Wuhan Coronavirus Resource Thread

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Gyan
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Re: Wuhan Coronavirus Resource Thread

Postby Gyan » 07 Mar 2020 11:54

We need to estimate two parameters:-

1. How many persons equally exposed to virus catch the disease? That is % of population which is naturally immune.

2. How many who catch disease, are in need of medical care? Say 20% are serious and 80% mild.

3. How of that 20% will die? Say, Around 3%-10%.

That would mean death rate of infected is less than 1%.


If we estimate that 10% people exposed to disease will catch it while 90% is immune then death rate is less than 0.1% of the whole population. No wonder, Chinese slave labour is being put back to work. One million, mostly, oldies dead in China is not even a blip on their Capitalist radar.

This also indicates that disease in China is way older, perhaps patient zero got infected around Sept 2019 rather than December 2019.

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Re: Wuhan Coronavirus Resource Thread

Postby chola » 07 Mar 2020 17:36

Amber G. wrote:For perspective:
South Korea performed 140,000 + tests up till now - (Sensitivity about 95%)
While US about 1,500 (up from about 500 in a day or so) (Lot of problems and difficulties in initial stages - Sensitivity estimated *much* lower)


Good News that there are indications that some states are getting better (eg NY can conduct 500 tests a day) .

BTW Death rate computed from ROK data is about 0.6%


I am scared stiff of the system in the US. It's really broken when travellers from Italy are practically unscreened and not even asked to self-quarantine. Two of the three confirmed cases in Massachusetts were connected to Italy.

https://www.bostonglobe.com/2020/03/06/metro/just-italy-time-self-quarantine-first-youve-got-make-it-home/


Just in from Italy? Time to self-quarantine. But first, you’ve got to make it home
A light touch at Logan and other airports for travelers from one of the global hot spots for coronavirus

By Adam Vaccaro and Steve Annear Globe Staff
March 6, 2020, 5:45 p.m.

The federal government says travelers coming from Italy should self-quarantine, and keep their distance from other people. But in practice, passengers arriving at Logan International Airport and in other cities must still re-enter the country through a busy, crowded airport, with some travelling home by public transit, ride-sharing cars or shuttle services.

While Italy is one of the global hot spots for the coronavirus, and two Massachusetts residents are presumed to have the illness after returning from trips there, some passengers who disembarked from a sparsely-filled flight from Rome on Thursday said they were asked only cursory questions by customs workers at Logan International Airport.

“Like where you went, or where you had been,” said one of a group of high school students traveling home from a school trip cut short. A friend of hers said she wasn’t even asked those questions as she came through Customs.

The students, who like nearly all of the travelers who spoke with the Globe declined to give their names, said US Border and Customs Protection agents did not advise them of the self-quarantine guidance. The group of four was picked up at the airport by two of their mothers

...

The US has set harsher travel restrictions for China and Iran, also designated as Level 3 advisory countries, banning foreign nationals who have been in either country in the previous two weeks and diverting US citizens to one of 11 airports in the country with enhanced testing and screening procedures; Logan International Airport is not among them. These travelers are also subject to 14 days of health monitoring, according to government guidance.

As of Friday afternoon, Italy had more than 4,600 of the some 101,000 cases of the COVID-19 coronavirus documented around the world, and at 197, the second highest death toll, after China, according to a coronavirus database maintained by Johns Hopkins University.

Flyers on the Alitalia trip to Boston Thursday estimated roughly 30 to 35 people were onboard, giving most passengers their own row to sprawl across. It included many students whose school trips or study abroad semesters had been upended by the virus; they said their respective schools contacted them about the self-quarantine and emphasized that they stay home for the full two weeks before returning, and planned to follow the guidance.

“My town is small, and I’m not going to be Patient Zero,” said Skyla Lewis, a University of South Carolina student who had been studying abroad in Florence and now planned to spend the next two weeks at home in Newbury. “I’m [feeling] fine though.”

But not everybody planned to follow the quarantine advisory. One man on the flight said he did not plan to self-quarantine.

“No, I feel perfect,” he said after emerging from the Customs section of Terminal E into the general concourse.



https://www.wbur.org/commonhealth/2020/03/05/presumed-positive-coronavirus-covid-19-massachusetts

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Re: Wuhan Coronavirus Resource Thread

Postby arshyam » 07 Mar 2020 18:41

Looks like the irresponsible behaviour of the US CDC when it comes to screening is going to cause problems for the rest of the world. Here we are putting everyone through a thermal scanner amongst other things... Time for India to stop all non-stop flights from the US citing poor checking.

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 07 Mar 2020 20:02

^ Just strengthens my suspicions. Has any patient in the US actually been confirmed to have the actual Coronavirus, not "suspected" etc? I am worried about catching a cold: they will stick you in a pen with really sick people.

https://www.cnn.com/2020/03/06/business ... index.html

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 07 Mar 2020 20:22

And I just ate pizza yesterdin!! Clearly Italy is a CV center.

The man went to a doctor a few days after arriving home, and also had been notified that people at the same conference he had attended in Italy had tested positive for COVID-19, Ford said. The man and his son then tested positive and are recovering at home. Health officials have tested two other family members in the household, and were awaiting those results Tuesday.

Officials with the state Department of Public Health said one person had traveled to Milan, Italy, where they believe the person was infected, and then spread the disease to another member of the same Fulton County household after returning home.

Both patients are under home quarantine, officials said, and in good condition with mild symptoms.

The governor's office said the Department of Public Health is working to identify anyone who may have been exposed to the patients while they were infectious. People who are identified as having been exposed will be contacted directly by a Department of Public Health epidemiologist and monitored for fever and respiratory symptoms, according to a press release from Kemp's office.

