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Coronavirus (COVID-19) Thread

02 Apr 2020 00:11

Cantra wrote:
Source of the post Just a personal thing, I find that very hard to believe. Everything about this and the situation is very suspicious. 

Pandemics happen from time to time, why should it be suspicious?  It's only 10 years since we had the swine flu.  Covid-19 and the swine flu differ in some way.  Covid-19 spreads more rapidly and seems more deadly, but it can be argued that the swine flu was more dangerous in the sense that it affected children and young adults more than older people, whereas fatalities amongst the young from covid-19 is rare, and extremely rare if good healthcare is available.
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Coronavirus (COVID-19) Thread

03 Apr 2020 14:32

midtskogen wrote:
Cantra wrote:
Source of the post Just a personal thing, I find that very hard to believe. Everything about this and the situation is very suspicious. 

Pandemics happen from time to time, why should it be suspicious?  It's only 10 years since we had the swine flu.  Covid-19 and the swine flu differ in some way.  Covid-19 spreads more rapidly and seems more deadly, but it can be argued that the swine flu was more dangerous in the sense that it affected children and young adults more than older people, whereas fatalities amongst the young from covid-19 is rare, and extremely rare if good healthcare is available.

The trade deal with China was signed shortly before this Pandemic occurred, and there is a bio warfare laboratory near to Wuhan. 
 
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Coronavirus (COVID-19) Thread

04 Apr 2020 00:57

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Source of the post The trade deal with China was signed shortly before this Pandemic occurred, and there is a bio warfare laboratory near to Wuhan.


Okay and?

The Wuhan institute of virology was not equipped to deal with these pathogens, it did however work on sequencing and has worked in sequencing.  During my own time working in virology we had data from them regarding the 03 SARS outbreak and in 2012 the MERS outbreak, but it doesn't mean they worked on it.  This institute is an L4 facility.


Before going further, brush up a bit, here is the wiki article and Public Health Emergency governmental website on the levels regarding biosafety

https://www.phe.gov/s3/BioriskManagemen ... evels.aspx
https://en.wikipedia.org/wiki/Biosafety_level


See I worked in an L3 facility, we did sequencing and data work for other facilities as we were better equipped for it than they were, but we never actually had the physical viruses or bacteria, or even prions.

But lets go deeper shall we?


I have been ahead of this outbreak since late December, our Discord community can back that up.

I pointed out the poor actions of the Chinese government in January
Image

I even pointed out the things to expect from the virus
Image



I have a website here which has sequencing data

http://recombinomics.co/topic/4351-wuha ... sequences/
https://recombinomics.co/forum/479-sequences-covid/

Another which shows the phylogeography of the virus
http://virological.org/t/phylogeography ... r-2020/444


When you modify a pathogen you make markers, you have inserts, things which point to how it leaped when using comparative genomics.  

If this virus were designed they did an absolutely incredible job at it.  They must have had a couple dozen wet markets with Asian creatures crammed together and somehow kept this all hidden while injecting environmental markers from specific locations out of China, and intersplicing pieces of random Chinese citizens who they knew later would be infected.  Then at this point released it into a wet market they knew which would cause an outbreak.


But sure, lets say it was an accidental release.  The same notions still apply, we have clear markers linking it to specific species, clear markers linking it to geography, and clear markers showing no input from humans.

These conspiracy theories need to die
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Coronavirus (COVID-19) Thread

04 Apr 2020 01:53

Tests in Iceland indicate that half of those infected are asymptomatic, but this study indicate that as many as 80% are asymptomatic.  If that's really true, lockdowns wont do much.

I'm somewhat skeptical.  But maybe there are different mutations with different percentages.  Over here things exploded when people got home from Austria, and there were large groups in which most got ill, some very ill.  So assuming that every single one in those groups got infected, less than half were asymptomatic.  Still, a relatively high percentage explains well the rapid spread.
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Coronavirus (COVID-19) Thread

04 Apr 2020 06:16

 
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Coronavirus (COVID-19) Thread

06 Apr 2020 17:14

Was linked on Discord, and thought it worth sharing here as well:

What it feels like to survive COVID-19’s dreaded “cytokine storm”
 
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Coronavirus (COVID-19) Thread

08 Apr 2020 15:59

midtskogen wrote:
A-L-E-X wrote:
Source of the post  Is there some legitimacy to the idea that the Chinese importing poached animals from Africa caused this?

