COVID-19 Coronavirus Containment Efforts

[Vanadium 50]

Prosecutors have begun an investigation into whether the failure to lock down two towns near the northern city of Bergamo contributed to thousands of deaths related to the disease.

That's Italy, where failure to predict earthquakes is grounds for prosecution.

 

[russ_watters]

Evidently the cell phone tracker api is active...with no announcement. I think for apple users you have a usable app, but for Google it is just the api.

 

[vela]

Evidently the cell phone tracker api is active...with no announcement. I think for apple users you have a usable app, but for Google it is just the api.

Nope, it's just an API in iOS too. It's up to health agencies to develop apps.

 

[mfb]

Someone made an international version of the previous graph

Sweden's new case counts are still going up, not surprising that they are treated as exception when reopening borders. Parts of that will be coming from the increased testing, but the fraction of positive tests didn't drop that much (18% in early April, 12% recently at twice the number of positive tests).

 

[bhobba]

Here in Aus R0 has gone above 1 to 1.15 and a second wave may be coming. It's starting in Victoria because people seem to be sick and tired of the restrictions:
https://www.abc.net.au/news/2020-06...s-increase-again-with-more-new-cases/12376316

One thing I will say about the Victorian premier is he is VERY strong on using police to enforce restrictions. Police will randomly visit residences, suburbs will be locked down etc. If that doesn't work he will introduce even stronger measures. I would hate to be a protester now - we are starting to have a few - strong force will be used to disperse them. I pray it does not come to that. BTW it's not the protesters leading to the possible second wave - it's ignoring basic restrictions such as having people over for parties etc. It's even happening where I live, and it's still well under control here, but we have a number of young people who like to party with their boomboxes. A couple of weeks ago it was dead quiet - now especially Friday, Saturday and Sunday it's easy even from my locked room to hear it.

Thanks
Bill

 

[bhobba]

Was it irrational? Once others started hoarding, you should too.

Yes. As soon as the word got out people were hoarding ridiculous amounts and shops, even chemists, soon ran out. The chemist explained to me one issue was they do a lot of just in time ordering these days. Stock would arrive - your usual just in time amount - then go virtually straight away. Then you get the next lot and so on until the warehouse runs out. It happened in about a week here. The way it was solved eventually was the police just walked into large supermarkets and handed out the paper - no large amounts. With that in place, and limits imposed by shops, it slowly came under control, but during its peak was scary.

Thanks
Bill

 

[kyphysics]

Satellite data suggests Coronavirus may have hit China earlier: Researchers
https://abcnews.go.com/Internationa...t-china-earlier-researchers/story?id=71123270

Dramatic spikes in auto traffic around major hospitals in Wuhan last fall suggest the novel coronavirus may have been present and spreading through central China long before the outbreak was first reported to the world, according to a new Harvard Medical School study.

Using techniques similar to those employed by intelligence agencies, the research team behind the study analyzed commercial satellite imagery and "observed a dramatic increase in hospital traffic outside five major Wuhan hospitals beginning late summer and early fall 2019," according to Dr. John Brownstein, the Harvard Medical professor who led the research.

Brownstein, an ABC News contributor, said the traffic increase also "coincided with" elevated queries on a Chinese internet search for "certain symptoms that would later be determined as closely associated with the novel coronavirus."

Though Brownstein acknowledged the evidence is circumstantial, he said the study makes for an important new data point in the mystery of COVID-19's origins.

a.) This is a theory - not proven.
b.) Nonetheless, every time I see pieces like this that theorize/attempt to place the initial virus outbreak date further back in time, it makes me wonder if much more people have had it than we know and perhaps the infection fatality rate is not as bad as we thought (and we're closer to herd immunity that we may know).

 

[bhobba]

Woman still has Covid after 3 months:
https://people.com/health/asthmatic...after-coronavirus-diagnosis-theres-no-answer/

Amazing. I had a very bad case of sinusitis that lasted nearly that long. I also got bad depression after about a week or two. Thought it was just from it hanging around so long but saw a psychiatrist anyway who said - let me guess - here are the symptoms you had. He listed them exactly. He said he has had tons of patients who never had any issue with depression before but got it with this bug that was doing the rounds. He was pretty sure it jumbled up brain chemicals. He put me on some antidepressants but said the symptoms will hang around for a while - it did - and it will take an extra few months on top of that for your brain chemicals to normalise so you can come off the anti depressants - that took about a year. Interestingly I saw another psychiatrist while I was in hospital for a totally unrelated reason and he said the evidence for that cause is weak - he thought I was just depressed because the sinusitis took so long to go away.