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Re: Wuhan Coronavirus Resource Thread

Postby SriKumar » 07 Mar 2020 20:34

sudarshan wrote:So the initial reassuring "facts" which were being posted to scare people don't seem to be true anymore.
1. This virus spreads through the air
Since you write, I thought I'd point out an interesting use of phrases 'reassuring facts' and 'to scare people' ....seemed a bit of a contradiction in terms. Usually, reassuance is the opposite of trying to scare :D . My position on this is that if something can travel through air, e.g. respiratory droplets (they call it aerosol) in a sneeze, I consider that as 'infection via air'. But this is not a technical defintion obviously. I am looking at it specifically from a prevention angle. In a hat-tip to your use of phrase, I present/pesh this limmerick to capture my thought above...arz kiya hai.

An unguarded sneeze,
Aided by a breeze
Can put in motion,
the viral potion*
and make it spread with ease.

(*line could read: the Wuhan potion)

THat Boston Globe article on Italian travelers is crazy. Boston Globe is a major publication and I think those stories are real and not exaggerated. Lot of students go to ITaly who are now returning. one person name is revealed (Skyla Lewis). She'll be a paraih in her town for 2 weeks.

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Re: Wuhan Coronavirus Resource Thread

Postby saip » 07 Mar 2020 21:05

People seem to be already scared. Yesterday I was at local Walmart to buy some rice. What do you know? All the rice shelves are empty and all I could get was one 2lb bag hiding way back in the shelf.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 07 Mar 2020 22:37

Amber G. wrote:
sudeepj wrote:

As for India.. I am hopeful that the hot weather and lack of air conditioning saves us.


Here is my take on "hot weather" ... (Based on current data and traditional thinking).

There has been quite a bit of data/study about spread of "corona viruses" and humidity and temperature .. There is some understanding (and mathematical models) on how water droplets (with viruses) behave etc..Of course this is a new f virus and more data will always be more helpful.

I have posted some graph(s) before here.and there is additional data. Things to me look quite optimistic. The data is quite stark. Rate of spread in southern hemisphere (where it is summer) and equatorial region is *much* less. Now it is quite probable that cases in tropical countries yet have not been reported (or are not in our database) so confidence level is still modest.

But another week or so if it goes without *domestic* outbreaks in tropical countries, the more confidence level!

(I am also looking at "doubling" time .. some of the graphs which have not been that popular among those published - More familiar tools - used in studying radioactive decay / nuclear fission rates.. can be helpful here).


This is probably it, but in India, flu takes off in the rainy season, compared to winters in latitudes farther north. If Coronavirus behaves in a similar fashion, we have a respite for a few months till it attacks us too!

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 07 Mar 2020 22:39

kit wrote:
Amber G. wrote:
Here is my take on "hot weather" ... (Based on current data and traditional thinking).

There has been quite a bit of data/study about spread of "corona viruses" and humidity and temperature .. There is some understanding (and mathematical models) on how water droplets (with viruses) behave etc..Of course this is a new f virus and more data will always be more helpful.
...

(I am also looking at "doubling" time .. some of the graphs which have not been that popular among those published - More familiar tools - used in studying radioactive decay / nuclear fission rates.. can be helpful here).


looks like even grandma's rasam has a found a place as a 'remedy " for corona virus :mrgreen:


Oh yes.. I am consuming a teaspoon of haldi with cream every day ever since this whole thing started! In the absence of anti-virals and the disease galloping, its probably the more traditional things that will help us. Get Sun/Vit D, sleep, exercise, eat well, maintain hygiene and keep social distance.
Last edited by sudeepj on 07 Mar 2020 23:04, edited 1 time in total.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 07 Mar 2020 23:03

Amber G. wrote:For perspective:
South Korea performed 140,000 + tests up till now - (Sensitivity about 95%)
While US about 1,500 (up from about 500 in a day or so) (Lot of problems and difficulties in initial stages - Sensitivity estimated *much* lower)


Good News that there are indications that some states are getting better (eg NY can conduct 500 tests a day) .

BTW Death rate computed from ROK data is about 0.6%


These things are very idiosyncratic and its going to be very hard to estimate when the disease is still in motion. Wuhan death rate is much higher, probably because health care facilities were overwhelmed and another intriguing reason. Apparently, Wuhan has a lot of migrant workers, who are younger, and this infected population left for their 'home cities' and left the patient population in wuhan much older. As a result, more fatalities were seen in this population. In SK, I have seen speculation that its the members of that church who are most of the patients, and these members are younger, so fatality is much lower.

Right now, several times worse than the seasonal flu and disproportionately impacting older people appears to be the only statement we can make with 100% certainty. This is unlike the flu, which impacts younger people harder, because the older people have developed some kind of immunity over the most prevalent strains over the years.

This is still a very alarming picture! Imho, fatality is just one aspect of this.. The other aspect is the number of ICU stays and hospitalizations required. This is being claimed variously as 10% hospitalizations and 5% into ICU. Considering the disease doubling rate of 7 days (reported variously), this could potentially overwhelm most health care systems in short order! Hopefully, the weather Gods save us soon!

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Re: Wuhan Coronavirus Resource Thread

Postby Amber G. » 07 Mar 2020 23:15

Amber G. wrote:For perspective:
South Korea performed 140,000 + tests up till now - (Sensitivity about 95%)
While US about 1,500 (up from about 500 in a day or so) (Lot of problems and difficulties in initial stages - Sensitivity estimated *much* lower)


Good News that there are indications that some states are getting better (eg NY can conduct 500 tests a day) .

To me the incredible part is it is relatively quite easy to produce these kits.. Many schools - eg Stanford had those kits (for quite some time) .. UCSF is reportedly ready to release this for actual use.. These kits can produce results - from what I know - in about an hour.

It is beyond shameful for CDC/Trump admin/ etc to not be ready, drag their feet.. It is criminal.


****
Recently a nurse who treated a patient who (the patient) was later tested positive for CV. The nurse requested to be tested herself too. (Not only the nurse but the other patients - some of whom may be elder or more vulnerable will be at risk if she is exposed). CDC incredibly said something to the effect " well if you were wearing mask and PPE you are not at risk and you do not fall under our guidelines to be qualified for a test .... we can not authorize testing for you"..