Many blame the live animal markets in China.  Maybe, but the facts are obscured by much activism to ban such markets for other reasons than diseases.

Yes but those markets should be banned, especially the ones involved in poaching and ridiculous religious practices that are involved.
The areas that are hardest hit are very densely populated.....going back to what we talked about months ago, this was a powder keg just waiting to explode.  I hope this changes our society permanently and people take the positives of these changes and create a more positive and less polluted environment, as has seemed to have happened the last few weeks.

We need deep healthcare reform.   it's also why minorities have lower life expectancies and far worse coronavirus outcomes.  Underlying conditions due to a diet high in processed foods (diabetes, heart disease and obesity from cheaper fast foods and soda, because they face income inequality and that's what they can afford) and higher pollution levels (and higher rates of asthma) are partly responsible.

While the UK united after WW2, America became much more divisive.  UK got the best healthcare in the world, America went south.

Mid take a look at these for why viruses should be considered alive:

https://www.sciencealert.com/are-viruses-alive

https://www.scientificamerican.com/article/are-viruses-alive-2004/

Just to add to the above, I watched an excellent interview with the CDC's director about how both our bad lifestyle habits and pollution have made this so much worse than it had to be.  High levels of air pollution from car exhaust especially near densely packed cities with high levels of NO2 causing high levels of asthma made our lungs weaker to begin with.  On top of that, half of all Americans have existing medical conditions like obesity, diabetes, high blood pressure, etc, because of a bad diet.  Urban dwellers are more likely to consume ultra processed food with HFCS, high levels of salt, etc., which has caused these underlying conditions to begin with.  On top of that, not having universal healthcare, where many people have not even ever gone to doctors to treat these underlying conditions has caused this virus to find every weakness in our society and exploit it.

When I was in high school and college I used to travel a lot and saw these disgusting open air markets in Asia.  Hygiene is in a very short supply.  Not only are the animals very poorly treated, the atmosphere is dangerous to the health of human beings.  No wonder so many Far Easterners wore face masks long before this virus raised its ugly head.  Glad I'm a vegan now and dont have these disgusting habits and my blood pressure has gotten a lot lower (without meds) since I eliminated processed food from my diet.

Both the UN and the American Journal of Microbiology and Dr Fauci of our CDC have all said that China needs to end these nasty dirty "wet markets" on exotic mammals.  I saw a video where thousands of these disgusting bats were being showed off in a slaughter shop- the same ones where this virus supposedly came from.  We need to stop encroaching on lands that belong to wild animals or we will keep having these pandemics.  Dr. Rick Knabb who was the head of the National Hurricane Center said that unless we put a check on our population growth, climate change, pandemics and pollution will ALL be much harder to fight.

At the Bronx Zoo, the disease has spread from animal workers to 4 tigers and 3 lions, they have developed a dry cough and lack of appetite.  So obviously transmission between creatures can and does happen.

Ironically our pollution levels have gotten a lot better because of this pandemic.  I hope we learn our hard learned lessons and hold onto that after the pandemic ends.

Found this out the other day, did you know that 8 MILLION people a year die from pollution?!
 
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Coronavirus (COVID-19) Thread

16 Apr 2020 14:28

I've been following New York governor Andrew Cuomo's daily briefings for a while now, which have been truly fantastic. Today's briefing gave a good overview of the development of the plan to gradually transition New York and the surrounding states back to a full working economy.



This process of course must be taken slowly, incrementally. A good analogy is like bringing a nuclear reactor online -- carefully, and constantly watching the effect that each small action you take has. In a reactor you move control rods and watch the reaction rate. Here, we expand what we consider essential businesses, and we watch the infection rate, or rather, a proxy for it. Widespread testing is essential, as is contact tracing. The way businesses operate must be considered, and whether they can be made safer. There is a lot that needs to be done to make this work, but like midts has mentioned, the future we transition into could be a better one.
 
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Coronavirus (COVID-19) Thread

22 Apr 2020 01:40

There was a one hour special on PBS Frontline on the chain of events in the US's first outbreak in Washington State, and the interplay between state government and federal government response. Very well put together.

