covid-19 epidemiologic data

[hyksos]

The bubonic plague ravaged Europe in a century in which there were no cars or airplanes, or airports, or even metropolitan cities for that matter. Urbanization only came after the Industrial Revolution. Traveling by buggy was reserved for the wealthy and the landed gentry. Despite the rural situation of the 1300s Europe, the plague spread over the continent in as little as 7 years. In fact, the entire Black Death only lasted 7 years, 1346 to 1353.

We live in a very different earth now. The Spanish flu virus criss-crossed the globe in a mere 3 years, from January of 1918 to December of 1920. At the end claiming an unknown number of victims. The low estimate is 17 million deaths, and the high estimate being 50 million.

While the Spanish flu viral pandemic took place in a post-industrial world, one needs to consider what the most advanced aircraft at the time looked like.



That is not a passenger jet by any stretch. 1919 cities had nobody waiting in line to board at an airport takeoff gate. No people were squashed together in subway cars after a baseball game let out. A "large concert venue"? What's that? There were no regular television shows at that time, and no live audiences daily sardined into the seats.




Some are suggesting COVID-19 will claim 600,000 lives by summer, just in the United States. That number is often quoted as being the worst-case scenario for the continental 48. Chinese media is suggesting that the virus has already "run its course" in mainland China.

[Serpent]

That Chinese source is almost certainly misinformed. Or just thinking wishfully.
They do not yet know whether, in the course it just ran, it learned any new tricks. They don't yet know whether people who have had it are virus-free, or it's just gone dormant. They haven't had time to study the level of immunity that survivors have. They don't know how soon and how effective the vaccine will be.
And that's before the second and third waves.

Previous pandemics have been characterized by waves of activity spread over months. Once the level of disease activity drops, a critical communications task will be to balance this information with the possibility of another wave. Pandemic waves can be separated by months and an immediate “at-ease” signal may be premature.http://www.euro.who.int/en/health-topics/communicable-diseases/influenza/data-and-statistics/pandemic-influenza/about-pandemic-phases

This thing is nowhere near through, anywhere!
We're likely to see alternating expansion and contraction.
Think of the forecast as "a mix of sun and cloud, with 60% chance of thundershowers".

[BadgerJelly]

The worst is over in China as far as I can tell. Vietnam is tentative, but things have been dealt with VERY well since the beginning - strange how praise is heaped on nations like Taiwan and South Korea yet no one seems to appreciate the unbelievable job done here (again, this is due to the previous experience of SARS and taking this seriously from the outset).

In a month I think they’ll be just a handful of cases left in Vietnam. I didn’t expect the government here to handle this so well tbh.

Keep in mind they don’t have endless resources here, it’s been a case of closing borders, quarantining new arrivals and practically everyone with easy access to face masks (which is a reasonably common practice prior to the outbreak).

National interest as opposed to global unity will be many people’s downfall sadly.

[TheVat]

Perhaps people who are Italian, or of "Mediterranean" ancestry, are more susceptible to COVID-19 than others. For example, the highest concentration of Italians and Italian-americans in the entire Western hemisphere is no other than New York City. The data is . . . suggestive of this hypothesis. Under this hypothesis, NYC is experiencing unprecedented outbreak because it has more people of Italian ancestry than does Seattle, and not say because of temperature/humidity/sunlight. ...

Interesting speculation. If you run across more analytics on this, I hope you'll share them here. North End of Boston is pretty close to NYC, in terms of concentration of Italian-Americans, but appears to have less of an outbreak. One would expect higher numbers in South Philly, Rhode Island, Connecticut, and NJ as well. I lived in a largely Italian (and other Mediterraneans) neighborhood for three years, in Newton, Mass.

One should also consider purely cultural factors here, too. Like body distance, rates of hugging, rates of RC Mass attendance before they started going to online services, etc.

IIRC, you are a New Englander, so hope you're being careful.