Wonder if Covid can do the same type of thing.

Thanks
Bill

 

[wukunlin]

Satellite data suggests Coronavirus may have hit China earlier: Researchers
https://abcnews.go.com/Internationa...t-china-earlier-researchers/story?id=71123270a.) This is a theory - not proven.
b.) Nonetheless, every time I see pieces like this that theorize/attempt to place the initial virus outbreak date further back in time, it makes me wonder if much more people have had it than we know and perhaps the infection fatality rate is not as bad as we thought (and we're closer to herd immunity that we may know).

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An interesting study. Although, to make any conclusion out of that I would like to see:
1. Actual amount of appointments with doctors in all hospitals in Wuhan. A lot of people do not drive to hospitals.
2. Running average of the data. Just so it doesn't look like the data is cherry picked on certain dates.
3. Several more years of data to observe any seasonal effects or general trends.
4. Aside from hospitals, Chinese tend to go to what they call "Community Health Centres" for vaccines, flus, and minor illnesses, the doctors there are somewhat like GPs, they deal with all kinds of health issues, and if they see anything particularly nasty, people get referred to hospitals. People who are confident about what problems they have or if they think doctors in those health centres are incompetent, go to hospitals directly. Ideally (probably easier said than done...), we should take a look at these numbers to see what's going on. And let's not forget a lot of these folks may simply ask for herbal remedies from a local pharmacy.
4. Some control group to compare against (other regions of China or Asia?)

 

[Astronuc]

Jeremiah DeLap, died Jan. 7 in Orange County while visiting his parents. He had been healthy, suffering on a Friday [Jan 3] from what he thought was food poisoning, and found dead in bed the following Tuesday [Jan 7], drowned by fluid in his lungs.

It seem he had a type of pneumonia.

Preserved samples of DeLap's lungs are among tissue from more than 40 California deaths waiting for a decision by the U.S. Centers for Disease Control and Prevention on whether to test for COVID-19. Orange County has nine of the cases, as does Los Angeles County. Kern County has identified two respiratory deaths that might suggest COVID-19, both of young women, one of whom died Dec. 21.

https://news.yahoo.com/mysterious-deaths-infants-children-raise-140052428.html
Health officials in 3 counties in California are now scrutinizing fatalities of children and babies.
Understatement: "A positive finding in any of the cases would dramatically rewrite the narrative of COVID-19 in the United States."

In Washington State:

The Yakima Health District reported that Virginia Mason Memorial, Yakima’s only hospital, ran out of intensive care and other beds late in the week. The county had 61 patients hospitalized with confirmed cases of COVID-19, even after transferring at least 17 patients out of the county.

https://www.tri-cityherald.com/news/coronavirus/article243677112.html

From the NY Times, today -

New Coronavirus cases surged in 22 states over the weekend, and the U.S. accounted for 20% of all new infections worldwide on Sunday, according to New York Times data, even as the country’s population makes up about 4.3% of the world’s.

 

[bobob]

A couple of comments...

Regarding facemasks, I think it's obvious that the viral particles themselves have no difficulty passing through the masks, but that is not how the virus is transmitted. The virus is transmitted in droplets of moisture, which can be stopped or reduced by masks and if the moisture dries while airborne, the virus is stopped at that point. Furthermore, a single virus is not sufficient to cause an infection. All operating rooms and surgical centers are not 100% sterile. What is done is to reduce the the load from infectious organisms as much as possible so that the load is reduced to the extent that it's unlikey to be sufficient to create an infection in the patient. That suggests that whatever the actual efficacy of the masks, wearing them provides at least some benefit, even if that is at most to decrease the distance of the droplets coming from a person who coughs or sneezes while wearing a mask.

Second, in case it hasn't already been mentioned, for those interested in the models which are most accurate, the very best so far is the YYG model. It's predictions have been pretty much spot on with the LANL model coming in at a close second. The IHME model which has been what the media and whitehouse has been using to throw out numbers has been among the worst and consistentlt does worse than just using the previous week's average to predict the next week. The YYG website has a comparison of about 10 different models and the predictions several months into the future. One really odd thing about several models is that the uncertainty in some of the _decreases_ into the future, where it seems like common sense that you would be less certain about a prediction for say, August 1, than for next week.

