlier outbreaks of SARS and MERS,
Likewise, there has not been a lot of spread from cases discovered in other countries
in tourists from China or people returning from China.
the problem isn’t testing reagents — the country has indicated it has adequate supplies —
but the sheer number of tests that need to be run.
So there are clear indications obviously that the disease numbers are growing.
But there is also some contradictory evidence as well that doesn’t completely align with
the kinds of R0s that are being estimated,”
(what circumstances would lead the WHO to declare this event a
pandemic )-That kind of discussion, would be a distraction.
“If that becomes the discussion, then we’re all going to lose focus,”
We have to remain laser-focused on containment and slowing down the spread of disease.”
 “Almost all of the mortality is in the over 40s,” and a strong preponderance of males.”
the data the WHO are seeing suggests some people who have been publicly labeled “
asymptomatic” were actually already experiencing some symptoms.
“We still believe, looking at the data, that the force of infection here, the major driver,
is people who are symptomatic, unwell, and transmitting to others along the
human-to-human route,” That is the pressure wave.”
 surprised by the speed with which the outbreak has taken off.
For me it’s been unusual to see a new disease emerge and, on the face of it,
move so quickly,”  If the scientists studying the genetic sequences of the viruses are right
and the outbreak began sometime in late November or early December, “then this is a very
rapid emergence and very rapid infection of a lot of people.”
-----------------------------------------------------------------------------------------------

------------------------------------------------------------------
Feb-07, Beverley Paterson,  Australian epidemiologist who works with governments to
prepare for pandemics.
The answer to whether a pandemic will happen, unfortunately, is probably “yes.”
--------------------------------------------------------------------------------------------
Feb-07 , Lawrence Gostin, a public health law professor at Georgetown University.
Travel bans and quarantines are a centuries-old answer to the spread of disease.
They’re also exactly what the World Health Organization asked everyone not to do.
The same WHO committee that recommended calling the virus a Public Health
Emergency of International Concern explicitly said the measures to stop it should
include treatment, tracing of contacts, and social distancing, but not “any travel or
trade restriction.” That’s because almost no one in the game thinks that works.
“The travel ban on foreign nationals is counterproductive, unethical, and violates
international law. There’s little evidence that a person who’s been to mainland China
but not in the hot zone would be exposed to the virus, and there are far less restrictive
measures we could use,” . “I think it’s a huge overreach, and I worry that the White
House is lurching from complacency to panic and overreaction.”
------------------------------------------------------------------------------------------------------
Feb-07 , Jennifer Nuzzo, an epidemiologist at the Johns Hopkins Center for Health Security
Travel bans and quarantines haven’t worked to contain other recent outbreaks. “I don’t think
we’ve seen compelling evidence that travel bans work at all, and they’re less likely to work
for respiratory viruses like this, because they move too quickly,”
 -----------------------------------------------------------------
One 2011 study by a team of modelers in Europe and the US said that H1N1 travel bans
 reduced air travel to and from Mexico by 40 percent—with huge economic consequences—
but didn’t slow the disease’s spread at all. A 2014 British meta-analysis of 23 different
studies of the effect of travel restrictions on influenza outbreaks concluded that they
slowed disease spread by no more than 3 percent—less if the restrictions came late
in the outbreak, and less in big cities. And an international team looking at the travel
restrictions that came with the 2014 West African Ebola outbreak found much the
same thing: They delayed the disease’s spread to other countries only by weeks, if at all.
https://www.scielosp.org/pdf/bwho/2014.v92n12/868-880D/en
------------------------------------------------------------------------
Feb-07 , https://science.sciencemag.org/content/367/6478/610

