Coronavirus - worldwide spread and control

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(Bad) news from France

Beaten Back, the Coronavirus Regains Strength in France

Faced with an increase in infections, especially among young adults, French health officials are expanding mask rules and warning against complacence.

The signs of a new wave of infection emerged over the summer as people began resuming much of their pre-coronavirus lives, traveling across France and socializing in cafes, restaurants and parks. Many, especially the young, have visibly relaxed their vigilance and have not followed rules on mask wearing or social distancing.

In recent days, France has recorded about 3,000 new infections every day, roughly double the figure at the beginning of the month, and the authorities are investigating an increasing number of clusters.
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https://www.nytimes.com/2020/08/17/world/europe/france-coronavirus.html?smid=tw-share

Masks have just been declared madatory in working places from the 1st of september.

Nothing is prepared for schools and universities. That is really insane. The education minister has spent his summer doing sports in front of the media.
 
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Yesterday I had a short look at wikipedia pages. Although new infections seem to rise, it doesn´t seem to correspond so far to deaths (or even hospital admissions).

The curve of deaths, as has been pointed out, has gone down in a textbook like manner. I still could´t find any investigations on effectiveness of measures, and still wonder if the initial rough measures and common carefulness might already have done the job in countries that havn´t been idle.

euromomo.eu

cdc.gov//covid19/excess_deaths

It is true that in the US the excess rate is still above the "upper average", in contrast to what I had said a few weeks ago, but the curve nevertheless has gone down - or still goes down? - in the textbook like manner, which makes the question arise - I think - if the now displayed excess deaths are directly due to covid-19, or if they might occur from indirect effects of the pandemic (and the US health care system is not well organised ... , is it?).

I still think that on the long run the measures might turn out to have done more harm than good, we ´ll see in a few years.
 
That banquet took place on January 18, 2020, and clearly qualifies as a superspreader event. What we are seeing in the available data is that there were many infected individuals there, and multiple strains. We also have at least one definite case in France prior to that event, and likely elsewhere. Granted you have to make assumptions to make models work, and these are hard to document when some data is suppressed. My judgment is that the assumptions necessary to put the origin late in December 2019 are wildly improbable. Another problem is that you would have to assume a high value of R0 early on, which suddenly decreased after the banquet, but before the world woke up to the crisis. (We have plenty of evidence lots of people still haven't awakened.) You would also have to assume the rate of mutations was high at the beginning, then suddenly dropped, to generate the number of strains we trace back to common ancestors.

That simply isn't how epidemics work. Pathogens generally mutate to become more infective, but less lethal, so that carriers have more time to spread infection. Changes in the mutation rate for one strain are possible, but should not affect other strains existing at the same time. When you have two unexplained shifts in the pathogen that happen at the same time for reasons nobody can state, it is safer to assume there is missing data.

My best guess remains an origin in mid-November resulting in thousands of cases in China prior to that banquet. There is plenty of evidence of government incompetence almost everywhere you look. China is no exception. I'll have more to say about U.S. incompetence and garbled data in a later post.
 
Florida has had a strange combination of reported data which has caused me to question the way it is being reported. Testing and case numbers have declined, but both deaths and hospital admissions have remained high. Today the DoH reported 3,383 new cases and 219 deaths. Monday they reported 2,678 cases and 82 deaths. There is always a dip in reporting caused by weekends, but this seemed excessive. Those declining case numbers, from a peak of 15,300 in a day, have paralleled a drop in testing. There is a departure in positivity rates between antibody tests (>20%) and RT-PCR tests (<8.22%). Florida is approaching a total of 10,000 COVID-19 deaths. Unfortunately, we have been seeing another surge in infections in long-term care facilities. Here's a more recent article in the Miami Herald.

I've looked for similar problems in Texas, a state that just passed 10,000 deaths due to COVID-19. Here's one report of the problem they have. I have another article to link, but you would likely hit a paywall. Here's a quote: “Without really good data, it’s going to be hard to navigate and know where we are in the response,” Lakey said. “If you don’t know that you can trust that positivity rate and trust the case counts, then you’re flying blind.”

California has already admitted to a serious problem with their data some time back.

I'm afraid major sources of pandemic data in the U.S. are not reliable. What I cannot say is how much is due to political interference versus sheer incompetence. The problem is that whatever data we have is being used to guide policy on opening schools with in-person classes.

Nothing convinces me this problem is about to go away.
 
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New hyper-infectious coronavirus strain may be 'a good thing', says disease expert

http://www.msn.com/en-gb/news/newsl...g-says-disease-expert/ar-BB186ByK?ocid=ASUDHP

A strain of the novel coronavirus spreading across large parts of the globe may be ten times more infectious but less deadly, a top disease expert has said.