Finally, for anyone interested in just playing around with some epidemiological models, there's an ipad app that provides a solver for coupled first order differential equations. They provide an example of an SIR model, (Succeptible, Infectious, Recovered where recovered include being dead), but it's easy enough to add additional compartments (additional differential equations), so for example, if you are interested in Covid-19 which adds an Exposed compartment (SEIR model) to account for the latency between exposure and becoming infectious (which is what many of the models being used do). You can extraxt a reproduction number from the ratio of transition rates between compartments. For more in depth explanation of the models, see the wikipedia page on epidemiological compartment models.

 

[Astronuc]

As of Tuesday evening, there are 28,870 confirmed cases of Coronavirus in Washington, and more than 4,000 hospitalizations, according to the state's Department of Health. Yakima County, which sits just southeast of Seattle, has the second highest numbers in the state — and said it has run out of hospital beds to help battle the virus.

https://www.cbsnews.com/news/washin...-masks-after-county-runs-out-of-hospital-beds

Washington Governor Jay Inslee says the entire state is going to take a more aggressive approach to handling the pandemic. Everyone in the state, minus a few exceptions, will now have to wear a face mask, and will be charged with a misdemeanor crime if they fail to do so.

Arizona's had 84% occupation of ICU beds.
https://www.azdhs.gov/preparedness/...se-epidemiology/covid-19/dashboards/index.php

Florida cases may overtake Massachusetts.
https://floridahealthcovid19.gov/

Texas Governor Greg Abbott is advising people to stay home, otherwise wear a mask when out in public.
By the end of Monday afternoon, the state Department of Health Services had reported the precise number: 5,489 new cases. Hospitalizations reached 4,092, marking the 12th straight day of a new peak.
https://www.texastribune.org/2020/06/23/texas-coronavirus-greg-abbott-home/
https://www.theeagle.com/news/state...cle_ab776c9e-6da1-5ffc-a62d-dd4b5cdf8d8f.html
https://txdshs.maps.arcgis.com/apps/opsdashboard/index.html#/ed483ecd702b4298ab01e8b9cafc8b83
https://www.dshs.state.tx.us/coronavirus/

There is ample evidence of community spread in 24 states.

 

[mfb]

With the large populations of California, Texas and Florida the overall US numbers are going up quickly. It's quite likely that this week will set a new record of daily new cases. Note the weekly pattern, the last dot is just one day after the weekly minimum.

 

[Vanadium 50]

But the positivity rate is falling:

 

[russ_watters]

But the positivity rate is falling:

View attachment 265239

That graph is missing the last few data points, but no, that graph shows the positivity rate bottoming-out. In the past few days it has started rising again (er -- it's a 7 day moving average and yours probably is too):

https://coronavirus.jhu.edu/testing/individual-states

And just to make sure our interpretations are aligned: positivity rate does not equal infection rate unless you are testing a random sampling of the population. When testing was limited and rationed, a lot of cases were missed. So the "true" case count at the first peak was likely several times higher than what was measured. But today, with less discriminating testing the positivity rate should be much lower regardless of if the case count is higher or lower. The "true" case count can be rising even with a falling positivity rate.

This is pretty worrisome.

 

[Vanadium 50]

positivity rate does not equal infection rate unless you are testing a random sampling of the population.

Agreed. But it shows (and your plot shows more directly) that the number of tests is changing dramatically over time. In that context, one shouldn't conclude that a change in the number of positive tests is due to a change in the number of infected.

I think we have discussed in another contest (Pennsylvania?) that different populations being tested have different positive (and presumably infected) rates and one can see wiggles in these plots as these samples are added - especially when they are added on a single day. I didn't find statistics on those tested, but those who test positive skew 4 or 5 years older than the population as a whole.

The death rate is flat. That's delayed by two weeks or so it does tell us something about the conditions in early June, but won't tell us much about the reason for the uptick happening ~now.

 

[russ_watters]

Agreed. But it shows (and your plot shows more directly) that the number of tests is changing dramatically over time. In that context, one shouldn't conclude that a change in the number of positive tests is due to a change in the number of infected.

The two sides of the coin are not equal/exactly opposite:
1. A decrease in positive test rate does not necessarily imply a decrease in actual new cases.
2. An increase in positive test rate does imply an increase in new cases.

Combining the case count and rate:
1. An increasing case count with a decreasing case rate may or may not mean the actual new cases are increasing.
2. An increasing case count with an increasing case rate does almost certainly mean the actual new cases are increasing.

I think we have discussed in another contest (Pennsylvania?) that different populations being tested have different positive (and presumably infected) rates and one can see wiggles in these plots as these samples are added - especially when they are added on a single day.