Covering Coronavirus: A Tale of Two Washingtons - PBS

How did the U.S. become the country with the worst known coronavirus outbreak in the world? FRONTLINE investigates the American response to COVID-19 — from Washington state to Washington, D.C. — and examines what happens when politics and science collide.
 
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Coronavirus (COVID-19) Thread

22 Apr 2020 09:33

Watsisname wrote:
I've been following New York governor Andrew Cuomo's daily briefings for a while now, which have been truly fantastic. Today's briefing gave a good overview of the development of the plan to gradually transition New York and the surrounding states back to a full working economy.



This process of course must be taken slowly, incrementally. A good analogy is like bringing a nuclear reactor online -- carefully, and constantly watching the effect that each small action you take has. In a reactor you move control rods and watch the reaction rate. Here, we expand what we consider essential businesses, and we watch the infection rate, or rather, a proxy for it. Widespread testing is essential, as is contact tracing. The way businesses operate must be considered, and whether they can be made safer. There is a lot that needs to be done to make this work, but like midts has mentioned, the future we transition into could be a better one.

Did you see how he mentioned (on Earth Day) how the highest rates of it are in highly polluted areas, where the asthma rates are 3x worse?  Very much on point and exactly why we need tougher regulations.
Since you mentioned PBS did you see their excellent 2 hour show on America's diabetes epidemic and how the pharma industry is price gouging life saving medication like insulin (we're suing them now)?  Also, they mentioned how diabetes rates have tripled because of the poor Western highly processed diet, especially in rural AND in urban communities- the "food deserts."  This is very appropriate, especially considering how diabetes makes the outcome of this pandemic far worse.  Seems like the only ways to get real change is to either sue these companies or boycott them.

It's also very illustrative that the nations doing best are nations that took quick action, like South Korea, New Zealand, Norway, Denmark, Finland, Iceland and Germany.  Sweden's outcome has been worse, and the UK even worse than that.

Much will change in this country and the world after this, much more than most people realize.  I see even a significant percentage of conservatives (25%) now realizing that we need universal healthcare- something that was obvious to the rest of us a long time ago.  When you strongly regulate unhealthy foods, you wont have the logjam often mentioned about some people being refused healthcare. Ban non nutritious food, strongly regulate pollution causing chemicals and ban plastic and you have much fewer sick people (lower rates of diabetes, high blood pressure, obesity, heart and lung conditions, etc.)  It's good to see oil falling flat on its face, global pollution has been significantly lowered because of this pandemic- a positive and foreshadowing of what we need to do in other to live sustainably.  Air pollution being halved is one positive outcome of this pandemic.  We need to continue this trend after this ends.
 
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Coronavirus (COVID-19) Thread

22 Apr 2020 16:22

A-L-E-X wrote:
Source of the post It's also very illustrative that the nations doing best are nations that took quick action, like South Korea, New Zealand, Norway, Denmark, Finland, Iceland and Germany.  Sweden's outcome has been worse, and the UK even worse than that.


Yes, another useful case study is to compare and contrast Norway with Sweden. As Midtskogen described earlier, Norway went more heavily toward total societal shutdown, while Sweden leaned towards keeping things open and trying to protect the more vulnerable. How well did it work? Well, their growth curves for cases started out at around the same time and for a while looked fairly similar, with the typical exponential growth that eventually flattens out toward something more linear. But now that more time has gone by we see the differences quite clearly. Norway's rate of new cases has been dropping -- now down to about 100 per day from a peak of about 300 per day around March 27. Sweden however has only just plateaued, at around 500 per day. It appears that Norway's strategy has proved more effective at flattening the curve.

Testing, however, may differ from place to place. A more accurate but grim comparison may be the deaths. Sweden's number of deaths so far is much greater than Norway's -- by a factor of 10! We might expect their difference in strategies to be reflected in their numbers of deaths, but such a large discrepancy is shocking to me. I don't fully understand it. It is probably due to a complex combination of factors.

Sweden's approach now seems to be the same as what the UK initially planned on -- to let the virus spread, suffer the impact now and hope for herd immunity to reduce the severity of following waves. It's a very risky experiment, and many in the academic community have sent pleas for them change their course. If they go forward with it, only time will tell how it works out.
 