[Serpent]

The possible variables are certainly many and there's a lot of cross-over among factors - e.g. the ethnic communities that share a cultural heritage also share quite a lot of genetic traits.
Statistics can highlight clusters of facts, but can't indicate which of those clusters, and which facts within a given cluster are significant. It can point to areas that merit study, but they can't lead to conclusions.
You may find this article interesting - both for the methodology and the findings.
https://www.the-scientist.com/news-opinion/coronaviruss-genetics-hint-at-its-cryptic-spread-in-communities-67233

[Serpent]

BBC is a good source for all kinds of stats.
https://www.bbc.com/news/world-51235105

[Serpent]

Here's another trajectory graphic.
https://newsinteractives.cbc.ca/coronaviruscurve/

[TheVat]

I live in an odd statistical blip in the United States.

What's weird is that Rapid City, in the heart of Lakota (an indigenous tribal people) country, has the lowest rate of COVID of any metro in the US, AFAICT. City around 75k, metro about 150k, and a total of 7 cases. I looked at comparable places like Missoula, Bismarck, Sioux Falls, Fort Collins, Grand Island, et al. Much higher numbers all of them. In Arizona, remote Apache County has 52 cases, with half the population of Rapid city metro. Martin County, MN, has 35 cases with a population of only 20k, and is more off the beaten path than Rapid City.

If anyone finds a lower rate than RC for a comparable sized metro, please let me know. It's mystifying, considering we're on a major interstate, regional hub, and did get some winter tourism until late February anyway. We are near Native reservations with many families living in close quarters and having short water supplies (though not as short on water as the Navajo nation, where there is a serious outbreak) for handwashing. Pine Ridge rez, and Standing Rock rez have each had one case. Same for Rosebud rez.

So I'm wondering if this is just a matter of radically lower rates of testing. Or one of those statistical blips that just happen. I will try to find out.

[zetreque]

I live in an odd statistical blip in the United States.

What's weird is that Rapid City, in the heart of Lakota (an indigenous tribal people) country, has the lowest rate of COVID of any metro in the US, AFAICT.

Maybe not for long?
https://www.boston.com/news/national-ne ... oronavirus

Just a couple things I've noticed.

[*]Testing numbers are way off as so many people can't get tested and won't test or are being told not to.
[*]Deaths overall from all causes is WAY UP globally this year from first reports coming in from areas like Italy and the UK. The finger seems to be pointing at covid19 secondary and indirect effects.
[*]IMO the less people take this seriously the more times they shoot themselves in the foot for impacts to the economy, personal freedom/privacy, and environment for greater lengths of time.

[TheVat]

Yes, the stark contrast between hot spot Sioux Falls and Rapid City seems to be mainly from that one pork processor. We're sort of equidistant between the SF cluster and the Greeley, Colorado cluster (beef processor). More testing and contact tracing would certainly help us here, in containing those hot spots.

Those meat plants are nasty workplaces (I've been in one, years ago, a summer job in college), and people work elbow to elbow. I'd vote for a patriotic wave of eating vegetarian, and getting those workers fast tracked on unemployment claims.

[Serpent]

I'd vote for anybody redirecting the workers at the tar sands to building hydroponic greenhouses...
But they just seem to be stuck in a non-viable meme.

They're not unique!

I'M not sure whether this belongs here; a friend just sent it to me today. It's a PBS interview that shows the man who today announced himself in absolute charge and how he reacted over the last few months.

We waited until the roof was burning and the structure was on fire in New York state and New York City before we called the fire department. And that was a decision that the president made, was to not move ahead with those announcements.

https://www.pbs.org/newshour/show/what-new-reports-reveal-about-trumps-response-to-covid-19

[TheVat]

The Andean nation has officially confirmed around 560 deaths from complications related to covid-19. In poverty — and now grief — stricken Guayaquil, Ecuador’s largest city, corpses have been lining up in homes and streets as the virus has overwhelmed sanitation authorities, The Washington Post previously reported.

Health Minister Juan Carlos Zevallos said Thursday that, in an effort to work around limited testing, authorities were contacting families of people who recently died to see if the deceased reported any symptoms.