Yes, I've pointed it out for Pennsylvania or more specifically Montgomery County, but those wiggles smooth themselves out with time and larger sample sizes. E.G., the dramatic uptick in cases in Montgomery County on the day they got the results from testing every prisoner did not register at the state level. It's very unlikely that a sudden, substantial, ubiquitous and unreported change in testing policy has happened in the past week in the US to cause the uptick we're seeing now.

The death rate is flat. That's delayed by two weeks or so it does tell us something about the conditions in early June, but won't tell us much about the reason for the uptick happening ~now.

Yes, we'll have a much better idea in a few weeks. There's also hospitalization/ICU rates which are also rising in some states, but I don't know that there's a national count.

 

[Vanadium 50]

I don't quite follow your argument. Your first #2 seems contradicted by your second #1.

Your second #2 I agree with, insofar as your sample is representative. If you were going county-by-county in NYS (and this is an extreme example for illustrative purposes) starting in Brooklyn and working your way upstate you would incorrectly conclude things are improving much faster than they actually are.

 

[russ_watters]

I don't quite follow your argument. Your first #2 seems contradicted by your second #1.

Your second #2 I agree with, insofar as your sample is representative.

1-1. A decrease in positive test rate does not necessarily imply a decrease in actual new cases.
2-1. An increasing case count with a decreasing case rate may or may not mean the actual new cases are increasing.

The first one has one criteria and the second has two. Maybe the language should have been more similar to make the alignment clearer. A decrease in positive test rate can obviously result from a decrease in actual new cases. But a decrease in positive test rate can also result from a testing rate that increases faster than a simultaneous increase in actual new case rate.

E.G. if your testing criteria is pretty well targeted(and isn't changed) and the positive rate drops from 10% to 9% while the number of positives doubles, odds are you are testing more people because more people fit the criteria because more people have the disease.

 

[WWGD]

Welcome to the club

I half seriously wonder if some sort of version of windshield wipers for glasses would make sense. Could be dangerous to walk around with during rain, with low visiility.

 

[Astronuc]

But the positivity rate is falling:

According to the Texas Tribune article I cited, "The positivity rate — or the ratio of cases to tests, presented by the state as a seven-day average — reached 9.76%, back to the level it was at in mid-April." I believe it had been down around 3%.

Where we are now - https://aatishb.com/covidtrends/?region=US

 

[DrClaude]

I half seriously wonder if some sort of version of windshield wipers for glasses would make sense.

 

[Ygggdrasil]

Looking at the US as a whole is probably not so useful for detecting a new virus hot spots. Until recently numbers in the US have been dominated by hot spots like New York, so the dynamics of the US statistics have largely reflected what is going on in New York. However, when looking for new outbreaks, we want to see signs of (initially small) increases in places where there are many fewer initial infections. Some of these dynamics can be seen better when breaking the US down into geographical regions:

There are many regions that show steadily decreasing COVID-19 hospitalizations, but there are also regions that show relatively flat hospitalizations (the West) or increasing hospitalizations (the South and Southwest).

Instead of looking at just one metric like cases, it's probably useful to look at a combination of statistics to see what's going on. For example, see my post from last week comparing Texas and California. While both states show increasing number of cases, Texas shows an increased fraction of positive tests in recent weeks (suggesting that the increase in cases is not due solely to an increase in testing) along with an increase in COVID-19 hospitalizations. In contrast, hospitalizations and the fraction of positive tests in CA were flat, suggesting that the increase in cases was likely due mostly to an increase in testing.

It is pretty clear from the data that there are some areas of the country (e.g. Texas and Arizona) that are experiencing significant community spread, which appears to be showing exponential growth in the number of COVID-19 hospitalizations.

These data are also consistent with a study I posted about back in April. The study, which tracked the course of recent influenza epidemics in Australia, showed that the outbreaks generally had earlier outbreaks in high density urban centers (with large amounts of international travel) and later, as those initial location were recovering from their peak in infections, the disease would spread to affect areas of lower population density. Similar dynamics seem to be at play in the US.

 

[russ_watters]

According to the Texas Tribune article I cited, "The positivity rate — or the ratio of cases to tests, presented by the state as a seven-day average — reached 9.76%, back to the level it was at in mid-April." I believe it had been down around 3%.

Where we are now - https://aatishb.com/covidtrends/?region=US

The cases and positive % in PA and my local area appear to have bottomed-out and started rising again as well, despite my area still being in the "yellow" phase and preparing to go into the "green" phase tomorrow.

Meanwhile, we finally have an API for a limited cell-phone based tracking system, but no app to use it, voluntary or mandatory. And no robust manual contact tracing system either.

I wonder which state will be the first to cave and how.