After lot of push back from other staff from the hospital (and story getting out in public via news outlets) test was finally authorized for her. :shock:
Unfortunately these are not isolated cases. People have been billed thousands of dollars for the test.. (Now they are saying that insurance companies can not charge a copay for CV test).

Hope things changes soon here in US. If you have loved ones who are elderly or have heart condition or diabetes please be extra careful.

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Re: Wuhan Coronavirus Resource Thread

Postby Amber G. » 07 Mar 2020 23:44

chola wrote:

I am scared stiff of the system in the US. It's really broken when travellers from Italy are practically unscreened and not even asked to self-quarantine. Two of the three confirmed cases in Massachusetts were connected to Italy.

Thanks for posting the story. Yes, it is quite serious. If there are elderly or vulnerable people in your home, this is scary.
Hope things changes, and changes fast.
***
Things are sort of hitting too close to home.. Have doctors in family who are *very* concerned with chaos and they have not seen this kind of unpreparedness in the past.

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Re: Wuhan Coronavirus Resource Thread

Postby Amber G. » 08 Mar 2020 00:42

sudeepj wrote: Considering the disease doubling rate of 7 days (reported variously), this could potentially overwhelm most health care systems in short order! Hopefully, the weather Gods save us soon!


If you get a chance - Can you give link/details for doubling rate.. it will be interesting to see and monitor that site. TIA.

I have been looking at raw data and analyzing the doubling rate. ROK, Singapore and India data is much more reliable/complete than few other countries. From: ROK data it looks around 7 days at present (perhaps becoming a little bit more as the things become more stable).. Japan looks slower now (perhaps 10+ days)..

US part looks really scary if you just consider the raw data (about 2 days) but it is clear that the growth does not represent news cases.. it is just that we are finding more results as more tests are becoming available.

I don't know if in US we may see 5-6 weeks of big epidemic type outbreak (like we see in Iran or Italy or it may last 4 months (or longer) and turn into Flu type outbreak (which may repeat seasonally over years).. just a bit worse than bad flu season.
(I still remember 69 Flu outbreak in US - it was not fun)

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 01:10

Amber G. wrote:
sudeepj wrote: Considering the disease doubling rate of 7 days (reported variously), this could potentially overwhelm most health care systems in short order! Hopefully, the weather Gods save us soon!


If you get a chance - Can you give link/details for doubling rate.. it will be interesting to see and monitor that site. TIA.

I have been looking at raw data and analyzing the doubling rate. ROK, Singapore and India data is much more reliable/complete than few other countries. From: ROK data it looks around 7 days at present (perhaps becoming a little bit more as the things become more stable).. Japan looks slower now (perhaps 10+ days)..

US part looks really scary if you just consider the raw data (about 2 days) but it is clear that the growth does not represent news cases.. it is just that we are finding more results as more tests are becoming available.

I don't know if in US we may see 5-6 weeks of big epidemic type outbreak (like we see in Iran or Italy or it may last 4 months (or longer) and turn into Flu type outbreak (which may repeat seasonally over years).. just a bit worse than bad flu season.
(I still remember 69 Flu outbreak in US - it was not fun)


The disease doubling rate itself is dependent on social distancing and Pub Health measures so even in the same disease center, it will vary over time. Here is one estimate from current Washington State. (The estimate is generated by looking at the viral genome, and counting the number of mutations per jump from known cases, looking at the genomes from infected people and estimating the number of jumps the virus has made so far. So it has wide error bars, but is better than nothing.)

https://www.seattletimes.com/seattle-ne ... tist-says/

Since then, Bedford believes, the virus has been moving through the community at a rate in which the number of cases doubled roughly every six days. Bedford concluded that rate of infection, taking into account a projected margin of error, would mean that there are as many as 570 infected individuals as of Sunday, and that number is growing. One of Bedford’s colleagues, using another method of tracking and projecting infections, came up with a more conservative estimate of 330 infections since roughly Jan. 15.


Here is another estimate from Los Alamos, which is much more scary!:

https://www.medrxiv.org/content/10.1101 ... 1.full.pdf

he novel coronavirus (2019-nCoV) is a recently emerged human pathogen that has spread widely since January 2020. Initially, the basic reproductive number, R0, was estimated to be 2.2 to 2.7. Here we provide a new estimate of this quantity. We collected extensive individual case reports and estimated key epidemiology parameters, including the incubation period.Integrating these estimates and high-resolution real-time human travel and infection data with mathematical models, we estimated that the number of infected individuals during early epidemic double every 2.4days, and the R0 value is likely to be between 4.7 and 6.6. We further show that quarantine and contact tracing of symptomatic individuals alone may not be effective and early, strong control measures are needed to stop transmission of the virus.


It is somewhat telling that the Chinese effort to control it did not stop at quarantine and contact tracing, and included very strong control measures. This is something neither Italy, nor the US have done. I think western democracies may simply be incapable of putting in place such measures. It is also telling that nearly all US states are reporting high numbers of 'Influenza like Illnesses'. We will see what happens..

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 01:23

Here are some numbers from Italy:

https://twitter.com/tancredipalmeri/sta ... 4652234753
The #coronavirus in Italy

Day1 14cases/1dead
D2 76/2
D3 153/3
D4 231/7
D5 374/12
D6 528/17
D7 821/21
D8 1128/29
D9 1577/34
D10 1835/52
D11 2263/79
D12 2706/107
D13 3296/148
D14 3916/197
D15 5061/233

The percentage of dead in the number of detected cases starts out really high, stabilizes for a week at 2-3%, then jumps really fast to 5% on day 15. To me, this is an indication of a run away epidemic. Clearly, there are many more cases that are not being caught! (because we know, that covid is not as deadly as 5% of cases..).

On the flip side, some Chinese from Wuhan say, rumors in the city point to 20,000 dead! And many cases were not counted correctly and hurriedly buried/cremated.

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 08 Mar 2020 01:41

And now this!

