COVID COVID-19 Coronavirus Containment Efforts

[atyy]

Tom Cruise scolds Mission Impossible crew for not social distancing in leaked audio
https://www.nbcnews.com/pop-culture...t-outburst-covid-era-anxieties-power-n1251456

 

[Astronuc]

Oddly, Kansas reports only 7 hospitalizations (Sheridan reports 25) which seems low for 20 deaths.

I believe the 7 hospitalizations reflects 'active' hospitalizations as opposed to cumulative.

I searched and found Gove County Health Department data and made a timeline. Between March 01 and October 04, there were a total of 101 positive cases and no deaths. The first (2) deaths occurred between October 4 and 7. As of November 25, there were 20 deaths, but then none since. In the timeline below, the second active refers to active hospitalizations.

Oct 04, 2020 - 101 positive cases cumulative, 67 active cases; 12 hospitalizations cum., 4 active, and 0 deaths
Oct 07, 2020 - 115 positive cases cumulative, 77 active cases; 16 hospitalizations cum., 3 active, and 2 deaths
Oct 12, 2020 - 136 positive cases cumulative, 63 active cases; 21 hospitalizations cum., 3 active, and 2 deaths
Oct 16, 2020 - 148 positive cases cumulative, 39 active cases; 26 hospitalizations cum., 5 active, and 9 deaths
On October 18, Gove County Sheriff Allan Weber was flown to the Swedish Medical Center in Denver Colorado in respiratory distress due to Covid 19 complications. Upon arrival, he was intubated, put on a ventilator and placed in the Intensive Care Unit.
Oct 21, 2020 - 162 positive cases cumulative, 34 active cases; 28 hospitalizations cum., 6 active, and 10 deaths
Oct 23, 2020 - 171 positive cases cumulative, 29 active cases; 29 hospitalizations cum., 5 active, and 11 deaths
Oct 28, 2020 - 182 positive cases cumulative, 28 active cases; 30 hospitalizations cum., 2 active, and 12 deaths
Oct 30, 2020 - 185 positive cases cumulative, 23 active cases; 31 hospitalizations cum., 2 active, and 12 deaths
Nov 02, 2020 - 202 positive cases cumulative, 25 active cases; 35 hospitalizations cum., 3 active, and 16 deaths
Nov 04, 2020 - 213 positive cases cumulative, 33 active cases; 37 hospitalizations cum., 4 active, and 18 deaths
Nov 06, 2020 - 220 positive cases cumulative, 39 active cases; 41 hospitalizations cum., 3 active, and 19 deaths
Nov 16, 2020 - 245 positive cases cumulative, 29 active cases; 59 hospitalizations cum., 9 active, and 19 deaths
Nov 20, 2020 - 263 positive cases cumulative, 40 active cases; 61 hospitalizations cum., 12 active, and 19 deaths
Nov 23, 2020 - 272 positive cases cumulative, 40 active cases; 62 hospitalizations cum., 8 active, and 19 deaths
Nov 25, 2020 - 283 positive cases cumulative, 49 active cases; 62 hospitalizations cum., 8 active, and 20 deaths
Dec 02, 2020 - 294 positive cases cumulative, 35 active cases; 69 hospitalizations cum., 6 active, and 20 deaths
Dec 07, 2020 - 297 positive cases cumulative, 17 active cases; 73 hospitalizations cum., 7 active, and 20 deaths
Dec 09, 2020 - 299 positive cases cumulative, 17 active cases; 75 hospitalizations cum., 5 active, and 20 deaths

12/14: "On 12/13/20 Allan went into cardiac arrest while he was at PAM Speciatly Hospital. They do not know the exact amount of time he was without oxygen. His code lasted 15 mins after they found him unresponsive, after three rounds of epinephrine and shocking him they were able to get him back. He was transferred to Denver Health and the care at Denver Health has been beyond amazing."

I hope Sheriff Allan Weber pulls through.

Ref: https://www.facebook.com/govecocovid19/

 

[mfb]

Here's Covid mortality vs. the number of negative tests, state by state:

Wouldn't it make more sense to divide negative tests by population, too?
Number of negative tests is very similar to the total number of tests now. Early in the pandemic that was different.

 

[Vanadium 50]

We have a winner! (Sort of)

The mortality rate is correlated with population. As are the number of positive tests (0.96) and negative tests (0.90) However, it turns out the population is only correlated with mortality rate at 0.08, so I suspect that about 2/3 of the effect is random noise.

