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How many will die of Covid19 in the 2020s directly and indirectly

Less than 10,000
10 (14.7%)
10,000-100,000
9 (13.2%)
100,000-1,000,000
9 (13.2%)
One to ten million
13 (19.1%)
Ten to a hundred million
14 (20.6%)
Hundred million to one billion
9 (13.2%)
Over a billion
4 (5.9%)

Total Members Voted: 61

Voting closed: March 03, 2020, 12:39:52 AM

Author Topic: COVID-19  (Read 346832 times)

Archimid

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Re: Chinese coronavirus
« Reply #300 on: January 31, 2020, 12:14:26 PM »
Quote
Because of 5-6 days incubation period and the fact infection can hardly spread anymore we should be very close to peak coronavirus.

+1
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Tom_Mazanec

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Re: Chinese coronavirus
« Reply #301 on: January 31, 2020, 12:57:46 PM »
Latest from second favorite doomer:

The W.H.O. Just Prioritized Money Over Human Life
https://www.peakprosperity.com/the-w-h-o-just-prioritized-money-over-human-life/
Quote
Today the World Health Organization (W.H.O.) declared that the Wuhan coronavirus is indeed now a pandemic.
Scary news, right?
Well…not if you kept listening. The W.H.O. then proceeded to downplay the risk to public health and took pains to make it clear it doesn’t recommend placing restrictions on global trade & travel at this time.
What?!? When we may be in dealing with a viral outbreak as (or more!) virulent than the Spanish Flu? (aka The Great Influenza)
Folks, this is nothing less than a political decision to keep business/commerce flowing without regard to public health. The W.H.O. has chosen money over people’s lives:
Also in the news today: science journal The Lancet just released a study that finds initial evidence that men are substantially more vulnerable to coronaviruses than women.
Why? Watch the video below. Chris Martenson walks through the science behind the findings:
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wili

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Re: Chinese coronavirus
« Reply #302 on: January 31, 2020, 01:49:11 PM »
Pretty close to 10,000 world wide by now. 9,809 confirmed cases in China alone.  https://www.nbcnews.com/news/world/coronavirus-updates-latest-news-outbreak-global-response-n1127226

From NYT:

How Bad Will the Coronavirus Outbreak Get?

Here Are 6 Key Factors
Quote

•    How contagious is the virus?
    It seems moderately infectious, similar to SARS.

•    How deadly is the virus?
    It’s hard to know yet. But the mortality rate is probably less than 3 percent, much less than SARS.

•    How long does it take to show symptoms?
    Possibly between 2 to 14 days, allowing the illness to go undetected.

•    How much have infected people traveled?
    The virus spread quickly because it started in a transportation hub.

•    How effective will the response be?
    The W.H.O. has praised China’s efforts, but critics fear lockdown measures may not be enough.

•    How long will it take to develop a vaccine?
    A vaccine is still a year away — at minimum.

It seems to me, they missed another crucial factor here (at least one): How contagious are people before they are symptomatic, and for how long?

So we have a clear answer on this? As I recall, some Chinese authorities are saying it is contagious before symptoms emerge, but non-Chinese experts seem to be dubious.

https://www.nytimes.com/interactive/2020/world/asia/china-coronavirus-contain.html
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Sigmetnow

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Re: Chinese coronavirus
« Reply #303 on: January 31, 2020, 02:00:55 PM »
I'm In China. Here's What's Really Happening As The Country Faces The Coronavirus.
https://www.huffpost.com/entry/wuhan-coronavirus-china-experience_n_5e32ed53c5b69a19a4ab3a04
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Archimid

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Re: Chinese coronavirus
« Reply #304 on: January 31, 2020, 02:13:32 PM »
Fact. Paralyzing all trade and travel will stop nCoronavirus from spreading. If the trade is held for a month the threat will be over one way or the other.

Fact.  Paralyzing all trade and travel will starve millions to death.


This is not a choice. Travel and trade must continue while they can. Local quarantine is needed only because the break out already started.
I am an energy reservoir seemingly intent on lowering entropy for self preservation.

Archimid

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Re: Chinese coronavirus
« Reply #305 on: January 31, 2020, 02:30:51 PM »
Good reporting by the NYT in that article. They make the important caveats needed for the sars vs ncoronavirus comparison.
I am an energy reservoir seemingly intent on lowering entropy for self preservation.

Tigertown

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Re: Chinese coronavirus
« Reply #306 on: January 31, 2020, 04:55:46 PM »
Your own immune system will kill the virus. The problem is to get past the lipid coating. One simple trick is to get something in your body to compromise the viral lipid coating. I have been reading for years about MCT's and one substance found in coconut oil as well as milk. It is monolaurin, which the coating readily absorbs, trying to increase its protection, but resulting in the coating's destruction. Your immune system then attacks the actual virus. I have gotten this to work against the basic flu, but obviously have not had the new virus.

In the words of someone smarter than me,
 "While Monolaurin is most widely used as an anti-viral agent, it
also has beneficial effects against pathogenic bacteria, yeasts
and fungi; other fatty acids such as caprylic and sorbic acids are
more effective against yeasts, but ineffective against viruses.
In a study performed at the CDC, which focused on Monolaurin tested
strains of viruses, Monolaurin was able to solubulize the
enveloped membrane of 14 human RNA and DNA viruses (3).
These include influenza, RSV, Rubeola, Newcastle’s, Coronavirus,
Herpes Simplex types 1 & 2, Epstein-Barr Virus (EBV)
and cytomegalovirus. (Monolaurin has no effect on
naked viruses, such as polio, encephalitis virus, coxsachie, or pox
viruses.) Monolaurin works by disintegrating the lipid
envelope coat of viruses. Data from these studies suggest that the
loss of virus infectivity is associated with the solubilization
of Monolaurin into the envelope. The virus absorbs the fatty acid
for its own replication, but winds up destroying its own protective
coat.  "

The big problem with monolaurin is that it is available at a very low price and big pharmacy has no motive to promote it, though many agencies and clinics such as the Mayo clinic are aware of it.
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Bruce Steele

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Re: Chinese coronavirus
« Reply #307 on: January 31, 2020, 06:26:10 PM »
Chinese New Year is a very important market for worldwide sales of seafood to China. Local prices to fishermen for rock lobster have locally dropped by about half to $10.50lb . Lobster are shipped live and canceling the holiday celebration has undoubtably left importers holding large supplies. Lobster and Dungeness  crab are seasonal fisheries and so a price drop and demand destruction will hurt local fishermen. Aquaculture is also affected but aquaculture can hold off processing and still sell their fish when conditions improve. Wild caught fisheries lose their season , Calif. Dungeness crab was already operating on a truncated season because whale entanglement issues in Monterey Bay and low meat to shell ratios.
 https://www.intrafish.com/markets/live-updates-chinas-coronavirus-chaos-sucks-in-salmon-shrimp-lobster/2-1-746616

Shared Humanity

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Re: Chinese coronavirus
« Reply #308 on: January 31, 2020, 06:29:55 PM »


... If it takes root here it will fall hardest on the working poor, who don’t get paid if they don’t show up and/or fear losing their jobs if they don’t go to work. The lack of paid sick leave policies is a danger to all of us.


If I were a cook or cleaning person for the wealthy in DC and thought I might be sick, I'd start smearing phlegm and nasal secretions on surfaces all over the house.

Shared Humanity

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Re: Chinese coronavirus
« Reply #309 on: January 31, 2020, 06:36:26 PM »
The number of hospital beds in the US is under a million. There were nearly a million hospitalized cases of flu in the 2017-'18 season.

In general, based on such stats and from what I hear from healthcare professionals, we're already stretched to the max, and any significant further pressure will overwhelm the system.

That is no doubt even more true of some other places around the world that are now seeing their first cases arrive on their shores.