Cheen Quarantine hotel collapses, burying dozens. :(

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 08 Mar 2020 01:46

IMO this is far more dangerous and frightening than COVID.
Literally eats you in a matter minutes. :eek: :shock:

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 08 Mar 2020 02:06

Oh cool! Now they are bringing out the helicopters, HUMVEES and machine guns in true American tradition


Police-Enforced Quarantine Hits California Neighborhood – Residents Ordered to Stay Inside Due to Coronavirus
Jim Hoft
Sacramento police ordered all residents in a California neighborhood to stay inside on Thursday due to a coronavirus death in the area.
The local health department issued a statement after the police presence in the area.
This is a frightening development.
Sacramento County Sheriff deputies and Rocklin Police, some wearing protective gloves, converged on a residential street Thursday as a sheriff’s helicopter circled overhead, ordering people to get inside.

It was later learned that the first California coronavirus patient to die from the illness lived on this block.

The Placer County Health Department issued a brief statement shortly after the police presence, stating: “Law enforcement partners are currently responding to enforce a health officer’s order. We cannot share any additional information to protect patient confidentiality.”

The orders were given under sections of California Health and Safety Code that allows Placer Health to “enforce regulations requiring strict isolation, or quarantine if the action is necessary for the protection of the public health.”

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Re: Wuhan Coronavirus Resource Thread

Postby Amber G. » 08 Mar 2020 02:46

sudeepj - short note to say thanks. (One study - Washington State case , I posted it here too ..)

I have been looking up / analyzing this (doubling time period) too, over some time - the death data is more reliable.
Short thing pops out - Italy, South Korea and Iran are now "out of control'" - designation
Japan - Almost there - can go either way
To watch: France, Germany, Spain and the US
(May post some graphs here by country - based on data we have)
Meanwhile:
Here is one interesting update on one graph: About death rates:
Image

How important it is to take quick timely action: (death rate in 2 US cities in 1918 epidemic
Image

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Re: Wuhan Coronavirus Resource Thread

Postby Cain Marko » 08 Mar 2020 03:09

Amber G. wrote:sudeepj - short note to say thanks. (One study - Washington State case , I posted it here too ..)

I have been looking up / analyzing this (doubling time period) too, over some time - the death data is more reliable.
Short thing pops out - Italy, South Korea and Iran are now "out of control'" - designation
Japan - Almost there - can go either way
To watch: France, Germany, Spain and the US
(May post some graphs here by country - based on data we have)
Meanwhile:
Here is one interesting update on one graph: About death rates:
Image


Amberji, correct me if I'm wrong, but this confirms my fears that the virus is far deadlier in non China populations. Iirc in the USA, it's 380 cases with 17 deaths. I wonder if it's because of the demographic differences, lots of older people in the US thanks to the bbs.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 03:15

sudeepj wrote:Here are some numbers from Italy:

https://twitter.com/tancredipalmeri/sta ... 4652234753
The #coronavirus in Italy

Day1 14cases/1dead
D2 76/2
D3 153/3
D4 231/7
D5 374/12
D6 528/17
D7 821/21
D8 1128/29
D9 1577/34
D10 1835/52
D11 2263/79
D12 2706/107
D13 3296/148
D14 3916/197
D15 5061/233

The percentage of dead in the number of detected cases starts out really high, stabilizes for a week at 2-3%, then jumps really fast to 5% on day 15. To me, this is an indication of a run away epidemic. Clearly, there are many more cases that are not being caught! (because we know, that covid is not as deadly as 5% of cases..).

On the flip side, some Chinese from Wuhan say, rumors in the city point to 20,000 dead! And many cases were not counted correctly and hurriedly buried/cremated.


Trying to do some analysis on the Italian death rates, I compared the deaths reported on day N with the deaths reported on day (N -1) to get at disease spreading rate. Here, deaths is used as a proxy for the total number of infections. Given that most infections are not being detected, this looks like a better measure than the total number of detected cases.

Day1 14cases/1dead Death Ratio over previous day
D2 76/2 2
D3 153/3 1.5
D4 231/7 2.33
D5 374/12 1.71
D6 528/17 1.41
D7 821/21 1.23
D8 1128/29 1.17
D9 1577/34 1.52
D10 1835/52 1.52
D11 2263/79 1.51
D12 2706/107 1.35
D13 3296/148 1.38
D14 3916/197 1.33
D15 5061/233 1.18

If we ignore the first 5 days (too noisy, and numbers too small to give any reliable statistics), The ratio of deaths on day X over all deaths till day X-1 looks like it varies from 1.17 - 1.52. An average over days 6 to 15 yields 1.36 as the ratio of infections from one day to the next! Doubling every three days!

Remember, this is for a population that is not yet alarmed, as presumably it takes perhaps 10 days from infection to death. Most of the dead till now are those who were infected ten days to two-three weeks ago! Now that the population is properly alarmed and taking many more precautions (no gatherings, hand shakes, face kissing every one you meet), this number should go down. But even if it is reduced by 75%, the doubling rate is now every eight days! This is the reason we are seeing serious measures such as curfews and lockdowns to control this disease.

Even after quarantines and lockdowns, most people will infect their close relatives and families. So the numbers will continue to grow for a week or two before dropping dramatically as in wuhan. Past that, we will have to rely on frequent hand washing, no face touching etc. to reduce the spread of the disease to a 'its only pandemic flu bro' levels.

The recovery rate seems to be 3-4 weeks after being infected. So if we can get the doubling rate down to 3-4 weeks, we will see an equal number of new patients as recovered patients and some sort of steady state equilibrium will be achieved in demand for hospital beds/health care etc. It remains to be seen if such delay in spreading the infection can be achieved. At the very least, large social gatherings - cinemas, restaurants, churches, mosques, schools, should be avoided.

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Re: Wuhan Coronavirus Resource Thread

Postby vinod » 08 Mar 2020 03:22

sudeepj wrote:Here are some numbers from Italy:

https://twitter.com/tancredipalmeri/sta ... 4652234753
The #coronavirus in Italy

Day1 14cases/1dead
D2 76/2
D3 153/3
D4 231/7
D5 374/12
D6 528/17
D7 821/21
D8 1128/29
D9 1577/34
D10 1835/52
D11 2263/79
D12 2706/107
D13 3296/148
D14 3916/197
D15 5061/233

The percentage of dead in the number of detected cases starts out really high, stabilizes for a week at 2-3%, then jumps really fast to 5% on day 15. To me, this is an indication of a run away epidemic. Clearly, there are many more cases that are not being caught! (because we know, that covid is not as deadly as 5% of cases..).