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Coronavirus (COVID-19) Thread

23 Apr 2020 03:22

A-L-E-X wrote:
Source of the post Did you see how he mentioned (on Earth Day) how the highest rates of it are in highly polluted areas, where the asthma rates are 3x worse?  Very much on point and exactly why we need tougher regulations.

The correlation may simply be that both pollution and virus spread are correlated with population density.  It means that the regulations need to be local.  There are many places where the toughest regulations will be pointless.

Watsisname wrote:
Source of the post Norway went more heavily toward total societal shutdown, while Sweden leaned towards keeping things open and trying to protect the more vulnerable. How well did it work? Well, their growth curves for cases started out at around the same time and for a while looked fairly similar, with the typical exponential growth that eventually flattens out toward something more linear. But now that more time has gone by we see the differences quite clearly. Norway's rate of new cases has been dropping -- now down to about 100 per day from a peak of about 300 per day around March 27. Sweden however has only just plateaued, at around 500 per day. It appears that Norway's strategy has proved more effective at flattening the curve.

Sweden has played a more dangerous game.  Protecting the vulnerable has not been very successful with many deaths in the >80 years group.  Their other goal, achieving herd immunity without collapsing healthcare, is yet to be judged.  If it turns out that herd immunity is hard to achieve for this virus, then the strategy is a big failure.  That remains to be seen.  The number of new cases in Norway and Sweden, even if you correct for roughly double the population in Sweden, is difficult to compare as the testing is different and many are asymptomatic.  It may well be possible that the cases in Sweden has passed the million mark, whereas in Norway it's just in the tens of thousand range.  In that case deaths in Sweden will drop, whereas Norway will simply slowly catch up with all the pain of strict regulations.  I think we need to look at the death numbers when this is over and all data are in to judge who where right.  Sweden does have a much higher number of deaths per million than Norway, but Norway may simply have postponed the problems.  Currently Norway has 125 people hospitalised with Covid-19, 33 of which getting breathing aid.  Many are above 80 who would not have received this kind of attention for similar symptoms in a normal situation, which raises some ethical questions concerning how elderly are treated.  The capacity is higher, and a lot of other appointments have been postponed to free up resources in case Covid-19 gets really nasty.  This is also bad, and premature deaths due to this are likely not counted.

Schools will partially reopen here on Monday.

EDIT 2020-04-24: Today the first deaths of anyone under 50 years were reported in Norway.   The current breakdown is:
40-49: 2
50-59: 6
60-69: 13
70-79: 44
80-89: 70
90+: 56

The average age is 83.  Life expectancy in Norway is also 83.
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Coronavirus (COVID-19) Thread

24 Apr 2020 13:57

midtskogen wrote:
Source of the post The number of new cases in Norway and Sweden, even if you correct for roughly double the population in Sweden, is difficult to compare as the testing is different and many are asymptomatic.  It may well be possible that the cases in Sweden has passed the million mark, whereas in Norway it's just in the tens of thousand range.

The question of how many true infections there have been is important. To help answer that, New York began a new study performing antibody tests on a random sample of the public at the grocery and other stores in counties all across the state (so by design the sample only includes people who are out in society rather than staying in their homes, and therefore the infection rate derived from this is likely to be an overestimate rather than an underestimate). Preliminary results from 3000 tests are discussed starting at 11:09 here:



Results: Across the sample, 13.9% tested positive, meaning they have had an immune response to the virus. NYC had the highest rate of 21.2%, Long Island 16.7%, Westchester/Rockland 11.7%, while the rest of the state had 3.6%.

Out of a state population size of 19.45 million people (as of 2019), that implies 2.7 million infections.  With 15,000 deaths in New York, that implies a true mortality rate of 0.55%. Smaller than most WHO and CDC estimates. However, remember two caveats -- first, this is likely overestimating the fraction infected, since by design it sampled people who are out and about the most. Second, we have not counted the few thousand COVD-19 deaths that may have occurred outside of hospitals and nursing homes. Estimates currently put the number of these deaths at around 5000. 

So by these data I think we can safely conclude the mortality rate is not less than 0.5%, and it is likely to be higher, perhaps consistent with the older estimates of 1-3%. Also crucial to note: even in the most hard hit areas in NY, the fraction of infected is around 20%. These areas are not even close to reaching herd immunity.