There are 6 confirmed cases in the U.S. We all need to take a deep breath.

sark

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Re: Chinese coronavirus
« Reply #310 on: January 31, 2020, 06:55:14 PM »
I am not a scientist

Alexander555

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vox_mundi

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Re: Chinese coronavirus
« Reply #312 on: January 31, 2020, 08:40:44 PM »


... If it takes root here it will fall hardest on the working poor, who don’t get paid if they don’t show up and/or fear losing their jobs if they don’t go to work. The lack of paid sick leave policies is a danger to all of us.


If I were a cook or cleaning person for the wealthy in DC and thought I might be sick, I'd start smearing phlegm and nasal secretions on surfaces all over the house.
Couldn't agree more. An excellent 'cure' for hyperpartisanship



Remember; don't forget the doorknobs!
« Last Edit: January 31, 2020, 09:34:11 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

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Alexander555

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Re: Chinese coronavirus
« Reply #313 on: January 31, 2020, 09:05:25 PM »
The local government in Wuhan even arrested 8 people because they informed other people what was going on. https://www.aljazeera.com/news/2020/01/diary-wuhan-native-week-coronavirus-quarantine-200131045152448.html

KiwiGriff

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Re: Chinese coronavirus
« Reply #314 on: January 31, 2020, 09:06:54 PM »
Animals can be driven crazy by placing too many in too small a pen. Homo sapiens is the only animal that voluntarily does this to himself.
Notebooks of Lazarus Long.
Robert Heinlein.

vox_mundi

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Re: Chinese coronavirus
« Reply #315 on: January 31, 2020, 09:15:43 PM »
US Underprepared for Coronavirus Due to Trump Cuts, say Health Experts
https://www.theguardian.com/world/2020/jan/31/us-coronavirus-budget-cuts-trump-underprepared

US preparedness to deal with the threat of coronavirus has been hampered by the personnel and budget cuts made by the Trump administration over the past three years, according to health experts.

... “You have to at least now be anticipating and responsibly planning against a sort of pandemic level scenario reaching the US,” Jeremy Konyndyk, who ran foreign disaster assistance in the Obama administration, said.

“The fact that they explicitly dismantled the pandemic office in the White House that was tasked with preparing for exactly this kind of a risk is hugely concerning,” said Konyndyk, now a senior policy fellow at the Center for Global Development. “Both the structure and all the institutional memory is gone now.”

Funding has also been cut drastically to the Centers for Disease Control and Prevention (CDC), forcing it to reduce or discontinue epidemic-prevention efforts in 39 out of the 49 countries it had been helping. Among the countries where CDC efforts were scaled back were Haiti, Rwanda and the Democratic Republic of Congo as well as China, where the agency provided technical assistance.

In its 2020 budget the Trump administration proposed a further 10% cut in CDC funding, equivalent to $750m. It zeroed out funding for epidemiology and laboratory capacity at state and local levels.

Funding will also dry up this year for a tiered epidemic response within the US. The system was set up in the aftermath of the Ebola scare, and involved identifying patients infected by “special pathogens” in frontline hospitals and their transfer up a chain of specially equipped regional hospitals where they could be safely treated.

After this year’s cuts, 10 advanced treatment facilities will still receive funding, but not the 60 other treatment centres one tier below.



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

Trump Administration Temporarily Barring Foreigners Who Visited China.
https://www.nytimes.com/2020/01/31/world/asia/coronavirus-china.html#link-20802680

President Trump has temporarily suspended entry into the United States for any foreign nationals who have traveled to China, the administration announced on Friday.

The action will restrict all foreign nationals who have been to China — other than immediate family of American citizens and permanent residents  — from entering the United States.

Beginning on Feb. 2, any United States citizen returning home who has been in the Hubei province of China within the past 14 days will be quarantined for up to 14 days, administration officials said. Those who have been to other parts of China within the past 14 days will be subject to “proactive entry screening” and up to 14 days of monitoring and self quarantine.

The United States will also funnel all flights from China to just a few airports, including Kennedy Airport, Chicago’s O’Hare and San Francisco International Airport.

The State Department on Thursday night issued a travel advisory telling Americans not to travel to China because of the public health threat posed by the dangerous new coronavirus. The department set the new advisory at Level 4, or red — its highest alert, reserved for the most perilous situations (like North Korea or Yemen).


« Last Edit: January 31, 2020, 10:29:50 PM by vox_mundi »
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vox_mundi

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Re: Chinese coronavirus
« Reply #316 on: January 31, 2020, 09:30:16 PM »
First Case of Coronavirus Confirmed in Sweden
https://www.thelocal.se/20200131/first-case-of-coronavirus-confirmed-in-jonkoping-sweden

A patient at the Ryhov county hospital in Jönköping, central-southern Sweden, has tested positive for the coronavirus, the Public Health Agency of Sweden (Folkhälsomyndigheten) confirmed to the website.

The patient is a woman who landed in Sweden on 24 January after visiting the Wuhan area in China. At that point she had no symptoms, said the agency.

But she later developed a cough and contacted the health services in Jönköping.

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

US Announces 14-day Quarantine on 195 Virus Evacuees
https://medicalxpress.com/news/2020-01-day-quarantine-virus-evacuees.html

The US on Friday issue a rare federal quarantine order of 14 days for 195 Americans who were evacuated from the Chinese city at the center of a global virus epidemic that has killed more than 200 people.

It is the first time in 50 years the Centers for Disease Control and Prevention (CDC) has issued such an order, and the two-week period began the day they left Wuhan, said senior CDC official Nancy Messonnier.

The latest move came after one individual tried to leave the base and was placed under quarantine by the state of California, said a second CDC official, Marty Citron, but he denied that that event had been the impetus.

"The last time that quarantine was used for a suspect case was in the 1960s for smallpox evaluation"

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

Lawmaker, local factory team for reusable, antibacterial masks, though efficacy against viruses unknown
https://www.scmp.com/news/hong-kong/health-environment/article/3048481/coronavirus-lawmaker-local-factory-team-reusable

Hong Kong’s textile industry could start making and selling reusable surgical masks using an antibacterial fabric within 10 days amid the city’s ongoing shortage, a lawmaker for the sector said on Friday.

Textile and garment industry legislator Felix Chung Kwok-pan told an RTHK radio programme he was working with a local manufacturer to make reusable face masks out of a fabric previously developed by researchers at the Hong Kong Polytechnic University, which cautioned the fabric has not yet been proven to prevent viruses.

“The government has said that 30 million masks are on the way, but the problem is these masks need to be thrown out after eight hours of use. If everyone in the city needs a mask, that's 200 million a month,” the Liberal Party leader said.

“If the virus continues for months, supply will never be stable.”

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

China Goes Global in Search for Protective Suits, Masks and Goggles as Coronavirus Infections Begin To Take Off
https://www.scmp.com/news/china/society/article/3048379/china-goes-global-search-protective-suits-masks-and-goggles

In Beijing, the Ministry of Industry and Information Technology estimated that Hubei was in need of 100,000 pieces of protective clothing and equipment every day, but that the country’s 40 manufacturers could only produce 30,000 items a day.

Unicef, South Korea, Japan and Chinese embassies are sourcing and shipping more, while Taiwan says it must focus on its own needs

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

India’s Homeopathic ‘Cure’ for Coronavirus ‘Immature and Irresponsible’
https://www.scmp.com/week-asia/health-environment/article/3048398/indias-homeopathic-cure-coronavirus-immature-and

The Indian Medical Association has assailed the Indian ministry that promotes traditional healing for peddling “immature and irresponsible” homeopathic remedies to prevent infections of the novel coronavirus.

As India reported its first case of coronavirus this week and China and other nations accelerated efforts to stop the spread of the outbreak, New Delhi’s Ministry of Ayurveda, Yoga & Naturopathy, Unani, Siddha, Sowa Rigpa and Homoeopathy (AYUSH) on Wednesday publicised its recommended cure for the disease: homeopathic treatments and other alternative medicines.

Along with generic recommendations and personal hygiene tips, the communique advised that patients ingest various herbal concoctions to “strengthen the immune system” and other traditional medicines “useful in [the] symptomatic management of coronavirus infection”.