On the flip side, some Chinese from Wuhan say, rumors in the city point to 20,000 dead! And many cases were not counted correctly and hurriedly buried/cremated.


Local news channels reporting that govt officlals planning shutdown of northern regions in Italy starting from midnight today until 3rd April.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 03:34

Amber G. wrote:sudeepj - short note to say thanks. (One study - Washington State case , I posted it here too ..)

I have been looking up / analyzing this (doubling time period) too, over some time - the death data is more reliable.
Short thing pops out - Italy, South Korea and Iran are now "out of control'" - designation
Japan - Almost there - can go either way
To watch: France, Germany, Spain and the US

How important it is to take quick timely action: (death rate in 2 US cities in 1918 epidemic
Image


The Philadelphia vs St Louis graph is pure gold. It 'feels' like the area under the St Louis curve is about half that under Philadelphia, which makes sense.

Personally, I am not so concerned about South Korea, as they have caught 7000 patients and 40 reported deaths. To me, it suggests they have ramped up testing really fast, alarmed their population really fast.. And may well have controlled the outbreak! If it werent for that stupid church, it wont even have gotten this bad in the first place!

To me, Italy and the US are really concerning. By all accounts, the disease hits people with diabetes & hypertension really hard and about a third of the US population are obese/hypertensive/diabetic. Add that testing wont hit top gear till next week, how disorganized everything feels (almost India like! :| ).

The cultural impacts of this, if the Asiatics and the orientals come out ahead in managing the disease compared to the West are going to be interesting. Expect full tilt propaganda.

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Re: Wuhan Coronavirus Resource Thread

Postby Cain Marko » 08 Mar 2020 04:58

Thought providing thoughts Sudeepji. Can you do any predictive analysis using the data from Italy and China for the US? It seems to me that we may start seeing stronger, preemptive measures in US soon.

The baby-boomers will be disproportionately affected considering that with age come the ailments you speak of. Perhaps gen xers too.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 05:24

US doesnt have as much public transport, church going (on the coasts), cheek-by-jowl living as many Asian and European countries do, so just a hunch that it should not spread as fast here. On the flip side, lack of free basic medical care means people dont access healthcare proactively.. the morbidity burden of obesity & associated diseases is also very high. Believe me, you aint seen a fat man till you seen some fat americans! It also 'feels' extremely disorganized with incompetence permeating every level of governance. I cant do any predictions.. except to say, I am worried. Ill be happy if we come out the other end without a mark.

Somewhat Ironically, for the 'disease is contained' camp, a larger mortality is better, because then it means we are catching most cases. If the mortality rate is 'only' 0.5%.. we are missing a very large number of infected people and either we have to lockdown or do some other drastic measure to slow the disease down.

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Re: Wuhan Coronavirus Resource Thread

Postby Cain Marko » 08 Mar 2020 05:29

sudeepj wrote: On the flip side, some Chinese from Wuhan say, rumors in the city point to 20,000 dead! And many cases were not counted correctly and hurriedly buried/cremated.

:shock: here is some more disturbing news from China



Damn. Wish China was a little more transparent.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 05:33

Here is a series of tweets from a Microbiology prof on twitter.
https://twitter.com/florian_krammer/sta ... 5924972545
1) I am getting a little annoyed at people responding to my tweets saying 'why do you even believe the Chinese numbers' and 'China was hiding this' etc. There is something we all need to keep in mind: China bought us time and we wasted it.

2) It is easier to believe numbers from the Chinese government than in no numbers at all. I am sick of people blaming the Chinese. Chinese health care workers are heroes and many of them payed with their lives for responding fast to this.

3) Millions of Chinese people were and are under a lockdown that bough us time. Would any of our Western countries have done the same? Did we contain this? China uses lockdowns and great technology to manage this. We can't even test large numbers of people.

4) So, please stop pointing fingers and motivate your own governments to act. These comments are wrong and not constructive, especially not at this point in time. I will block anybody who makes them.

Like I said, the cultural impacts of this could be interesting to watch.

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Re: Wuhan Coronavirus Resource Thread

Postby Cain Marko » 08 Mar 2020 06:04

3) Millions of Chinese people were and are under a lockdown that bough us time. Would any of our Western countries have done the same? Did we contain this? China uses lockdowns and great technology to manage this. We can't even test large numbers of people.


All this is well and good but considering traditional lack of transparency wrt China, it is going to raise suspicions. The good Prof, with good intentions, is effectively saying we should make do with what we have.

Others are saying, is there something we don't know.....Afterall, millions of Chinese are regularly in lock down in China, no?

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Re: Wuhan Coronavirus Resource Thread

Postby sudarshan » 08 Mar 2020 06:58

Amber G. wrote:Sudarshan ji - Few comments:
No reputable scientist will claim to know exact numbers of "facts",, And it is not scientific to claim to know these numbers just because one has a good hunch. IMO, at least for me, It is NOT a contest of whose guess was correct and "I told you so type statement" - unless based on scientific reasoning are not that helpful. Most of these numbers we don't know, as we get more data we will be surer..:) But let me comment on your post.


Yes, I understand that, but if that is the case, then why do these experts present all these conjectures to reporters (and to the general population) without waiting for verification? I mean, conjectures such as - "this virus seems to be spreading through the air" or "the incubation period could be 24 days, which is big trouble!" If as you (correctly) say, we don't know these numbers and we need to get more data to be sure, then why perform these releases to the press as soon as the conjecture arises?

Technically most say that it is NOT (at least not the primary or significant) mode. But CDC/WHO also recommend 6+ feet distance. Scientifically all one can talk about is probability .. yes you are correct this is sharing air is *not* as dangerous as some other dreaded diseases, definitely no evidence that it is anywhere close to that but it is *not* zero. How small, jury is still out.