And random noise is clearly a factor, since the correlation with nonsensical quantities like state names is even larger than the "signal" being bandied about.

 

[Ivan Seeking]

We have a winner! (Sort of)

The mortality rate is correlated with population. As are the number of positive tests (0.96) and negative tests (0.90) However, it turns out the population is only correlated with mortality rate at 0.08, so I suspect that about 2/3 of the effect is random noise.

And random noise is clearly a factor, since the correlation with nonsensical quantities like state names is even larger than the "signal" being bandied about.

Geography correlates with behavior. There is nothing silly about it.

People who are infected and don't wear masks, spread the virus. Right?

 

[mfb]

Moderna studied how many people tested positive at the time of the second dose (28 days after the first one). The vaccinated group had ~1/3 the rate of positive tests of the placebo group, suggesting that the vaccine is very effective against asymptomatic infections as well (even after the first dose). That's good news for other mRNA vaccines, too.
Source

Vaccination trackers have started.
Worldwide - at the moment only the UK has data at 0.2% of the population
By US state - they seem to use doses and people interchangeably which confuses me. There should be a factor 2. All data there are plans. Generally the expectation seems to be that states get enough doses by the end of the year to give ~5% of their population the first dose. Most of these will be healthcare workers.

 

[PeroK]

Geography correlates with behavior. There is nothing silly about it.

People who are infected and don't wear masks, spread the virus. Right?

The problem is that the data is complex enough that it may be genuinely difficult to extract conclusive evidence for that; and, someone with a particular poltical agenda can look at the data differently to reject the conclusion.

The best/worst example I can remember of this was when the Scottish government began paying undergraduate university fees. The English Conservative government was/is opposed to this - and in England students have to take out a student loan.

One English Conservative looked at the data and concluded that students from poorer backgrounds were less likely to go to university in Scotland because their fees were being paid!

I've always remembered that because that's about as mad as politics can get.

I might say that, for an unknown reason, Scotland was still struggling to get more students from poorer backgrounds to go to university despite their fees being paid. Not because of it.

 

[Borg]

Tom Cruise scolds Mission Impossible crew for not social distancing in leaked audio
https://www.nbcnews.com/pop-culture...t-outburst-covid-era-anxieties-power-n1251456

I had heard about it but didn't check out the audio until this morning. He does sound a bit upset.

 

[Jarvis323]

I can't believe people are still arguing "My political tribe is doing better! You just have to look at the data the right way!"

OK, so my numbers proved unconvincing. Here's the scatter plot. Cook Political index is on the x-axis and deaths per million is on the y-axis.

View attachment 274435Do you see a trend there? I sure don't. People who are arguing that their political tribe is doing best are starting with the conclusion and fiddling with the data to support it. They sure aren't looking at the above data and drawing conclusions from it.

I guess, due to the many confounding factors, it is difficult to compare political influences. Rural areas are usually more republican leaning. Rural areas are also less densely populated. And it seems that for the most part, they are getting hit later, with right now being the beginning of a surge. There is also a difference in attitude once it starts hitting. At my hometown, even staff at the clinic weren't taking it seriously and even believed it was a hoax. But as soon as someone close to them was hospitalized, they started freaking out.

I propose instead that you should be comparing based on the measures and adherence to them. If there are compelling correlations with mask use, distancing, etc, and there are correlations with political affiliation and those measures, then you might have something fairly solid to talk about.

In my personal opinion, I think that preventative measures work, but are limited in effectiveness when not taken far enough and/or not adhered to strongly enough. We see clearly from the success of many countries (particularly in Asia) that measures can work very well. But perhaps due to culture differences, many countries tend to have populations which act more or less responsibly overall. And also, which have worse or better guidance and resources.

In places like the US, we see a somewhat half baked response, coupled with half baked adherence. There is no doubt also some political correlation, but the entire county is not doing so good. We have public officials (poor response, messaging, etc) and the public (poor adherence) both to blame I guess. It makes sense to talk about the political influence, but yes, lying with statistics is pretty easy (e.g. cherry picking, not correcting for population density, accounting for time, etc, etc. etc.).

 

[Jarvis323]

I had heard about it but didn't check out the audio until this morning. He does sound a bit upset.

It's funny because the day before, there was a lot of media buzz about Tom's cake gifting. He sends cakes to a whole bunch of people for Christmas. I guess that was his PR team doing some preemptive damage control. Even though I doubt it will hurt him anyways.