... “Why do the systems of medicines which do not even recognise microbes as disease-causing agents… [say] they can treat the coronavirus?”

... Asked about the possible side-effects of the recommended treatment for the coronavirus – a highly diluted solution of arsenic trioxide used by homoeopaths that has in the past resulted in arsenic poisoning due to negligence – Joshi said the suggested quantity would not have serious consequences.

The fortunate part about homoeopathy is, one need not worry much about the type of virus,” Joshi claimed. “Through the generalised symptoms of all the patients, we’ll be able to find an effective remedy” for any virus that can be used as “a preventive medication for all the population”.
« Last Edit: January 31, 2020, 10:10:01 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

vox_mundi

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Re: Chinese coronavirus
« Reply #317 on: January 31, 2020, 09:44:53 PM »
Just a random thought ...

With the list of airlines (over 20) that have suspended flights to China growing daily and the likelihood of this occurring globally in the months ahead; this would be a good time to get some quantitative correlation data in regards to 'global dimming'

https://www.reuters.com/article/us-china-health-airlines-factbox/factbox-airlines-suspend-china-flights-over-coronavirus-idUSKBN1ZT1RZ
https://www.scmp.com/news/asia/east-asia/article/3048417/coronavirus-global-travel-restrictions-imposed-chinese
https://www.theguardian.com/environment/2012/may/11/global-dimming-pollution

This may add 0.1-0.5°C by this summer (in the NH)

Just a thought.  :)
« Last Edit: January 31, 2020, 10:01:09 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

Bernard

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Re: Chinese coronavirus
« Reply #318 on: January 31, 2020, 10:37:27 PM »
Looking at the figures published by John Hopkins CSSE at https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

As I write, 204 out of 213 deaths took place in Hubei province, with 5806 confirmed cases out of 9925.
So, in the province, where the epidemy started the mortality is over 3%.

The second province in number of confirmed cases is Zheijang with 538 cases, but not a single death yet. How do you folks interpret this?

oren

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Re: Chinese coronavirus
« Reply #319 on: January 31, 2020, 10:45:11 PM »
Some ideas: Either the virus is not as violent when transferred person to person as opposed to the initial contagion (implausible), or not enough time has passed to generate casualties, or the medical treatment was prompt, or the actual number of cases in Hubei was much higher than reported (with mild cases unreported).

Tom_Mazanec

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Re: Chinese coronavirus
« Reply #320 on: January 31, 2020, 10:50:36 PM »
US Declares Public Health Emergency, Travelers Returning From Hubei To Be Quarantined
https://www.zerohedge.com/health/watch-white-house-holds-coronavirus-public-briefing
Quote
Anyone who expected Trump's task force to give algos the all clear to BTFD, will be disappointed because moments ago Trump's coronavirus tzar, Azar said the US is declaring a public health emergency, US citizens returning from Hubei will be quarantined for 14 days and all flights coming from China will be funneled to 7 airports:

I know Zerohedge is supposed to be unreliable, but this kind of news seems hard to fake.
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crandles

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Re: Chinese coronavirus
« Reply #321 on: February 01, 2020, 12:12:01 AM »
Mainland China outside Hubei 3977 confirmed cases 9 deaths. So it isn't just Zhejiang but all provinces other than Hubei.

Going back to 26 Jan Hubei had 76 deaths and 1423 confirmed cases. Rest of mainland China 4 deaths from 927 confirmed cases. So it isn't recent. Only 5 deaths while confirmed cases increase by 3050 from 927 to 3977 is I think to be expected: If well enough to travel, milder and it probably takes more time before death.

Ability to test wouldn't be available until well after virus identified. Testing probably started close to same time everywhere which leaves less of a time gap between virus arrival in other provinces and testing starting. Hubei ability to test sufficiently also likely strained. So I think it likely there are many more actual infections to confirmed cases in Hubei than elsewhere.

So a number a factors:
Time before death
If well enough to travel, perhaps milder infection more likely and longer before death
Hubei more undercounted in number of confirmed cases
Medical facilities available and consequent quality of treatment

With these explanations, I am not sure if we need extra possible explanations like virus mutated to be less deadly and more transmissible which might be sensible evolution for the virus.

vox_mundi

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Re: Chinese coronavirus
« Reply #322 on: February 01, 2020, 12:12:30 AM »
China virus death toll rises to 258
https://www.theguardian.com/world/live/2020/jan/31/coronavirus-live-updates-china-wuhan-death-toll-who-global-health-emergency-latest-news

The number of confirmed deaths from China’s coronavirus outbreak has risen to 258, as authorities in hardest-hit Hubei province reported 45 new fatalities, AFP reports.

In its daily update, the provincial health commission also said newly confirmed cases of infection in Hubei continued to grow at a steady pace, with 1,347.

That puts the national total over 11,000, based on numbers previously issued by the central government.

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

Coronavirus: Canada Reports Fourth Case, a Patient Who Tested Negative at First
https://www.scmp.com/news/world/united-states-canada/article/3048506/coronavirus-outbreak-canada-gets-chinas-nod

The female university student in her 20s arrived in Toronto on January 23 from Wuhan, China, the epicentre of the outbreak. Initially asymptomatic, she reported to hospital the next day, where she initially tested negative. A second test at Canada’s National Microbiology Laboratory in Winnipeg, Manitoba, confirmed the case as positive.

“It is clear that we are learning more and more about the coronavirus each day, and our testing procedures are evolving and getting more and more precise,” Ontario’s Chief Medical Officer of Health Dr David Williams said in a statement after a news conference in Toronto.
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

Sam

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Re: Chinese coronavirus
« Reply #323 on: February 01, 2020, 01:02:33 AM »
Looking at the figures published by John Hopkins CSSE at https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

As I write, 204 out of 213 deaths took place in Hubei province, with 5806 confirmed cases out of 9925.
So, in the province, where the epidemy started the mortality is over 3%.

The second province in number of confirmed cases is Zheijang with 538 cases, but not a single death yet. How do you folks interpret this?

One of the difficulties with a fast moving virus like this is that the numbers can be very confusing until you remember that it is behaving mostly as an exponential growth curve and that there are time delays involved. Also, the parameters involved have ranges, and specific conditions in different areas can either mask the numbers, or make them look worse, or distort them in other ways.

Over time as various control strategies are employed, as people do various things, the basic parameters will or at least can change values. If the virus mutates, that can also have a large impact - though, so far that is not the case here.

More than this, non-obvious things like differences in age distributions, gender ratios, health status, other life style and disease factors (smoking, diabetes, ...) come into play and can have large importance.

Do not take any of what follows as correct, true, or valid for predicting anything. These are crude numbers and a very simple model to get a ballpark idea of what is happening, and to help answer Bernard's question - (tryin to make sense of the numbers).

Taking all of that, plus inherent randomness and other factors into account - the disease outbreak looks to be something like this:

1) The virus is spreading person to person.
2) The "average" contact transmission (R0) seems to be between 2 and 6 people infected by each person with the disease. The average R0 seems to be generally between 2.2 and 5.6 with an average from all of the available data of somewhere near 2.7
3) The growth of the number of people infected as reflected by "confirmed" infections was initially growing at about a factor of 1.32 per day. More recently it has averaged about 1.62 per day. Through the whole period factors in the range of 1.32 to 1.62 can reasonably match various parts of the data. Let's use a midpoint value of 1.42 (because it shows up a lot - but then too, so do 1.57 and 1.62).
4) Using that daily growth ratio and the R0, we can estimate the time from exposure to infectivity of the next generation - i.e. the generation time. Do that by taking the natural log of the R0 and dividing by the natural log of the growth factor - so ln(2.7)/ln(1.42) for example. In this case, that equals 2.83 days. That seems awfully fast. But then too, this is an "average" or more properly an equivalent behavior as the real distributions show. Another common pairing seems to be an R0 of 4.08 and a growth of 1.62 => 2.91 days per generation.