Feb-07 ,  Robin Thompson, a mathematical epidemiologist at the University of Oxford.
“There has obviously been a huge amount of spread within China, but [elsewhere], there's no
 evidence of any kind of substantial human-to-human transmission,” “The risk probably isn't
as high as some models have been projecting.”
-------------------------------------------------------------------------------------------
Feb-07 , Epidemiologist Marion Koopmans of Erasmus Medical Center
it may not be that hard to contain the virus in a new locale as long as the first cases are detected and isolated early—provided the virus is not highly transmissible. “We don't see it taking off in the 200 or so cases seeded outside of China,”  If that pattern holds, “there still is the possibility it will bend off.”
----------------------------------------------------------------------------------------------
Feb-07 ,  Joseph Wu, a modeler at the University of Hong Kong.
 [goes down in summer] “That is a big question mark we're trying to assess at the moment
-------------------------------------------------------------------------------------------------
Feb-07 , Alessandro Vespignani, a modeler of infectious diseases at Northeastern University.
2019-nCoV “will be very difficult to stop in China,”  But if asymptomatic transmission is rare,
 “isolation and social distancing can have a big impact.”
-------------------------------------------------------------------------------------------
Feb-07 , Aavitsland
“As the virus continues to spread in China, the risk of exportation to other countries
grows and sooner or later we will see it spread in another country,”
--------------------------------------------------------------------------------------------
Feb.07 , Lipsitch
so far there has been no sustained transmission outside of China, but I expect that to change:
“I would be really shocked if in 2 or 3 weeks there wasn't ongoing transmission with hundreds
of cases in several countries on several continents.”
[mild cases]  “So what looks like a horrific disease may be the horrific tip of a very large iceberg,”
------------------------------------------------------------------------------------------
If indeed 2019-nCoV becomes pandemic, humanity may be stuck with it indefinitely.
----------------------------------------------------------------------
Feb.09 , Adam Kucharski, an associate professor of infectious disease epidemiology,
Assuming current trends continue, we’re still projecting a mid-to-late-February peak”
of virus cases in Wuhan,  5% infected by then
-------------------------------------------------
Feb.10 , Professor Peter Piot, director of the London School of Hygiene & Tropical Medicine,
the outbreak is more likely to become a pandemic, with the increased and fast rate of infection.
----------------------------------------------------
Feb.10 , UK Department for Health and Social Care , The secretary of state
declares that the incidence or transmission of novel
Coronavirus constitutes a serious and imminent threat to public health, and the
measures outlined in these regulations are considered as an effective means of
delaying or preventing further transmission of the virus.
--------------------------------------------------------
2020/02/11 , Prof Gabriel Leung, chair of public health medicine at Hong Kong Univ
Outbreak Could Infect “Between 60%-80%” Of Humanity, Causing 51 Million Deaths
-----------------------------------------------
2020/02/10  WHO Director-General Dr. Tedros Adhanom Ghebreyesus
we might be seeing only ‘the tip of the iceberg’ in terms of number of cases
------------------------------------------------
2020/02/11 , Tedros, WHO
weltweit „ernste Bedrohung“. Trotz der hauptsächlichen Eingrenzung auf China
stelle das Virus eine „sehr ernster Bedrohung für den Rest der Welt dar“,
Das zweitägige Treffen soll zur Eindämmung der Krankheit beitragen.
-------------------------------------------------------------------------
 Der chinesische Ministerpräsident Li Keqiang hat am Sonntagabend mit seiner
deutschen Amtskollegin Angela Merkel telefoniert und sich dabei mit über die
Vorbeugung und Kontrolle der Epidemie durch das Coronavirus 2019-nCoV ausgetauscht.
-------------------------------------------------------------------------
6:30 pm: China’s top virus expert reportedly says outbreak may peak this month
China’s fast-spreading coronavirus may peak in February, before cases then start
to plateau and ease over the coming months, Beijing’s top economic adviser told
Reuters on Tuesday.
Zhong Nanshan, a leading epidemiologist who become known around the world for
his role tackling the SARS epidemic in 2003, said the situation in China was already
showing signs of improving, pointing to the number of new cases falling overnight.
He added that he believes the outbreak would peak either by the middle or the end
of February before the number of cases would then start to fall.
Zhong had previously predicted an earlier peak for the coronavirus, Reuters reported.
------------------------------------------------------------------------------------
Feb.11 , Xi,
Die Maßnahmen zur Prävention und Eindämmung würden positive Ergebnisse zeigen,
Sein Land werde den Kampf gegen das Virus gewinnen. Danach werde die Volksrepublik
besser dastehen al zuvor, die Regierung werde an den geplanten wirtschaftlichen
und sozialen Zielen festhalten.
-----------------------------------------------------------------------------------------------------
Feb.11 , Tedros, WHO
Wir sollten als ein Menschengeschlecht hart daran arbeiten, dieses Feuer zu bekämpfen,
bevor es außer Kontrolle gerät“
------------------------------------------------------------------------------------------------------
2020/02/12 , Mike Coston avianfludiary.com
seems increasingly likely that COVID-19 will spread globally,
-------------------------------------------------------------------------------------------------------
Feb.10 , Donald Trump, President USA
The heat, generally speaking, kills this kind of virus,”“A lot of people think that goes
away in April as the heat comes in.“in theory when it gets a little warmer it
miraculously goes away.”
Feb.07,Trump
I had just spoken on the phone with President Xi Jinping of China.
“Nothing is easy,  but Xi will be successful, especially as the weather starts to
warm & the virus hopefully becomes weaker, and then gone.”
------------------------------------------------------------------------
Feb.11 , Messonier , CDC
Warm Weather May Not Slow Outbreak
The theory that the coronavirus will slow down when warm weather sets in is mostly based
on the fact that other respiratory viruses such as influenza exhibit seasonal patterns,
not specific data about this new virus.
CDC is optimistic that lower case counts coming from China in the last few days mean
that the country’s quarantine is working, but that it’s “too soon to say that for sure,”
----------------------------------------------------------------------------
Feb.12 , Dr. Robert Redfield , director CDC
We’re still going to see new cases. We’re probably going to see human-to-human transmission
within the United States,”
at some point in time it is highly probable that we’ll have to transition to mitigation”
as a public health strategy, using “social distancing measures” — for example, closure
of certain public facilities — and other techniques to try to limit the number of people who
become infected.
“We’re not going to be able to seal this virus from coming into this country,” .
But, “we do gain time by prolonging the containment phase as long as we can,
provided that we still believe that’s a useful public health effort.
“That’s where we are right now in the United States.”
If the United States begins to see instances in several parts of the country in which a
single case ignites four “generations” of human-to-human infection,
then the CDC is likely to conclude containment of the virus has failed.
“Once we get greater than three — so four or more is our view — [generations of]
human-to-human transmission in the community … and we see that in multiple areas of the
country that are not contiguous, then basically the value of all of the containment strategies
that we’ve done now then really become not effective,” he said. “That’s when we’re in full mitigation.”