President-elect of the International Society of Infectious Diseases, Paul Tambyah, has said evidence suggests the proliferation of the D614G mutation in some parts of the world has coincided with a drop in death rates.
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anciendaze said:
My best guess remains an origin in mid-November resulting in thousands of cases in China prior to that banquet. There is plenty of evidence of government incompetence almost everywhere you look. China is no exception. I'll have more to say about U.S. incompetence and garbled data in a later post.
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Which then again brings me back to that really really nasty cold-y/flu-y bug that was doing the rounds in the UK, particularly in London, in early December ... :(
 
So the doctor isn't too keen on vaccinating the whole population, comparing it to 50% of the population with H.Pylori infection and not developing into stomach cancer for everyone.
 
People can make similar comparisons about all sorts of things, for example, should we ban cars because accidents cause many deaths and serious injuries every year, or should we ban certain food items because they might increase ill health.

I got the impression he was more-or-less saying that it was time the constant barrage of fear-inducing reporting was stopped, since he believed it wasn't justified now (in Spain). But I'm not the world's best at understanding what people are implying, so take that with a pinch of salt.
 
Snow Leopard said:
This model has far too many unverified assumptions to be any more than suggestive. Other models could just have likely predicted or assumed more undetected cases in late Jan/early Feb - not just in the USA, but Europe too. I would consider airports themselves as prime candidates for "superspreader" events.

There were multiple introductions from China and Europe - far more people were infected in China than reported. There was also an explosion in cases in Wuhan due to the communal banquets being held for Chinese New Year, right when the epidemic was blowing up and just before the city was locked down.

There is also the hypothesis (or more appropriately, propaganda) that keeps being pushed by the Chinese Government, despite the lack of evidence - namely that the virus originated in the USA or Italy etc. I guess the goal is to blame it on foreigners to preserve face.
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Is there a "new" form of the virus circulating i.e. which is more contagious but less likely to kill you? Heard some media reports - second hand ---- might check unofficial Sage for an update.
 
FMMM1 said:
Is there a "new" form of the virus circulating i.e. which is more contagious but less likely to kill you? Heard some media reports - second hand ---- might check unofficial Sage for an update.
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I doubt it. Usually variant strains with mutations in key epitope regions occur once there is strong immunological pressure, basically once a large proportion of the population has prior immunity and the virus has to mutate to survive.

Sequencing studies of SARS-2 mostly show genetic drift, rather than significant structural mutations in key epitope regions.

However it is hypothetically possible that prolonged social distancing measures may select for increased contagion (though this won't necessarily have any impact on mortality).
 
Strictly speaking viruses do not mutate. Our nucleic acid copying machinery mutates them by making occasional mistakes. I would not expect that human mutation rate to alter over millions of years. The issue must be the likelihood of any mutation coming to dominate by getting copied more often. When people talk of one virus mutating more than another I suspect that reflects whether or not they have proteins that can tolerate changes in structure that are not catastrophic to further replication. Nothing to do with the virus itself having a capacity to change more often, although there might be sequences more subject to (human) errors. Virus mutation tends to be discussed in terms of the tendency to form strains that can produce new epidemics, as in flu, but that is only one of many scenarios.

During a gradually unfolding pandemic such as this one I would expect the selection pressure for more infectious mutants to come to dominate to be high so this story sounds very plausible. I do not think that the situation for viruses that mutate sufficiently to escape immune surveillance and produce a new epidemics is necessarily relevant.
 
Snow Leopard said:
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When you have thousands of people with an illness, even 10% of those adds up.
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In the U.S. we have over 5 million cases, so 10% could be a major public health burden all by itself.

Incidentally, when I went to check hospitalizations I ran into a problem getting data. The place this should be is the CDC emerging infectious diseases program, which has set up COVID-Net. Here you will discover that Texas and Florida are not officially participating. California has only the minimum percentage of counties participating. These are three states with about 500,000 cases and 10,000 deaths each. This is a huge gap in data available to the CDC. There are other sources, but it is really hard to get reliable apolitical data.

I've been trying to estimate the percentage of infected requiring hospitalization from day one, and still don't have a solid answer.

Furthermore, we have had leaders, including one I shall not name, saying that case numbers were high because we were testing so many, and we would be better off by testing less. Since that announcement we have seen a decline in testing paralleled by a decline in case numbers. I still can't tell you what is going on in Florida, where I live. I'd feel better if we were not seeing over 100 deaths reported each day.

Dropping case numbers caused by restricting testing to those with symptoms should produce an increase in positivity of tests. We have a wrinkle in Florida DoH statistics that reduces positivity. Patients with positive results are only counted once, but negative results are counted multiple times. The result is that I still don't know if infection numbers are going up or down. I do know deaths and hospitalizations remain curiously high for a declining epidemic.

This picture has been complicated by wildfires in California and a number of tropical storms facing Florida, both of which complicate efforts to control infections.

Oh yes, we are also trying to reopen schools with face-to-face classes. So far, this is not going well. Results from early classes are mostly not in yet.
 
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