That now sets the basic form for the growth of the infected population. Even minor changes in those parameters can cause wild changes in the results. Do not rely on the results. They are cautions only. This is an exponential growth curve. So the trick then for this very simple (overly simple) model is to use the real data and various choices of parameters to best fit the parameters to the data, while also sanity checking that those make any sense. Even then, take the results with a huge dose of skepticism. This is an overly simple model.

Now, we have the basics, an Ro =2.7, A growth factor of 1.42/day, and a generation time of 2.83 days.

Next let's look at what we know from field reports. People apparently show symptoms about 5-7 days after exposure. Lets say that on average they go to hospital then. They get counted as "suspect cases". Over the next day, they are tested by PCR and the results return. They are either now cleared of having this virus, or they are confirmed. Given the size of the outbreak in Wuhan (Hubei), the vast majority of those are confirmed.

The confirmed population then is one day after the suspect count. I.e. it represents a population 1 day earlier in the growth and spread of the virus.

Next lets look at the people who died. We know hospitalizations last an average of 23.5 days. Using the data from the hospitals, we can estimate how far back in time their cohort of infected people was. One report put that at 6 days. Another suggested about 5.9 days. Let's say 6 days. So, take the count of those who died times the growth factor raised to the power of the number of days = 1.42^6 = 8.2 times the count of dead.

On January 29, the confirmed count was 8,650. The dead count was 170. And the survived count was 130. That report may still not show effects of the quarantine, and so should be good for our purposes.

Take the 8,650 count of confirmed infected persons today and move it back in time 6 days by dividing by 1.42^6 = 1,055 people in the cohort those who died came from. Now divide 170 by 1,055. The result = 16.1% of the cohort dying. Take that with a huge grain of salt. We know from SARS that it's death rate averaged about 10%. MERS averaged about 40%. So 16% is not unreasonable. But this is a really tentative calculation based on lots of assumptions using exponential growth data. It would likely be safe to assume that the actual death rate is somewhere in the range of 10-20% based on these parameters.

We do not have (or at least I have not seen) good data on the average time from admission to being declared disease free. But we can work the problem backward to get an estimate. Take the current count 8,650. We need to move back X days to the cohort that the survivors came from. Take the survivor count of 130 and divide by the fraction surviving to estimate the original cohort they came from. 130 /(1 - 0.161) = 155. Now 8,650 = 155 * 1.42^X, solve for X = 11.5 days.

Now sanity check that. Is it reasonable that people take 5.5 days longer to be confirmed recovered than to die based on what we know? It is well within the 23.5 days. But that raises a question why on average people are still in hospital for 12 days longer than on average being confirmed to have survived. That might be reasonable to avoid spreading infections by assuring they are no longer contagious. I simply do not know if that is reasonable. The large time span with an intense need for beds makes me suspect that tis points to a serious flaw in the assumptions - an error of some sort.

Anyway, what you can see from this is that the estimate of those currently infected with pure exponential growth and no intervening factors would be about 1.42^7 = 11.64 times the current confirmed infected count. The count of those suspected to be infected should be about 1.42 times the infected count. The count of those who have died should be about 1/45th of the current confirmed count. And the count fo those who survived should be about 70-90% of the count of those who died (76% by the math in this example).

So now lets go back and think about this again. We aren't dealing with just one generation of people. The counts represent the time summed total of many different generations. To do this calculation more correctly (still an overly simple model), we would have to do all of those in parallel and add them. We would also need to do a stochastic calculation using the uncertainty bands for all of this. As you can see, even using this "simple" exponential growth model, the problem gets complicated quickly.

But the complications get worse. We have information now that this disease predominantly kills people over age 55. The precise data for that is also messy, as the death rate has to be calculated using this same messy exponential math (or more complicated models). It is all too easy to get that wrong. That can be confused by things like how long it takes for elderly people to succumb compared to younger people. The younger people who presumably survive longer before dying represent an earlier smaller cohort of people. If we estimate their death rate from current data, it will look like they are more resistant even if they aren't. Etc...

We also seem to be seeing a strong gender difference with 70% of the fatalities being male. That too may be caused by artificial biases. For example, if men have "better" access to health care, they may get earlier treatment, where the women might die at home and be counted later. Or, the men might be the ones going out into areas where they become infected, while the women don't. I do not know that any of these are true for this population. Nor do I mean to speculate that they are or even might be. I just mean to point out that fairly simple biases like these can make large differences in the short term results while the virus is spreading exponentially.

Once the quarantine went into effect, huge changes happened. People know to wear masks and use good hygiene practices to avoid spreading the disease. And these are societally mandated and enforced. Also, because of other factors, people are staying indoors and not frequenting the usual places. This dramatically reduces the opportunity for viral spread. But with an at least 2.85 day generation time and a 5-7 day time for appearance of symptoms, the effects of these changes won't be seen at the earliest until 5-7 days after they began. That is just about now.

Does this help?

Sam

Bearing all of that in mind. We still know far too little to be certain about much. We can be certain that it is a fast spreading lethal disease.

Sam

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Re: Chinese coronavirus
« Reply #324 on: February 01, 2020, 01:09:44 AM »
It is morning in China. Here are the latest numbers.

截至 2020-01-31 16:01 全国数据统计
数据说明
11,821 确诊病例
17,988 疑似病例
     259 死亡人数
     243 治愈人数

As of 2020-01-31 16:01 National Statistics
the data shows
11,821 confirmed cases
17,988 suspected cases
     259 deaths
     243 cured

The effects of the quarantine may be beginning to show. This looks tentatively like an R0 reduction from 2.7 to 1.7.

Sam

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Re: Chinese coronavirus
« Reply #325 on: February 01, 2020, 01:14:37 AM »
Wow.
I am not a scientist

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Re: Chinese coronavirus
« Reply #326 on: February 01, 2020, 01:26:49 AM »
Thank you for the clear explanation Sam.
A complex topic laid out well enough that even I can understand your logic.
.
Animals can be driven crazy by placing too many in too small a pen. Homo sapiens is the only animal that voluntarily does this to himself.
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KiwiGriff

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Re: Chinese coronavirus
« Reply #327 on: February 01, 2020, 01:37:27 AM »
Animals can be driven crazy by placing too many in too small a pen. Homo sapiens is the only animal that voluntarily does this to himself.
Notebooks of Lazarus Long.
Robert Heinlein.

Sam

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Re: Chinese coronavirus
« Reply #328 on: February 01, 2020, 02:48:19 AM »
Thank you for the clear explanation Sam.
A complex topic laid out well enough that even I can understand your logic.
.

KiwiGriff

You are welcome. As I said, that is an extremely simplified version. I hoped it was simple enough to follow. I am grateful that it is. It won't be for most people. Though it gets the right shape of the problem, it isn't really right.  It is more of a thumbnail estimate. And, I think you can see all of the complexities that follow to do it correctly. Still, thumbnail estimates are useful, even if they aren't accurate - mostly for making the problem easier to understand.

More even, it I think helps point out that there are multiple ways to attack the problem. Tracing individual cases with all of their complexities gives a much more accurate estimate of the answer. But that takes a lot of time and effort. Early in a rapidly expanding pandemic, that simply won't be fast enough. Understanding the general shape of the problem can give sufficient insights to help guide thinking about the problem and what to do in response. And more importantly - help avoid making some really big blunders.

One such insight that appears to flow from the data and even this simple analysis is the idea that the generation time is shorter than the time to appearance of symptoms. Recognizing that is hugely important in deciding what to do, as it suggests that there are silent carriers that will spread virus without showing symptoms.

That has now been confirmed several times. So the insight wasn't wrong, though it could have been.

The impact in the potential error that might come from making such a judgement and acting on it, is small compare to the gain in doing things to stop the early spread of the disease into new populations.

That involves things like precautionary quarantining small populations of people evacuated from hot zones. There is a real burden to that population. But that burden is small compared to the societal risk of not doing that.