China, which has reported more than 45,000 cases to date, has not been able to contain
the virus, despite massively restricting internal travel to try to stop it from spreading from
Hubei province
“Those countries that are still largely seeing cases that are really, like us, directly from Hubei province, there’s reason to still stay in the containment mode rather than turning that off and going right to mitigation. Because once you’re into mitigation, you will probably start to see more cases that may have been able to be contained,
----------------------------------------------------------------
Feb.12 , Messonier
This really isn’t a ‘let’s stop it and then we’re done.’ It’s a ‘if we can pause it a little bit, we buy ourselves some time to work on the rest of our pandemic planning,’
----------------------------------------------------------
2020/02/12 , Ferguson
With the numbers of people infected with coronavirus increasing, Professor Neil Ferguson -
 feels we’re in the “early phases of a global pandemic”
-----------------------------------------------------------
2020/02/11 , Lipsitch
Far more worrisome than Wall Street getting it wrong is that DonaldTrump
 has been saying it will go away naturally in spring.
-------------------------------------------------------------

https://twitter.com/mlipsitch
Krammer

https://www.medrxiv.org/content/10.1101/2020.02.09.20021261v1.full.pdf
The effect of travel restrictions on the spread of the 2019
novel coronavirus (2019-nCoV) outbreak
the travel quarantine delays the overall epidemic progression by only 3 to 5 days.
Modeling results also indicate that sustained 90% travel restric-
tions to and from Mainland China only modestly affect the epidemic trajectory unless
combined with a 50% or higher reduction of transmission in the community.

----------------------------------------------
Steven Riley, a professor of infectious-disease dynamics at Imperial College,
“Where we’ll look next is Hong Kong and Singapore,” Dr. Riley said. “We may see a growth phase there next,” although, he added, researchers haven’t yet seen exponential growth outside of mainland China.
“I think it is likely we’ll see a global pandemic,” said Marc Lipsitch, a professor of epidemiology at Harvard T.H. Chan School of Public Health. “If a pandemic happens, 40% to 70% of people world-wide are likely to be infected in the coming year. What proportion of those will be symptomatic, I can’t give a good number.”
--

195
studies,summaries / serology, Yunnan, 2015
« on: February 02, 2020, 01:57:46 am »

https://link.springer.com/content/pdf/10.1007/s12250-018-0012-7.pdf
(Nov.2017)  Serological Evidence of Bat SARS-Related Coronavirus Infection
in Humans, China

[my selection from that paper:]

 to date, no evidence of direct transmission of SARSr-CoVs from bats
to people has been reported.
 In October 2015, we collected serum samples from 218 residents in four villages
in Jinning County, Yunnan  located 1.1–6.0 km from two caves (Yanzi and Shitou).
 85.3% farmers and 8.7% students. Most (81.2%) kept or owned livestock or pets,
and the majority (97.2%) had a history of exposure to or contact with livestock
or wild animals. Importantly, 20 (9.1%) participants witnessed bats flying close
to their houses,
 As a control, we also collected 240 serum samples from random blood donors
in 2015 in Wuhan,  where inhabitants have a much lower
likelihood of contact with bats due to its urban setting.

Our study provides the first serological evidence of
likely human infection by bat SARSr-CoVs or, potentially,
related viruses. The lack of prior exposure to SARS
patients by the people surveyed, their lack of prior travel to
areas heavily affected by SARS during the outbreak, and
the rapid decline of detectable antibodies to SARS-CoV in
recovered patients within 2–3 years after infection strongly
suggests that positive serology obtained in this study is not
due to prior infection with SARS-CoV (Wu et al. 2007).
The 2.7% seropositivity for the high risk group of residents
living in close proximity to bat colonies suggests that
spillover is a relatively rare event, however this depends on
how long antibodies persist in people, since other indi-
viduals may have been exposed and antibodies waned.
 From our previous studies of bat SARSr-CoVs in
the two caves near these villages, we have found geneti-
cally highly diverse bat SARSr-CoVs and evidence of
frequent coinfection of two or more different SARSr-CoVs
in the same bat (Ge et al. 2013).

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