I believe the 6+ feet distance is to prevent droplet spread (large droplets, 5 to 10 microns in size, which spread with sneezes, coughs, even yawns or speech). Technically, 3 feet seems good in most cases, but just to be safe, do 6 feet. Air transmission is different - this mode depends on smaller droplets remaining in suspension for hours, and circulating through breezes or AC systems. This is the mode, for which there is no evidence right now (with COVID-19).

The measles virus can remain in the air (it seems) for up to 2 hours after an infected person has left the area. With COVID-19, currently, it seems the chance of infection is highest if you are exposed to the larger droplets (immediately after somebody coughs or otherwise sprays the area, since these droplets fall to the floor pretty fast). The next highest chance of infection seems to be if you touch surfaces where these droplets landed. With the smaller droplets remaining suspended in air, I agree, the chance of infection is still not zero, but it seems miniscule (with current data).

Let me just put the worldometer data - of course these are just numbers based on what data they are using -- This gives better understanding.

...

A statistician will say:
The mean incubation period was 5.2 days (95% confidence interval [(4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days.


I agree. There's a chance of higher incubation periods in some people, but these seem much rarer, and it's not like the general population has to contend with incubation periods longer than 2 weeks.

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Re: Wuhan Coronavirus Resource Thread

Postby sudarshan » 08 Mar 2020 07:10

SriKumar wrote:Since you write, I thought I'd point out an interesting use of phrases 'reassuring facts' and 'to scare people' ....seemed a bit of a contradiction in terms. Usually, reassuance is the opposite of trying to scare :D . My position on this is that if something can travel through air, e.g. respiratory droplets (they call it aerosol) in a sneeze, I consider that as 'infection via air'. But this is not a technical defintion obviously. I am looking at it specifically from a prevention angle.


Yeah, just being sarcastic :). But I do find it annoying when these experts, who seem to love the sound of their own voice, present preliminary conjectures to reporters (who don't have a clue) and thus to the general population (ditto), without waiting for verification. Something like air spread of the disease (respiratory droplets, the larger ones, fall pretty fast, so the risk of air spread only lasts a couple of seconds, it's the smaller droplets which can linger for hours, but usually, these don't have viable virus samples - the moisture, it seems, dries out in tenths of a second, and the virus gets deactivated). Does the general public need to immediately know the conjecture? Why not just outline the steps which the general public is expected to follow, if there's a fear in the experts' minds that there is going to be general air spread, like with measles or chicken pox? Does the public have to be scared stiff, especially since the conjecture turned out to be mostly false (again, based on what we know to date)? That was my grouse.

In a hat-tip to your use of phrase, I present/pesh this limmerick to capture my thought above...arz kiya hai.

An unguarded sneeze,
Aided by a breeze
Can put in motion,
the viral potion*
and make it spread with ease.

(*line could read: the Wuhan potion)


Nice :)! Now to really test your skill, could you come up with an English language rhyme for "Wuhan?" Or just complete this Limerick, which I started for you below :mrgreen:

There was once a virus in Wuhan....


I started the above, then went *oops* :oops: so now I'm relying on you to finish it.

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Re: Wuhan Coronavirus Resource Thread

Postby chola » 08 Mar 2020 07:47

Cain Marko wrote:
3) Millions of Chinese people were and are under a lockdown that bough us time. Would any of our Western countries have done the same? Did we contain this? China uses lockdowns and great technology to manage this. We can't even test large numbers of people.


All this is well and good but considering traditional lack of transparency wrt China, it is going to raise suspicions. The good Prof, with good intentions, is effectively saying we should make do with what we have.


Why should it matter now? If you don't believe in their numbers just assume the worst. That was pretty much the strategy of the US. From the same story where travelers from Italy were given a free pass:


The US has set harsher travel restrictions for China and Iran, also designated as Level 3 advisory countries, banning foreign nationals who have been in either country in the previous two weeks and diverting US citizens to one of 11 airports in the country with enhanced testing and screening procedures; Logan International Airport is not among them. These travelers are also subject to 14 days of health monitoring, according to government guidance.



All foreign nationals who from China and Iran are banned from the US while US citizens who traveled there are diverted to 11 US airports and then subjected to 14 days of quarantine. That is the proper way of dealing with this. It doesn't matter how many deaths they are hiding.

With Chinese (and Iranian) nationals banned from US soil and US citizens funneled through 11 specialize airports, you can't get much tougher unless you are blocking re-entry of US citizens from China and Iran.

But when Italy is also a Level 3 threat and travelers there are not subjected to the same strict process then the whole thing breaks down. The spread of the virus in America won't be by people from Cheen who were blocked very early by Trump but from secondary infected countries Europe like Italy and possibly, eventually, South America.

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Re: Wuhan Coronavirus Resource Thread

Postby UlanBatori » 08 Mar 2020 08:00

.... it was Americans returning from tours and conferences (same thing) from all over.

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Re: Wuhan Coronavirus Resource Thread

Postby Barath » 08 Mar 2020 08:12

UlanBatori wrote:^ Just strengthens my suspicions. Has any patient in the US actually been confirmed to have the actual Coronavirus, not "suspected" etc? I am worried about catching a cold: they will stick you in a pen with really sick people.

https://www.cnn.com/2020/03/06/business ... index.html


19 people in US dead from coronavirus.

https://www.nbcnews.com/health/health-n ... a-n1152081

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Re: Wuhan Coronavirus Resource Thread

Postby sudarshan » 08 Mar 2020 09:17

^ That is certainly worrying. They're identifying folks with "symptoms consistent with Coronavirus." God knows whether they're testing them at all, or giving those poor souls the runaround between various health departments. In the meantime, they just go ahead and report all of them as COVID-19 cases? The true cases seem to be slipping notice, and there's no confidence that the right people are being quarantined. It seems many of these patients also seem to think that this quarantining is "optional" - they're walking around, going shopping, and knowing Americans in general, not washing their hands even after restroom visits. As for their behinds... well, let's not go there.