The Chinese government took that a giant leap further in quarantining 56 million people. That too appears to have been a very good judgement on their part, though the long term impacts on the disease spread will take time to sort out. And the societal impacts and responses to that will no doubt take a generation to unfold. There are all sorts of serious societal issues to unravel and consider. That will give generations of sociologists, virologists, epidemiologist, politicians and others a lot to work on for a very long time.

Whatever answer and conclusions they reach will apply to them, and only less so to others in other countries with different societal dynamics and expectations.

Sam

« Last Edit: February 01, 2020, 02:53:56 AM by Sam »

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Re: Chinese coronavirus
« Reply #329 on: February 01, 2020, 02:50:17 AM »
Thanks for the analysis, Sam ...  +1

---------------------
Evolving Statistics
https://www.scmp.com/news/china/article/3048518/coronavirus-case-load-and-death-toll-china-rise-epicentre-hubei-province

Authorities in China’s coronavirus epicentre of Hubei province reported 45 new deaths from the illness and 1,347 new confirmed cases on Saturday, both daily record highs.

According to the National Health Commission in Beijing, 11,791 cases have been confirmed in China’s 31 provinces, municipalities and autonomous regions as of Friday (Globally: 11,943). The new deaths have brought the nationwide death toll to 259.

As of Friday, Hubei had 7,153 confirmed cases, with 36,838 still under observation for infection, according to the provincial health authority. Some 956 individuals with the illness are in “severe” condition and 338 are in “critical” condition.

Underscoring the apparent ease with which the illness may be spreading, a recent statement by the government of Xinyu, a city in Jiangxi province – which is adjacent to Hubei – said 17 new cases have been confirmed in the city, and that 15 of them were infected by a single person.

... Beijing has sent more than 7,000 medical workers to the province of Hubei to help fight the deadly disease.

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

'The City Is Suffocating': Diary of the Wuhan Coronavirus Lockdown
https://www.theguardian.com/world/2020/jan/31/the-city-is-suffocating-diary-of-the-wuhan-coronavirus-lockdown

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

Reuters is reporting that the northern Chinese city of Tianjin has ordered schools and non-essential companies to remain closed until further notice to curb the spread of the coronavirus that has already infected thousands in the country, a local government-run newspaper said.

Tianjin Daily, said the date when work and school could resume would be announced at a later stage, citing a local government committee responsible for controlling the epidemic.

Tianjin, which has a population of around 15 million and borders capital Beijing, had 32 confirmed cases of coronavirus as of 10pm local time on 31 January. (... that will cost Billions $)

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

Coronavirus: How Facebook Clickbait Fuels a Perfect Storm of Fake News On China’s Doorstep
https://www.scmp.com/week-asia/health-environment/article/3048453/wuhan-coronavirus-how-facebook-clickbait-fuels-perfect

High internet penetration and poor digital literacy provide fertile ground for wild claims and misinformation in Myanmar

Some people in Myanmar believe false rumours that onions and alcohol are antidotes, while others rely on celebrity news pages for ‘the truth’

-----------------------
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

sedziobs

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Re: Chinese coronavirus
« Reply #330 on: February 01, 2020, 02:55:29 AM »
The effects of the quarantine may be beginning to show. This looks tentatively like an R0 reduction from 2.7 to 1.7.

Are the confirmed cases limited by the number of tests that can be performed each day?

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Re: Chinese coronavirus
« Reply #331 on: February 01, 2020, 03:14:27 AM »
The effects of the quarantine may be beginning to show. This looks tentatively like an R0 reduction from 2.7 to 1.7.

Are the confirmed cases limited by the number of tests that can be performed each day?

I hope that is not the case, but there are reports of limited testing supplies available.

2 things trouble me today.

1) Can anyone confirm the validity of the videos circulating, shows bodies lying in the streets?  Those videos paint a much larger picture of what is going on if valid?

2)The 7th confirmed German case is apparently the child of one of the employees of the company where the virus was first reported.  The reason this troubles me so much, is if this child went to school at any point while carrying this virus.  Germany could be the next place we see a large cluster of cases outside of China. :-\

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Re: Chinese coronavirus
« Reply #332 on: February 01, 2020, 04:08:31 AM »
SH wrote:
Quote
There are 6 confirmed cases in the U.S. We all need to take a deep breath
.

About two weeks ago, there were only a hand full of cases of this virus in the world. Now there are well over 11,000 confirmed cases (and likely many times that unconfirmed).

Maybe...get a high quality face mask before taking that deep breath?? :)

Meanwhile: ...Wuhan coronavirus can spread even when people have no symptoms

https://www.cnn.com/2020/01/31/health/coronavirus-asymptomatic-spread-study/index.html
« Last Edit: February 01, 2020, 04:13:33 AM by wili »
"A force de chercher de bonnes raisons, on en trouve; on les dit; et après on y tient, non pas tant parce qu'elles sont bonnes que pour ne pas se démentir." Choderlos de Laclos "You struggle to come up with some valid reasons, then cling to them, not because they're good, but just to not back down."

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Re: Chinese coronavirus
« Reply #333 on: February 01, 2020, 04:28:23 AM »
China Virus Cases May Be Undercounted Even With 3,000% Surge
https://www.bloomberg.com/amp/news/articles/2020-01-31/china-virus-cases-surging-3-000-may-be-undercounting-infections

Shortage of testing kits creates bottlenecks to process

A shortage of testing kits and overworked hospital staff are straining China’s health system, hampering efforts to accurately track how many people have the pathogen. The result is a hectic and imprecise process that’s creating bottlenecks as health experts attempt to pin down the scope of a disease that has claimed more than 200 lives.

The challenge of keeping up with the tally can be seen in Hubei, at the center of the outbreak.

The province can process about 6,000 tests a day, health commission director Liu Yingzi told a press briefing Wednesday, noting that Hubei had about 50,000 test kits in stock. But with 5,806 confirmed cases and 32,340 people under observation, it’s uncertain if that is enough.



... Jonathan Yu, a doctor at a university hospital in Wuhan, is on the front lines, testing patients for the coronavirus. Accurately spotting the virus isn’t easy and can take several attempts, he said.

“A patient may be found as negative for the first or second test, and then found to be positive the third time,” said Yu. “It is like fishing in a pond: You did not catch a fish once, but that does not mean the pond does not have fish.”


Another doctor in the city who declined to be identified said her hospital was facing shortages of testing kits to confirm that people have the disease, as well as lacking in spare beds and respirators for patients.

Chinese human rights lawyer Chen Qiushi said in a video posted on social media Jan. 29 that some hospitals in the city of Wuhan don’t have enough kits and are telling patients that severe cases have to be prioritized. Chen, who has expressed anti-Communist Party sentiments in the past, cited interviews with people who suspected they have the virus as well as visits to local hospitals.



... China is making moves to improve the situation. Health officials approved two new kits on Tuesday, in addition to the existing four types, according to Xinhua News Agency. One of the two new kits can give results in about 30 minutes, shortening the time needed to diagnose cases, according to Technology Daily.

Roche Holding AG is also producing kits, and the government says it’s streamlining transport access to make sure relevant supplies get through. However, Roche said Thursday it was still having trouble getting its equipment to where it’s needed.

Yu, the Wuhan doctor, said the shortage of virus detection kits has lessened recently, although there is still a shortage of masks, glasses and other supplies.

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

Agence France-Presse reports that African countries are scrambling to avert an outbreak of the rapidly spreading coronavirus strain, as health officials warn that the poorest countries are ill-equipped to combat the deadly disease.

Across the continent, governments have stationed nurses at airports to check for feverish passengers and have suspended Chinese entry visas, while ordinary people grow increasingly nervous.

There have been no verified infections in Africa to date, but deep trade links with China and often overstretched healthcare systems are raising concerns about the capacity to respond to an outbreak.