 

[Vanadium 50]

Looking at the US as a whole is probably not so useful for detecting a new virus hot spots. Until recently numbers in the US have been dominated by hot spots like New York

I got beaten up for saying just that. But it's true.

Even regions seem to be too big. The case can be made that some states are too big - Missouri's timeline seems to hinge on three places: St. Louis, Kansas City, and meat processing in Saline County. Utah had two - one near SLC and one near Bluff. (I see now there may be a third near Bear River).

The problem with this line of reasoning is that it leads to the conclusion that this is a disease that preferentially hits cities.

 

[Astronuc]

The problem with this line of reasoning is that it leads to the conclusion that this is a disease that preferentially hits cities.

Isn't it more accurate to reason that the disease is more likely to spread in places where people congregate, particularly without wearing masks or social distancing, and such activities are more likely to occur in cities or metropolitan areas, i.e., areas of high population density?

Places where people congregate are: businesses (office buildings, particularly those with elevators, which are more likely found in cities), retail establishments, transportation centers, transportation systems (trains, subways, buses), entertainment venues (e.g., movie theaters, concert halls, . . .), gymnasiums (where people tend to exhale vigorously), restaurants, bars, and clubs. Churches would be another place where people congregate in close proximity, but churches are found throughout the nation(s). Meat packing and food processing plants are also areas of congregation, but they are usually in rural areas.

The virus would be less likely to spread if people would wear masks, which is not universally practiced (as I have witnessed on numerous occasions in several states and many locales).

Another factor with respect various examples mentioned above is the likelihood of interaction with folks from outside the community. Blaine county (Idaho) has a high rate of cases compared to surrounding counties, because there are numerous folks from outside of the state traveling to the county and apparently bringing the virus with them.

To do a thorough analysis of the spread of the virus, one would have to document the numbers of people wearing masks and not, and compare rate of positive cases in those areas with high and low rates of people wearing masks while congregating. That is not going to happen.

 

[Vanadium 50]

Isn't it more accurate to reason that the disease is more likely to spread in places where people congregate, particularly without wearing masks or social distancing, and such activities are more likely to occur in cities or metropolitan areas, i.e., areas of high population density?

If you like. I suspect "number of close interactions" is closer to the relevant factor than "where people congregate". But we're still talking about "cities".

 

[gleem]

I do not know if this has been reported but the Florida Health Department's COVID dashboard has not been updated fora week. However, weather.com seems to be able to provide info on Florida and my county's active cases and deaths.

 

[Vanadium 50]

However, weather.com seems to be able to provide info on Florida and my county's active cases and deaths.

Cloudy with a chance of Covid? A 40% chance of infection today?

 

[gleem]

What if we didn't have the internet?

 

[BillTre]

There are allegations that the Florida state government is manipulating it virus statistics for political ends.
Here is a page (or more) of links on this subject.

I consider this a data quality post and not a political story (however some might not).

 

[bob012345]

What if we didn't have the internet?

Well, some of us remember not having an Internet. Or cell phone. Or PC. Life was good. Slower, but good.

 

[mfb]

The virus would be less likely to spread if people would wear masks, which is not universally practiced (as I have witnessed on numerous occasions in several states and many locales).

There is a correlation between mask regulations and cases recently, but (a) all the caveats about cases apply and (b) a correlation can have many sources.

https://www.inquirer.com/health/cor...html?outputType=amp&__twitter_impression=true

It's interesting how the US and Europe's countries differ. Countries in Europe had one wave, roughly at the same time, with rapidly falling cases afterwards. The various US states all follow wildly different patterns.

----

Germany's new cases increased a bit. New cases on top, estimated reproduction rate at the bottom:

I don't see anything similar in surrounding countries.

 

[mfb]

I had a closer look at the cases in Germany, apparently they are from a few localized outbreaks only. This includes 1500 employees at a single meat processing plant (Tönnies) and 120 in a single apartment complex (German). Most places have fewer than 5 new cases per 100,000 per week, where 5 would correspond to ~120 cases per day in Germany. Everything above that is from a few regional clusters.

 

[kadiot]

What is your thought about steam inhalation?

It is medicine absorption also. That is why the person must put in a blanket over his body whilst sitting down naked waist above in order to absorb the medicines placed with or in the water. There is no studies yet that find it as bad or ineffective against covid19. The aerosolization effect is a mere hypothesis placed forward. If there is, let us see the abstract and that it has been peer studied.

Let us be clear: It is not a cure as a ventilator is not. For me, it is a prophylaxis and a treatment at the onset of symptoms. And also to our health department, steam falls when cooled or is evaporated.