Now on a different note. It seems that eating with your hands is much more hygienic than spoons or forks. The reasoning is - "you get to control the cleanliness of your own hands." How do you know how many mouths (hopefully, only mouths) those forks and spoons and knives have been in? Even with the spoons in your own house, you could still have guests who use them. On the contrary, with your hands, you control whose mouths they go into. If you stay careful about your personal hygiene - well, that's the best anyone can do for themselves. As far as plates and stuff go, in South India, people used to eat on banana leaves and throw them away after a single use. Also biodegradable. In North India, I believe, people drank out of mud pots, and made sure to shatter them after one use. Again, biodegradable. Whereas the western world has always regarded the use of cutlery as an essential indicator of civilization.

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Re: Wuhan Coronavirus Resource Thread

Postby tandav » 08 Mar 2020 09:25

sudarshan wrote:^ That is certainly worrying. They're identifying folks with "symptoms consistent with Coronavirus." God knows whether they're testing them at all, or giving those poor souls the runaround between various health departments. In the meantime, they just go ahead and report all of them as COVID-19 cases? The true cases seem to be slipping notice, and there's no confidence that the right people are being quarantined. It seems many of these patients also seem to think that this quarantining is "optional" - they're walking around, going shopping, and knowing Americans in general, not washing their hands even after restroom visits. As for their behinds... well, let's not go there.

Now on a different note. It seems that eating with your hands is much more hygienic than spoons or forks. The reasoning is - "you get to control the cleanliness of your own hands." How do you know how many mouths (hopefully, only mouths) those forks and spoons and knives have been in? Even with the spoons in your own house, you could still have guests who use them. On the contrary, with your hands, you control whose mouths they go into. If you stay careful about your personal hygiene - well, that's the best anyone can do for themselves. As far as plates and stuff go, in South India, people used to eat on banana leaves and throw them away after a single use. Also biodegradable. In North India, I believe, people drank out of mud pots, and made sure to shatter them after one use. Again, biodegradable. Whereas the western world has always regarded the use of cutlery as an essential indicator of civilization.


Off topic: but I believe (no research done) use of cutlery was more of a hunting/fighting/raiding civilizational moor ... as the users of cutlery typically did not soil their hands while eating and they could transition to fighting far more quickly. Use of hands for eating is far more common in settled/agricultural civilizational moor.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 09:34

sudarshan wrote:^ That is certainly worrying. They're identifying folks with "symptoms consistent with Coronavirus." God knows whether they're testing them at all, or giving those poor souls the runaround between various health departments. In the meantime, they just go ahead and report all of them as COVID-19 cases? The true cases seem to be slipping notice, and there's no confidence that the right people are being quarantined. It seems many of these patients also seem to think that this quarantining is "optional" - they're walking around, going shopping, and knowing Americans in general, not washing their hands even after restroom visits. As for their behinds... well, let's not go there.

...


This is from a nursing home/care facility/old age home type situation where a few people definitely tested positive to the virus. If the clinical observation - fever, no runny nose, dry cough, 'ground glass opacity in lung CT scans' - match the description of the disease, and the cdc supplied test doesnt, what are you going to trust? Remember, the tests are new, and its possible that the tests dont work as reliably as we would hope!

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Re: Wuhan Coronavirus Resource Thread

Postby schinnas » 08 Mar 2020 09:34

Indian govt seems to be doing better. Most Indians with some history of foreign travel have got a call from a 172-***-**** number with message on basic precautions and a number to the nearest coronavirus helpline.

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 09:41

Translation of an interview of an ICU doctor from Lombardi region in Italy.

https://www.corriere.it/cronache/20_mar ... resh_ce-cp

Antonio Pesenti, 68, is the coordinator of the Lombardy Region Crisis Unit for intensive care. Publicly praised by the scientist Alberto Mantovani as one of the best Italian men of science, he is a physician-resuscitator with strong nerves, accustomed to governing any type of emergency. But at nine on Saturday evening, after 17 days of non-stop work, his voice is broken by tiredness and worry: "If the population does not understand that they must stay at home, the situation will become catastrophic."

She, together with colleagues in the reanimations, is the author of a very harsh letter to the government of Giuseppe Conte: "The scientific projections are very alarming". What do you mean by that?
"The picture is of such gravity as to require an increase in resuscitation places up to ten times the current availability. The number of hospitalized patients expected on March 26 is 18 thousand Lombard patients, of which between 2,700 and 3,200 will require hospitalization in intensive care. Today there are already over a thousand patients between those in resuscitation and those who risk getting worse from one minute to the next. We monitor the situation 24 hours a day ».

In the letter he speaks of risks not only for coronavirus patients, but also for everyone else: "In danger there is the survival not only of Covid-19 patients - you write -, but also of that part of the population that in any case addresses the health system ».
"So far in Lombardy ambulances have always arrived in 8 minutes, now they risk not arriving within an hour. A huge danger for those who have a heart attack, and not only ».

In short, Lombardy's emergency-urgency system is no longer able to guarantee ordinary standards.
«Unfortunately, it is the truth. I am not saying this to alarm citizens, but to make everyone understand that it is not the time to go out, to go shopping or to go and drink the spritz, as we have been saying for days now. We need to change social relationships, with the shops and neighborhood markets closed. In Milan, where I live, at least so far there have been too many people needlessly around. You only have to go out to buy food. "

The beds in intensive care units increase day by day, but they are never enough.
«We are creating Covid-19 blocks everywhere. By now all the main hospitals in Lombardy have been involved, at least fifty. As known, infected patients cannot be mixed with others. It means having resuscitations where everything happens with particular protection systems: from filtered air to doctors and nurses who always dress and undress in the presence of another person to check that the procedures are correct because a minimum distraction is enough to become infected ".

By now we are forced to create intensive therapies in the corridor, in the operating rooms, in the recovery rooms. We gutted entire hospital wards to make room for the seriously ill. One of the best healthcare in the world, the Lombard one, is one step away from collapse.