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

https://www.news-medical.net/amp/news/20200130/Wuhan-coronavirus-is-genetically-different-from-human-SARS-MERS-CoV-study-found.aspx

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Lu, Roujian et al. The Lancet,
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

...All ten genome sequences were very similar, with 99.98 percent sequence identity, indicating a very recent emergence of the virus into humans. Also, the 2019-nCoV was closely related to two bat-derived SARS-like coronaviruses, the bat-SL-CoVZXC21, and bat-SL-CoVZC45, which shared 88% of the genetic sequence. These strain samples were collected in 2018 from Zhoushan, eastern China.

However, the scientists found that the current coronavirus strain samples were more distant from SARS-CoV and the MERS-CoV, with 79 percent and 50 percent identity, respectively.


The study findings unveiled that the Wuhan coronavirus fell within the subgenus Sarbecovirus of the genus Betacoronavirus, mostly similar to its closest relatives, the bat-derived coronaviruses, and genetically distinct from the human SARS. But the Wuhan coronavirus has a similar receptor-binding domain structure to that of human SARS, which means the virus utilizes the same molecular doorway as SARS to enter human cells.

"It is striking that the sequences of 2019-nCoV described here from different patients were almost identical. This finding suggests that 2019-nCoV originated from one source within a very short period and was detected relatively rapidly. However, as the virus transmits to more individuals, constant surveillance of mutations arising is needed," Professor Weifeng Shi, Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, China, said in a statement.

... “These data are consistent with a bat reservoir for coronaviruses in general and 2019-nCoV in particular. However, despite the importance of bats, it seems likely that another animal host is acting as an intermediate host between bats and humans," Professor Guizhen Wu, Chinese Center for Disease Control and Prevention, said.

She believes that though bats are the likely original host of the virus, there might be an intermediate host of the virus, between bats and humans. She noted that the first surge of coronavirus cases started late in December 2019, a period when most of the bat species are hibernating. Also, she emphasized that before the outbreak, there were no bats sold or found in the Huanan seafood market, while many mammals and other non-aquatic animals were sold.

In both the MERS and SARS infections, bats served as the natural reservoir, with another animal acting as an intermediate host. Therefore, she said that a wild animal might have acted as a hidden virus reservoir, posing threat to human populations.
« Last Edit: February 01, 2020, 04:43:10 AM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

sark

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Re: Chinese coronavirus
« Reply #334 on: February 01, 2020, 05:09:14 AM »
Thank you for this, vox_mundi

Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30260-9/fulltext

"This new modelling study estimates 75,800 individuals in the Chinese city of Wuhan may have been infected with 2019 novel coronavirus (2019-nCoV) as of January 25, 2020 - but authors caution that the true size of the epidemic remains unclear "

As of January 25th 75,800 in Wuhan alone?  The only bright spot might be that the true # of cases may already be very large, giving the disease a lower fatality rate overall.  International cases remains a clear barometer

https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases
I am not a scientist

Sam

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Re: Chinese coronavirus
« Reply #335 on: February 01, 2020, 08:02:15 AM »
China Virus Cases May Be Undercounted Even With 3,000% Surge
https://www.bloomberg.com/amp/news/articles/2020-01-31/china-virus-cases-surging-3-000-may-be-undercounting-infections

Shortage of testing kits creates bottlenecks to process

A shortage of testing kits and overworked hospital staff are straining China’s health system, hampering efforts to accurately track how many people have the pathogen. The result is a hectic and imprecise process that’s creating bottlenecks as health experts attempt to pin down the scope of a disease that has claimed more than 200 lives.

The challenge of keeping up with the tally can be seen in Hubei, at the center of the outbreak.

The province can process about 6,000 tests a day, health commission director Liu Yingzi told a press briefing Wednesday, noting that Hubei had about 50,000 test kits in stock. But with 5,806 confirmed cases and 32,340 people under observation, it’s uncertain if that is enough.



... Jonathan Yu, a doctor at a university hospital in Wuhan, is on the front lines, testing patients for the coronavirus. Accurately spotting the virus isn’t easy and can take several attempts, he said.

“A patient may be found as negative for the first or second test, and then found to be positive the third time,” said Yu. “It is like fishing in a pond: You did not catch a fish once, but that does not mean the pond does not have fish.”


Another doctor in the city who declined to be identified said her hospital was facing shortages of testing kits to confirm that people have the disease, as well as lacking in spare beds and respirators for patients.

Chinese human rights lawyer Chen Qiushi said in a video posted on social media Jan. 29 that some hospitals in the city of Wuhan don’t have enough kits and are telling patients that severe cases have to be prioritized. Chen, who has expressed anti-Communist Party sentiments in the past, cited interviews with people who suspected they have the virus as well as visits to local hospitals.



... China is making moves to improve the situation. Health officials approved two new kits on Tuesday, in addition to the existing four types, according to Xinhua News Agency. One of the two new kits can give results in about 30 minutes, shortening the time needed to diagnose cases, according to Technology Daily.

Roche Holding AG is also producing kits, and the government says it’s streamlining transport access to make sure relevant supplies get through. However, Roche said Thursday it was still having trouble getting its equipment to where it’s needed.

Yu, the Wuhan doctor, said the shortage of virus detection kits has lessened recently, although there is still a shortage of masks, glasses and other supplies.

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

Agence France-Presse reports that African countries are scrambling to avert an outbreak of the rapidly spreading coronavirus strain, as health officials warn that the poorest countries are ill-equipped to combat the deadly disease.

Across the continent, governments have stationed nurses at airports to check for feverish passengers and have suspended Chinese entry visas, while ordinary people grow increasingly nervous.

There have been no verified infections in Africa to date, but deep trade links with China and often overstretched healthcare systems are raising concerns about the capacity to respond to an outbreak.

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

https://www.news-medical.net/amp/news/20200130/Wuhan-coronavirus-is-genetically-different-from-human-SARS-MERS-CoV-study-found.aspx

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Lu, Roujian et al. The Lancet,
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

...All ten genome sequences were very similar, with 99.98 percent sequence identity, indicating a very recent emergence of the virus into humans. Also, the 2019-nCoV was closely related to two bat-derived SARS-like coronaviruses, the bat-SL-CoVZXC21, and bat-SL-CoVZC45, which shared 88% of the genetic sequence. These strain samples were collected in 2018 from Zhoushan, eastern China.

However, the scientists found that the current coronavirus strain samples were more distant from SARS-CoV and the MERS-CoV, with 79 percent and 50 percent identity, respectively.


The study findings unveiled that the Wuhan coronavirus fell within the subgenus Sarbecovirus of the genus Betacoronavirus, mostly similar to its closest relatives, the bat-derived coronaviruses, and genetically distinct from the human SARS. But the Wuhan coronavirus has a similar receptor-binding domain structure to that of human SARS, which means the virus utilizes the same molecular doorway as SARS to enter human cells.

"It is striking that the sequences of 2019-nCoV described here from different patients were almost identical. This finding suggests that 2019-nCoV originated from one source within a very short period and was detected relatively rapidly. However, as the virus transmits to more individuals, constant surveillance of mutations arising is needed," Professor Weifeng Shi, Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, China, said in a statement.

... “These data are consistent with a bat reservoir for coronaviruses in general and 2019-nCoV in particular. However, despite the importance of bats, it seems likely that another animal host is acting as an intermediate host between bats and humans," Professor Guizhen Wu, Chinese Center for Disease Control and Prevention, said.

She believes that though bats are the likely original host of the virus, there might be an intermediate host of the virus, between bats and humans. She noted that the first surge of coronavirus cases started late in December 2019, a period when most of the bat species are hibernating. Also, she emphasized that before the outbreak, there were no bats sold or found in the Huanan seafood market, while many mammals and other non-aquatic animals were sold.

In both the MERS and SARS infections, bats served as the natural reservoir, with another animal acting as an intermediate host. Therefore, she said that a wild animal might have acted as a hidden virus reservoir, posing threat to human populations.

Thank you for finding this info. It is very important. It is yet another of the growing list of complications and uncertainties. If the hospitals have a growing backlog of tests, that could delay reporting. Delays in reporting would (if and when they occur) falsely look like a slowing in the exponential rise of the number of infected people.