 

[Vanadium 50]

Same source different chart: top 13 states for death rate are republican and 13 out of 15 of the states with the lowest death rate are democratic.

You've seen the full data. It doesn't show what you want, so you can cut it until it does. "We're going to make it political if it kills us! Literally."

Top and bottom states? NJ and VT. Both Deomcratic. That doesn't work. Top two? Add ME and MA. Both Democratic. That doesn't work either.

OK, let's go to 3. HI and CT. No, that doesn't work. Both Democratic. Number 4? AK and ND. Both Republican. Fifteen states? Still even, although you can make the difference a state depending on what you do with NH (Cook index is zero) and whether you include DC or not.

The full dataset shows no effect. It's possible to get any effect I want by a posteriori deciding my cuts and metric. I can pick my starting date. If June doesn't show what I want, I can try May. Or July. Ten states don't? Try fifteen. Maybe eight. Whatever it takes.

We wouldn't accept that in "real science" and we shouldn't accept it now. (I know, "...but politics is important!")

 

[fresh_42]

We have a mutation in GB!

 

[OmCheeto]

We have a mutation in GB!

This one?: New Coronavirus strain spreading in UK has key mutations, scientists say

Odd. It's dated two days ago. Seems like we would have heard about this immediately.

 

[anorlunda]

What's with those Vermonters, not wanting to join the party?

I'm a Vermonter. I'm in Vermont June-October and in Florida November-May.

All summer in Vermont I saw nearly 100% compliance with social distancing and masks. Instantly when I returned to Florida on November 1 I was shocked to see maybe 2/3 of the people in public with no masks. I take that as a clue to how much people changed their behavior.

By the end of November, Vermont (population 500K) had only 2 people hospitalized with COVID.

p.s. The NY Times has a dashboard you can customize to the state/county level. It's useful for comparisons. I'm not sure if it has a paywall.
https://www.nytimes.com/interactive/2020/us/covid-cases-deaths-tracker.html

 

[fresh_42]

I'm not sure if it has a paywall.

It worked without paywall or other restrictions, even for me.

 

[Borg]

I think they allow a certain number of visits before you're blocked.

 

[mfb]

This one?: New Coronavirus strain spreading in UK has key mutations, scientists say

Odd. It's dated two days ago. Seems like we would have heard about this immediately.

Why? There is no indication that this particular mutation is different from the thousands of others people have seen.

Looks like new daily cases have stopped increasing in the US in December, stable at ~200,000. That means new deaths could stabilize at ~2500/day soon, too (as weekly average).

 

[OmCheeto]

Why? There is no indication that this particular mutation is different from the thousands of others people have seen.
...

Exactly!

 

[Astronuc]

Why? There is no indication that this particular mutation is different from the thousands of others people have seen.

I posted about that somewhere, either in this thread, or in one of the threads in Biology and Medical forum. The significance is that "The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19 spreading more easily between people."

 

[mfb]

"In theory" every mutation can do that, but without any evidence that this particular one does anything it's just one of many.

 

[Ivan Seeking]

You've seen the full data. It doesn't show what you want, so you can cut it until it does. "We're going to make it political if it kills us! Literally."

Top and bottom states? NJ and VT. Both Deomcratic. That doesn't work. Top two? Add ME and MA. Both Democratic. That doesn't work either.

OK, let's go to 3. HI and CT. No, that doesn't work. Both Democratic. Number 4? AK and ND. Both Republican. Fifteen states? Still even, although you can make the difference a state depending on what you do with NH (Cook index is zero) and whether you include DC or not.

The full dataset shows no effect. It's possible to get any effect I want by a posteriori deciding my cuts and metric. I can pick my starting date. If June doesn't show what I want, I can try May. Or July. Ten states don't? Try fifteen. Maybe eight. Whatever it takes.

We wouldn't accept that in "real science" and we shouldn't accept it now. (I know, "...but politics is important!")

Are you arguing that masks don't work or that party has no bearing on behavior? Are you denying that events like political rallies and Sturgis were likely superspreader events? I don't understand what you are trying to deny here.

Clearly you can't look at the first wave as you suggested given that no best practices were in place yet. How is that logically consistent? And infections are still spreading wildly, showing by far the highest density in areas that focused on rallies and public events.

 

[Vanadium 50]

Are you arguing that masks don't work or that party has no bearing on behavior?