In what conditions are you working?
«We work harnesses to protect ourselves from the virus. After 4 hours we are sweating soaked, the movements are slowed down and we have to get out of the resuscitation to hydrate ourselves. We are doing everything we can, and even more, but the contagions must be stopped. The only way is prevention. "

In one of the last meetings with the ICU doctors there were those who failed to hold back tears.
«By profession we are used to dealing with any situation in cold blood. But only those who are living in the front line can understand the drama of the events
».

Is it likely to think of transporting seriously ill people to the rest of Italy?
«They are very complex patients to move. Both for their physical conditions and for the protections that must be taken in order not to infect us. I see it difficult ».


To me, this looks like a hundred or a fifty year pandemic. Otherwise you wont have 68 year old ICU doctors on the verge of tears. This needs to be taken seriously and every effort made to prepare, prepare, prepare. No more 'its just a bad cold bro'.. Whats the worst that can happen if you prepare? Whats the worst that can happen if you dont?

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Re: Wuhan Coronavirus Resource Thread

Postby sudeepj » 08 Mar 2020 09:53

sudeepj wrote:
sudeepj wrote:Here are some numbers from Italy:

https://twitter.com/tancredipalmeri/sta ... 4652234753
The #coronavirus in Italy

Day1 14cases/1dead
D2 76/2
D3 153/3
D4 231/7
D5 374/12
D6 528/17
D7 821/21
D8 1128/29
D9 1577/34
D10 1835/52
D11 2263/79
D12 2706/107
D13 3296/148
D14 3916/197
D15 5061/233

The percentage of dead in the number of detected cases starts out really high, stabilizes for a week at 2-3%, then jumps really fast to 5% on day 15. To me, this is an indication of a run away epidemic. Clearly, there are many more cases that are not being caught! (because we know, that covid is not as deadly as 5% of cases..).

On the flip side, some Chinese from Wuhan say, rumors in the city point to 20,000 dead! And many cases were not counted correctly and hurriedly buried/cremated.


Trying to do some analysis on the Italian death rates, I compared the deaths reported on day N with the deaths reported on day (N -1) to get at disease spreading rate. Here, deaths is used as a proxy for the total number of infections. Given that most infections are not being detected, this looks like a better measure than the total number of detected cases.

Day1 14cases/1dead Death Ratio over previous day
D2 76/2 2
D3 153/3 1.5
D4 231/7 2.33
D5 374/12 1.71
D6 528/17 1.41
D7 821/21 1.23
D8 1128/29 1.17
D9 1577/34 1.52
D10 1835/52 1.52
D11 2263/79 1.51
D12 2706/107 1.35
D13 3296/148 1.38
D14 3916/197 1.33
D15 5061/233 1.18

If we ignore the first 5 days (too noisy, and numbers too small to give any reliable statistics), The ratio of deaths on day X over all deaths till day X-1 looks like it varies from 1.17 - 1.52. An average over days 6 to 15 yields 1.36 as the ratio of infections from one day to the next! Doubling every three days!

Remember, this is for a population that is not yet alarmed, as presumably it takes perhaps 10 days from infection to death. Most of the dead till now are those who were infected ten days to two-three weeks ago! Now that the population is properly alarmed and taking many more precautions (no gatherings, hand shakes, face kissing every one you meet), this number should go down. But even if it is reduced by 75%, the doubling rate is now every eight days! This is the reason we are seeing serious measures such as curfews and lockdowns to control this disease.

...

The recovery rate seems to be 3-4 weeks after being infected. So if we can get the doubling rate down to 3-4 weeks, we will see an equal number of new patients as recovered patients and some sort of steady state equilibrium will be achieved in demand for hospital beds/health care etc. It remains to be seen if such delay in spreading the infection can be achieved. At the very least, large social gatherings - cinemas, restaurants, churches, mosques, schools, should be avoided.


The very crude disease doubling rate I estimated above appears to match the the estimation of 2.4 days doubling rate in an 'unalarmed population' by some Los Alamos guys. Seven weeks ago, China was reporting 50 cases.. So I think the next couple of weeks are going to be crucial in the US. In Italy, the horse has already bolted and they now have to take Wuhan style measures in Milan. Apparently, the story leaked and the trains out of Milan (as in Wuhan too!) were packed! I expect New York/New Jersey to be hit next.. Lot more Italy/Europe travel from that part of the US.

https://www.medrxiv.org/content/10.1101 ... 1.full.pdf

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Re: Wuhan Coronavirus Resource Thread

Postby Amber G. » 08 Mar 2020 09:55

Sharing this powerful article which was shared on Twitter by the chairman of the US FCC. I invite you to read it as well.

OPENING THE DOOR

>>>On Wednesday this week, Li Zehua , a journalist who recently resigned from his job as a news anchor at China’s state-run China Central Television to report as a citizen reporter on the front lines of the epidemic in Wuhan, was apparently detained by officers from state security. His whereabouts are currently unknown.

Li, who had managed to livestream his dispatches, and who also reported continued harassment from local police and security guards, arrived at Wuhan’s Baibuting Community, an area hit particularly hard by the epidemic, on February 16. He livestreamed a story on February 18 from a crematorium in the city about how porters were being hired at high wages in order to transport corpses. On February 25, he did a report in which he interviewed migrant workers who were forced to set up camp in the underground parking garage at Wuchang Railway Station.

Li’s citizen journalism in Wuhan followed in the footsteps of two other journalists, Fang Bin and Chen Qiushi, both of whom are now missing.

As state security officers caught up with him and prepared to detain him Wednesday, Li Zehua recorded a final message speaking to the men outside his door.


In this message, he talks about his belief in the importance of speaking up and the inspiration he took from Chai Jing (柴静), the celebrity CCTV anchor whose documentary “Under the Dome,” about serious air pollution in China, drew more than 300 million views online before being deleted by authorities.

Our translation of Li Zehua’s message follows.

<,<< Please see the link >>>
_____________


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