Based on the rate of rise, the current Size of the population seeking care, and the potential testing rate limits, we may be very close to the point where the confirmed numbers cease to be useful, and may instead become misleading (lending to false confidence the pandemic is slowing when it isn’t).

Sam
« Last Edit: February 01, 2020, 10:55:30 AM by Sam »

morganism

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Re: Chinese coronavirus
« Reply #336 on: February 01, 2020, 11:14:04 AM »
2019 Corona virus has 4 inserts that match HIV, showing possible bio-hacking.

Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1

https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf

" The  finding  of  4  unique  inserts  in  the  2019-nCoV,  all  of  which  have identity  /similarity  to  amino  acid  residues  in  key  structural  proteins  of  HIV-1  is  unlikely  to  be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.  ".

Unexpectedly, all the insertions got aligned with Human immunodeficiency Virus-1 (HIV-1). F

"As none of these 4 inserts are present in any other coronavirus, the genomic region encoding these inserts represent ideal candidates for designing primers that can distinguish 2019-nCoV from other coronaviruses".

"This  indicates  that  these  insertions  have  been  preferably  acquired  by  the  2019-nCoV, providing it with additional survival and infectivity advantage. Delving deeper we found that these insertions were similar to HIV-1. Our results highlight an astonishing relation between the gp120 and Gag protein of HIV, with 2019-nCoV spike glycoprotein. These proteins are  critical for  the viruses  to  identify  and  latch  on  to  their  host  cells  and  for    viral  assembly  (Beniac  et  al.,  2006). Since surface proteins are responsible for host tropism, changes in these proteins imply a change in  host  specificity  of  the  virus.  According  to  reports  from  China,  there  has  been  a  gain  of  host specificity in case 2019-nCoV as the virus was originally known to infect animals and not humans but after the mutations, it has gained tropism to humans as well. "


Tom_Mazanec

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Re: Chinese coronavirus
« Reply #337 on: February 01, 2020, 12:05:49 PM »
The effects of the quarantine may be beginning to show. This looks tentatively like an R0 reduction from 2.7 to 1.7.

Are the confirmed cases limited by the number of tests that can be performed each day?
Even if they are not, lowering R0 to 1.7 is not enough. We have to get it below 1 to beat this thing.
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crandles

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Re: Chinese coronavirus
« Reply #338 on: February 01, 2020, 01:07:36 PM »
New confirmed cases in Hubei daily numbers
371
1291
840
1032
1220
1347

Rest of mainland China, new confirmed cases daily numbers
387
381
721
676
760
216

Not sure I trust that 760 to 216 figure, looks like some provinces haven't updated from previous day.

In Hubei 1347 is not much larger than 1291 4 days previously. The optimistic view is that the quarantine is working well but there has been some catching up on testing recently leading to continuing increase in confirmed cases.

Alexander555

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Re: Chinese coronavirus
« Reply #339 on: February 01, 2020, 01:45:19 PM »
That's strange ,in the province Zhejiang there were 428 cases on Thursday. Yesterday it jumped to 537. And today not a single one. Maybe it's running out of control, or maybe no test kits.

Tom_Mazanec

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Re: Chinese coronavirus
« Reply #340 on: February 01, 2020, 01:49:48 PM »
Still more from Michael Snyder:

Fear Of The Coronavirus Is Spreading Like Wildfire All Over The Globe
http://endoftheamericandream.com/archives/fear-of-the-coronavirus-is-spreading-like-wildfire-all-over-the-globe
Quote
This does not appear to be an ordinary virus.

Global authorities are not disclosing everything that they know, and this is another reason why fear is spreading like wildfire.  Most people just want accurate information so that they can make good decisions, and from the very beginning of this crisis the information that we have been getting has definitely not been accurate.

Will The Coronavirus Outbreak Cause A Massive Stock Market Crash?
http://theeconomiccollapseblog.com/archives/will-the-coronavirus-outbreak-cause-a-massive-stock-market-crash
Quote
Could it be possible that this coronavirus outbreak will be the trigger that finally bursts the biggest stock market bubble in U.S. history?  As I have discussed previously, stock prices in the United States were the most overvalued that they have ever been during the month of January, and our stock market has never been more perfectly primed for a huge meltdown.  But stock prices are all about what investors believe will happen in the future, and if they remain convinced that the future is bright then perhaps this stock market bubble could persist for a while longer.  Unfortunately for Wall Street, this coronavirus outbreak is starting to create a wave of fear in the financial community.  In fact, concern about the coronavirus pushed the Dow Jones Industrial Average down more than 600 points on Friday, and that represented the worst day for the Dow since last August…

EDIT:
And still more from Dr. Chris Martinson:
https://www.peakprosperity.com/new-coronavirus-ro-of-4-1-massive-contagion-risk/
Quote
As Chris says in the below video, this is an alert we’d hoped not to have to deliver.
A new study coming out of China reports that the Wuhan coronavirus has an Ro of 4.1. That means it’s much more contagious than previously feared:
If indeed the case, an Ro of 4.1 means there is NO way of stopping this virus from becoming a full-blown global pandemic.
This study has not yet had time to be peer-reviewed, so the data may change. But going with the data we have *right now* in this fast-developing situation, it is time to start preparing yourself and your loved ones.
Not time to panic, mind you. But start taking steps to prepare should you need to shelter in place for a period of days/weeks if the virus hits your community.
N95 masks, sanitizers, household cleaners, etc, body protection, food stores, etc.
Hopefully you won’t have to self-isolate. But if you do, be sure you’ve prepared in advance.
« Last Edit: February 01, 2020, 03:26:09 PM by Tom_Mazanec »
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vox_mundi

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Re: Chinese coronavirus
« Reply #341 on: February 01, 2020, 05:52:19 PM »
I've worked-in and managed hospital, pharmaceutical and toxicology labs for the last 45 years so here is some background information on the 'stage of the game' for 2019-nCov testing ...

- Several companies are providing experimental kits to identify 2019-nCov
- These kits vary in sensitivity and specificity - results from one companies kit is not exactly equivalent to another companies
- Normally a diagnostic kit takes 6-24 months to develop, scale-up, and be certified for human testing. They've pushed these products out in 1-2 weeks. This is beta testing on live subjects.
- PCR testing is (normally) not a high volume/high throughput test. It takes 5-6 hours to run a batch of 96 (384 with some instruments). This is a fundamental feature of the test. 18% of tests are QC (non-patient samples)
- If you want to increase the the number of tests performed each day you have to add more instruments (... and run them around the clock)
- Initial screening is with pan-CoV PCR primers (... meaning the PCR test is not entirely specific to 2019-nCov, but rather, the primers cross react - to varying degrees - with all coronaviruses)
Quote
... The nucleocapsid (N) protein for coronaviruses is highly conserved across coronavirus families and cross-reactivity between 2019-nCoV and SARS N proteins (90% homologous) should allow commercially available antibodies and antigens to SARS N protein to be used for diagnostic testing for Wuhan nCoV.
- Confirmatory testing is done with specific 2019-nCov complimentary primers

WHO Diagnostic Detection of 2019-nCoV by real-time RT-PCR Protocol:
 https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf?sfvrsn=a9ef618c_2

^How samples are screened and confirmed is on the last 3-4 pages.


Thermal Cycler


Analyser

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

BGI Genomics: In response to this situation, and immediately after the occurrence of unexplained pneumonia in Wuhan on December 31, 2019, BGI successfully developed a Real-Time Fluorescent RT-PCR kit for detecting 2019-nCoV, which can issue results in a few hours (5-6 hours).

https://www.bgi.com/global/company/news/bgi-develops-real-time-dna-based-kit-for-detecting-the-2019-novel-coronavirus/

Global HQ: Shenzhen, China
Regional HQs:
Europe: Copenhagen, Denmark
Asia Pacific: Hong Kong, China
Americas: San Jose, CA, USA
Active in 100+ countries

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

Meridian BioScience: Diagnostic Solutions for Novel Coronavirus Outbreak

Supplies primers

https://meridianlifescience.com/novel-coronavirus

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

Genomica just announced that it is planning to make a testing kit for the coronavirus commercially available in the next five to seven weeks. The test will have the capacity to analyze 96 patient samples at the same time, with results within five hours, according to the Madrid-based company. Genomica already markets a diagnostic kit for 20 viruses that cause respiratory diseases, including coronaviruses, and has a subsidiary located in Wuhan, the source of the outbreak of the novel coronavirus.