Did I say any of that? Tell ya' what. You make your points and I'll make mine. That way you don't have to

Clearly you can't look at the first wave as you suggested given that no best practices were in place yet.

A posteriori argument. Feel free to make it, but don't pretend it's anything else.

 

[Ivan Seeking]

Did I say any of that? Tell ya' what. You make your points and I'll make mine. That way you don't have to
A posteriori argument. Feel free to make it, but don't pretend it's anything else.

I posted a map showing the CURRENT infection rates. You are using data going back to the beginning before best practices. Use the data I posted and your argument is moot.

 

[collinsmark]

I can't believe people are still arguing "My political tribe is doing better! You just have to look at the data the right way!"

OK, so my numbers proved unconvincing. Here's the scatter plot. Cook Political index is on the x-axis and deaths per million is on the y-axis.

View attachment 274435Do you see a trend there? I sure don't. People who are arguing that their political tribe is doing best are starting with the conclusion and fiddling with the data to support it. They sure aren't looking at the above data and drawing conclusions from it.

There is a striking correlation (at the moment) in the US between political trends and Covid-19 outbreak severity. But you won't find it that way for a couple of reasons:

1. Trying to find correlation between US states is too broad of strokes. A given state can have large metropolitan areas with a given political leaning while having large swaths of counties in other areas with the opposite leanings; all within the same state. It's better to get a bit more granular, like comparing counties.
2. It's not useful to include data early on in the pandemic. Very early on, the pandemic was spread by travel hubs, people were unaware of the proper precautions, and none of it was politicized.

Do you remember what it was like for those couple of weeks back in March? The whole country banded together. We were going to beat this virus, or at least pound it into submission for awhile to gain some time. We were all going to do it together. As a team. (Well, everybody except Trump who was spewing out some sort of unsubstantiated nonsense about how we should figuratively stick our heads in the sand because the virus is going to magically go away by Easter, "like a miracle.") Oh, I haven't forgotten those times.

I took the liberty of gathering some information summarizing the virus' spread and mortality rate by date and county, and comparing that to the 2020 presidential election results, also by county. I focused on a narrower timeframe, starting at Oct. 1st, up to the present. That let's us focus on the latest surge. The results mostly speak for themselves.

Figure 1. Scatter plot showing correlation between recent Covid-19 cases and voting trends, per county. Each dot represents a single US county/parish/municipality. (Note: Data for individual counties in Alaska were not available, thus all of Alaska is represented by a single dot.)

The correlation becomes pretty obvious when you look at Fig. 1. Each dot represents a single county. Counties on the right are those that showed larger support for Trump in the 2020 general election. Those on the left showed more support for Biden. A dot at 80 means that in that county, Trump had 80% of the vote. A dot at 20 means Trump only had 20% of the vote for that county.

Dots that are higher on the graph are counties that are getting hit hard by the pandemic right now.

The green, dashed line is a linear trendline confirming the correlation. If the pandemic was independent of voting trends, that line would be level with the horizontal. It's not even close to level.

You might be wondering why most of the dots are to the right of the 50% mark since Biden won the election. That's merely because there are more numerous, sparsely populated counties that leaned politically to Trump. Those to the left of the 50% mark, supporting Biden, while fewer in number, are more heavily populated on average.

Fig. 2 shows a similar plot but for Covid-19 deaths.

Figure 2. Scatter plot showing correlation between recent Covid-19 deaths and voting trends, per county (Note: Data for individual counties in Alaska were not available, thus all of Alaska is represented by a single dot.)

I've also attached a spreadsheet where one can analyze the data, if one wishes.

So what about causation? Well, that's complicated. I mean we all might be tempted to say that the unity the country embraced at the beginning of the pandemic fell apart when the red and tinfoil hat, conspiracy theorists started shouting bloody murder and mouth breathing about how a small piece of cloth on their nose is the most intense hardship they've ever experienced since they lost Civil War I. But I might caution against that since the relationship between correlation and causation can be a tricky one. (But, yeah.)

But since this thread was questioning the correlation aspect of it, I can and will say this: Yes, the correlation is there. It is real and undeniable according to my data.