What does this imply for Sweden?  If the strain of the virus spreading there has a similar mortality rate as in New York, for which let's use the 0.55% figure, then their 2152 deaths (according to worldometers as of this writing) implies they have had 390,000 true infections so far. Not millions.
 
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Coronavirus (COVID-19) Thread

24 Apr 2020 15:01

Watsisname wrote:
Source of the post What does this imply for Sweden?  If the strain of the virus spreading there has a similar mortality rate as in New York, for which let's use the 0.55% figure, then their 2152 deaths (according to worldometers as of this writing) implies they have had 390,000 true infections so far. Not millions.

You leave out one important factor: Of all infected a small percentage get seriously ill and their survival highly depends on whether they get good treatment.  That's the whole point of the flatten the curve mantra.  Healthcare in Sweden is very good and hospitals have not been seriously overwhelmed.  I would not be surprised if the mortality rate will turn out to be well below 0.5% in some countries, and 1 - 2% in others.  Also, different countries might be hit by different variations of the virus with different mortality rates, so direct comparisons will be difficult.

Another factor: The mortality rate also depends not only on age, but on other health factors as well.  Americans aren't well known for their wise lifestyle choices. Wikipedia says the the US has a mean BMI of 28.8, Sweden 25.8.  Diabetes is more than twice as common in the US as in Sweden and so on.  These things can also influence the mortality rate in different countries.

To make things a bit more complex: Reported flu cases dropped sharply when restrictions began.  Two plausible explanations: distancing and better hygiene helps.  And fewer see doctors for the flu because of corona.  Or a combination.  This could also mean fewer deaths from the flu (amongst the particularily vulnerable 80+ group).  So when the total number of deaths whatever reason in 2020 will be compared with other years, there will still be attribution issues.
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Coronavirus (COVID-19) Thread

24 Apr 2020 16:15

midtskogen wrote:
Source of the post You leave out one important factor: Of all infected a small percentage get seriously ill and their survival highly depends on whether they get good treatment.  That's the whole point of the flatten the curve mantra.  Healthcare in Sweden is very good and hospitals have not been seriously overwhelmed.

The flood on the health care system in NY has been very high. Even now, on the decline of the curve, about 1300 new COVID-19 patients still come in to hospitals statewide every day. But with the expansions of capacity and coordinating patient and equipment movement across all hospitals in the region, they managed to avoid being overwhelmed. Patients who required it have been put on oxygen, and those that continue to decline have been put on ventilators. So I do not think many deaths can be attributed to insufficient care, except for those who died at home, which we have not counted yet. Maybe another explanation is perhaps there is more use of effective antiviral remedies in Sweden than NY? Offhand I don't have good info about that besides this page for NYC hospitals.

How strong could the effect be from the age distribution? Earlier we looked at South Korea and Italy, and found the difference in their population pyramids could account for about a 40% difference in mortality rate. For New York, the data from the antibody study as well as from hospitalizations do not suggest this would be very important. The former is a fairly uniform sampling by age, and it shows that for those interacting in society, the infection rate is also fairly uniform by age (within factor of 2). The latter shows that mortalities by age follow a consistent trend as what we expected.

Comorbidities can certainly be important. In NYC 34% of adults are overweight and 22% are obese. Asthma and diabetes factor in, too. I think that will surely change the calculus, but... will it change it by a factor of more than 2? That would really surprise me.

And of course the biggest caveat is this: These are preliminary data. The study is ongoing, so the data could change. Still, it's a sample size of 3000, which is a lot of data already and I think we can draw useful conclusions from them.

Anecdotally I have heard people in the US speculate that the true number of infected is so much higher than the reported cases that if we had all the numbers it'd turn out that this was no worse than a typical flu, or that some places have already hit or are very close to herd immunity, which if true would change the discussion about responses and reopenings. But these data do not show that to be true. The number of infections is higher, but not that much higher. I suspect that will be the case for most other countries so far, as well. I hope we can find out for sure by having similar antibody studies conducted elsewhere. The nice thing is it could soon be possible to do that in a more widespread manner -- we don't need to wait for the pandemic to play out to get those facts.

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