In full production, GENOMICA is able to manufacture individual batches of sufficient size to analyze up to 12,000 samples. This is achieved by means of a validation course that takes place between the stages of development and production of each kit, and which allows to ensure that changes due to significant increases in volumes as well as the use of robotic equipment for the automatic dispensing, do not affect those parameters critical for the kit performance, such as analytical and diagnostic reproducibility initially established during the development phase.

http://genomica.es/en/in_vitro_diagnostics_products_clart_pneumovir.cfm



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

Roche Diagnostics has an immunoassay test in development that (they claim) can output results in 30 min. Availability: March?

https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html

Quote
... A false negative result may occur if inadequate numbers of organisms are present in the specimen due to improper collection, transport or handling.

RNA viruses in particular show substantial genetic variability. Although efforts were made to design rRT-PCR assays to conserved regions of the viral genomes, variability resulting in mis-matches between the primers and probes and the target sequences can result in diminished assay performance and possible false negative results.

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

Needless to say, these tests require trained techs, full personal protection equipment and dedicated testing facilities.

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

I do not envy the poor slogs that have to run these tests day after day. Not only are they constantly exposed to a deadly disease; but, everyone, from their supervisor to the Chinese premier, are breathing down their neck for results. NO PRESSURE!!!!



----------------------------------
« Last Edit: February 01, 2020, 06:49:38 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late


vox_mundi

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Re: Chinese coronavirus
« Reply #343 on: February 01, 2020, 06:12:45 PM »
Updates:
https://www.theguardian.com/world/live/2020/feb/01/coronavirus-latest-updates-us-ban-china-death-toll-hits-259-live-news
https://www.scmp.com/news/china/article/3048518/coronavirus-case-load-and-death-toll-china-rise-epicentre-hubei-province

Global: 12027
China: 11860
Deaths: 259

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



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

British Foreign Office pulls staff out of China

The British Foreign Office is withdrawing staff from China hours after flying dozens of UK nationals home from coronavirus-hit Wuhan, PA Media reports.

Essential staff will remain to continue “critical work” but the FCO has warned that its ability to provide help to Britons in the country may be limited.

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

Authorities have detected the first suspected case of coronavirus in Tunisia (Africa), according to local reports.

The passenger is male and was returning to Tunis Airport via Qatar from China.

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

Public Health England (PHE) have confirmed that one of the two individuals recently reported to have tested positive for coronavirus is a student at the University of York, but that risk of infection on campus remains low.
https://www.york.ac.uk/alert/
https://www.gov.uk/guidance/wuhan-novel-coronavirus-information-for-the-public

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

New restrictions on the second worst-hit city in China. In Huanggang, only one family member per household will be allowed to go out every two days to get supplies, necessities.
https://twitter.com/globaltimesnews/status/1223515232661692416

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

A hospital in Xinyu, Jiangxi, has shut down after 14 of its staff were confirmed to be infected with the coronavirus, the deputy director of the Chinese Centre for Disease Control Cheng Huijian said on Saturday.

Forty staff at Number Four Hospital in the city had been isolated and its health commission director Jian Guisheng told Thepaper.cn that 15 of the 17 new confirmed cases involved hospital staff.

One of the hospital’s employees was confirmed to have contracted the virus on January 23 but Jian did not elaborate on whether the patient may be a “super-spreader” – a patient who has contact with others at the most virulent stage of the disease.

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

US Companies Suspend China Operations, Restrict Travel as Coronavirus Outbreak Becomes Global Crisis
https://www.cnbc.com/amp/2020/02/01/coronavirus-companies-suspend-china-operations-restrict-travel.html

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

Man Taken Off American Airlines Flight for Wearing Gas Mask
https://www.bbc.com/news/amp/world-us-canada-51342278

---------------------------
« Last Edit: February 01, 2020, 06:27:08 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

Bernard

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Re: Chinese coronavirus
« Reply #344 on: February 01, 2020, 06:29:41 PM »

Does this help?

Sam

Bearing all of that in mind. We still know far too little to be certain about much. We can be certain that it is a fast spreading lethal disease.

Thanks Sam. Yes, it did help me.

sark

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Re: Chinese coronavirus
« Reply #345 on: February 01, 2020, 06:39:38 PM »
https://twitter.com/SKonermann/status/1223344537772290048

"Just checked their results. The similarity is spurious. Out of 4 inserts they identify between NCov and SARS, 2 are found in bat coronavirus. Of the remaining two, only one is most similar to HIV, and is so short (6 AA) that the similarity is not higher than chance given database"

"The other novel insert between the bat coronavirus glycoprotein and NCoV is more similar to 13 viruses besides HIV and none of those similarities is higher than chance (given insert size/viral protein database size)"

https://twitter.com/Dereklowe/status/1223343979292434433

"Exactly. If these inserts are as described, it should be easy for a number of labs around the world to replicate these results, and rather quickly. We shall see."

https://twitter.com/Dereklowe/status/1223369665533050880

"TBH, I would expect an actual bioweapon to display far more obvious signs of engineering. But I would also expect such a weapon to be far nastier than this virus, bad news though it is."

The narrative of a bioweapon was always inevitable.  What I see looks more like an evolutionary cousin of SARS, better adapted to its host.



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blumenkraft

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Re: Chinese coronavirus
« Reply #346 on: February 01, 2020, 06:48:44 PM »
No, it must be the Chinese government conspiring with aliens from the andromeda galaxy. Only this can explain a virus.

/s

Tom_Mazanec

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Re: Chinese coronavirus
« Reply #347 on: February 01, 2020, 06:53:17 PM »
Quote
This is a fundamental feature of the test. 18% of tests are QC (non-patient samples)
Ahhh...why?
BTW, I wonder if other governments (especially mine) would be able to impose the extreme measures China is imposing on its population?
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KiwiGriff

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Re: Chinese coronavirus
« Reply #348 on: February 01, 2020, 06:57:49 PM »
Quote
[ Newly added 2 cases of cumulative confirmed 93 cases in Yunnan # ] On February 1 from 02:00 to 12:00, Yunnan Province reported 2 new cases of new coronavirus infection pneumonia. A total of 93 confirmed cases were reported across the province.
...Snip.
Newly diagnosed patients:
the 92nd case: a 63-year-old male, Wuhan, Hubei, traveling from Wuhan to Guizhou and Yunnan by car on January 15th, and successively to Luoping, Maile, Yuanyang, January 19th to January 24th, Jianshui, Longyang, Ruili and other places arrived in Tengchong on January 25, and were admitted to Tengchong medical institution for isolation and treatment on January 31.
Case 93: A 24-year-old male, a Red River Jianshui man, living in Lihaozhai Township, Jianshui County, taking a flight from Wuhan to Kunming on January 21, and a shuttle bus from Kunming to Jianshui on January 22, and the passenger returned by shuttle bus on the same day At Li Haozhai's home, he was admitted to a medical institution in Jianshui County for isolation and treatment on January 29.

You think this is contained within China's boarders?



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Robert Heinlein.

sark

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Re: Chinese coronavirus
« Reply #349 on: February 01, 2020, 07:08:48 PM »
https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases

Proper International cases for Feb 1st from the EU CDC.  I'm not sure if this graph is updating intraday.

There are today 167 cases outside of Mainland China.

What has everyone currently spooked is the asymptomatic superspreader that visited Germany, but during this CDC presser we heard that there is

asymptomatic transmission
fluxuating viral count / false negatives
there are certain to be more cases in the US

https://youtu.be/oMI-9Kvoj7Q?t=255
I am not a scientist