----------------------------------------------------------------------
Sources:

Covid-19 data taken from the New York Times Covid-19-Data repository on Github. It's updated every day, usually around midnight, Greenwich Mean Time.
https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv

Population data was taken from US Census estimate for 2019 (it would appear the 2020 Census data isn't available just yet).
https://www.census.gov/data/tables/time-series/demo/popest/2010s-counties-total.html

Finding 2020 election data by county was a bit tougher. I mean it's widely available, but finding it all in one place was the thing. I ended up using this data from Tom McGovern on Github
https://github.com/tonmcg/US_County...2020_US_County_Level_Presidential_Results.csv
I compared a sample of counties against websites such as this one (https://abcnews.go.com/Elections/2020-us-presidential-election-results-live-map/), and it seems to check out from my limited sample. If you have any questions about the data, again, I've included the Excel file so anyone can critique it.

 

[russ_watters]

It's not useful to include data early on in the pandemic. Very early on... and none of it was politicized.

Hehe.

Even if that were true, which is isn't, there's an underlying assumption that the first wave has no impact on subsequent waves. But each wave necessarily lessens the severity of subsequent waves by reducing the pool of potential victims. The more severe the prior waves, the less severe subsequent waves will be.

 

[mfb]

I suggest to end the Democrat/Republican discussion here. It's questionable if it is within the forum rules, and it's getting really repetitive and it seems to take over the thread. Posting largely the same arguments yet another time isn't helping anyone.

 

[fresh_42]

If this ...

The significance is that "The new variant, which UK scientists have named “VUI – 202012/01” includes a mutation in the viral genome region encoding the spike protein, which - in theory - could result in COVID-19 spreading more easily between people."

... is true, then this ...

"In theory" every mutation can do that, but without any evidence that this particular one does anything it's just one of many.

... is unfortunately wrong, simply because the currently hyped vaccines other than other vaccines primarily attack named spike protein, i.e. it is not clear whether currently planned vaccinations protect against that new strain. However, I saw this on a news channel and the professor who was interviewed said, that it is unlikely that a mutation changes the spike. Maybe he had been caught on the wrong foot and he was not prepared. But he expressed his concerns that it won't remain in UK over the holidays. "It's just one of many" is an a priori assessment. Let's hope it will become an a posteriori assessment, too.

 

[atyy]

... is unfortunately wrong, simply because the currently hyped vaccines other than other vaccines primarily attack named spike protein, i.e. it is not clear whether currently planned vaccinations protect against that new strain. However, I saw this on a news channel and the professor who was interviewed said, that it is unlikely that a mutation changes the spike. Maybe he had been caught on the wrong foot and he was not prepared. But he expressed his concerns that it won't remain in UK over the holidays. "It's just one of many" is an a priori assessment. Let's hope it will become an a posteriori assessment, too.

There are already mutations in the spike protein. Currently, they are thought not to affect the spike protein enough to affect vaccine effectiveness. These mutations do affect the behaviour of the virus in cell culture, but at the clinical level these are thought to be of minimal significance.

https://www.nature.com/articles/s41541-020-00246-8
Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein

In principle, spike protein mutations can cause a problem for vaccines, however, back of the envelope estimates by Trevor Bedford suggest that this is likely to take a few years:
"If I had to guess, I would predict that #SARSCoV2 will behave similarly to existing seasonal coronaviruses in its ability to mutate to avoid vaccines and immunity.
...
So, my prediction is that we should see occasional mutations to the spike protein of #SARSCoV2 that allow the virus to partially escape from vaccines or existing "herd" immunity, but that this process will most likely take years rather than months."

 

[Astronuc]

United (I believe other airlines require the same) requires all its passengers to complete a "Ready-to-Fly" checklist before checking into a flight, which prompts them to acknowledge they have not tested positive for COVID-19 nor have they had any related symptoms in the past two weeks.

https://abcnews.go.com/Politics/man-dead-medical-emergency-united-flight/story?id=74802890

Yet, a man with symptoms of Covid-19 died on a flight.

United Flight 591 (Orlando (MCO) to Los Angeles (LAX)) was diverted to New Orleans on Monday after a male passenger became ill. Paramedics transported the individual to a local hospital where he was pronounced deceased, the carrier said.

If he had symptoms, he shouldn't have been flying.

 

[fresh_42]

If he had symptoms, he shouldn't have been flying.

This virus is an excellent measure on how far a society is altruistic or selfish. All individual measures are mainly to protect others rather than oneself. E.g. people who refuse to wear a mask and protest against it justify that with their personal freedom. A freedom to the expense of others. One should not complain about it because it is in accordance to the general commitment on individualism versus social responsibility.