In the first 15 days of April, the government registered 6,700 deaths in Guayaquil and its surrounding province, compared with 2,000 fatalities in January and February, Reuters reported...

Showing the disparity between official counts and actual CV deaths in some areas of the world. We may never know how many in Ecuador died from CV.

[Serpent]

We'll probably never know the exact numbers from anywhere. Of course, some organs of information lie habitually, with a greater or smaller margin of deviance from the known truth. And some are incapable of collecting accurate information.

In Canada, the networks under provincial and federal health care authority (hospitals, group practices, clinics and independent physicians) is pretty well organized, well equipped for reporting -- But nursing homes, retirement homes and assisted living facilities are not well connected to that network, as many of them are privately owned, or fall under the auspices of a charity or municipal government. There, reporting can be anywhere from meticulous to haphazard to fraudulent - and that's even before considering the problem of differential diagnosis in chronically ill patients, or the severe shortage of staff trained in doing it properly. Right now, deaths are piling up in long-term care facilities, and there is no conceivable way to investigate how many are directly caused by covid, or previous conditions, or neglect, or lack of medication; how much anxiety and loneliness contributed. I imagine the same uncertainty applies to many deaths that take place at home.
Multiply that allowance for error by the number of district, municipal, township, county, regional, provincial/state agency the information passes through on its way to a national administrative hub and then to the media.

We'll have to settle for not knowing the true numbers. The approximate numbers are daunting enough!

[toucana]

This extrapolation based on the CSSE/JHU COVID-19 Dashboard model suggests that if the USA relaxes the current lockdown and social distancing regulations, and allows the spread rate of viral infection to increase by just 0.5% per day for two weeks, then the USA will experience in excess of 1 million COVID-19 related deaths by the 4th July

[Serpent]

That million was a given, even before the latest wave of arrogant, irresponsible stupidity in high places. State governments have had to step up, and some have done so, heroically, in very difficulty circumstances.

If anybody begins to think* this plague is anywhere near done with us, they have a big thud coming. Now it's had a pretty successful dress rehearsal, it's setting up for the real show.

This is the first study to provide an insight into how a mutation could impact the severity of the disease. For instance, the virus in New York is stronger and more aggressive, and it has the highest infection toll in the country.https://www.news-medical.net/news/20200422/Coronavirus-has-mutated-into-at-least-30-strains.aspx

That one's preliminary - not peer-reviewed - and regarded with a degree of suspicion:
https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/

But “the conclusions are overblown,” says Lisa Gralinski of the University of North Carolina, who is one of the few scientists in the world who specializes in coronaviruses.

We'll see, I guess.
Meanwhile:

The clinical trial marketing firm Antidote updated its digital screening app to include 335 active coronavirus studies in the USA, as of May 10, 2020. These studies include both preventive vaccines, such as a phase 4 BCG study in Texas, and various COVID-19 disease treatments. The main point is these open studies are generally no-charge to qualifying participants.

Quick reference: https://www.coronavirustoday.com/coronavirus-breaking-news




*I automatically exclude anti-vaxxers and eyebrow waxers and all the idjits with "fake crisis" signs: they obviously cannot think.

[toucana]

The scientist who created Florida's COVID-19 data portal wasn't just removed from her position on May 5, she was fired on Monday by the Department of Health, she said, for refusing to manipulate data.

https://eu.usatoday.com/story/news/nation/2020/05/19/florida-covid-19-coronavirus-data-researcher-out-state-reopens/5218897002/

Rebekah Jones said in an email to the USA TODAY Network that she single-handedly created two applications in two languages, four dashboards, six unique maps with layers of data functionality for 32 variables covering a half a million lines of data. Her objective was to create a way for Floridians and researchers to see what the COVID-19 situation was in real time.

Then, she was dismissed.

"I worked on it alone, sixteen hours a day for two months, most of which I was never paid for, and now that this has happened I'll probably never get paid for," she wrote in an email, confirming that she had not just been reassigned on May 5, but fired from her job as Geographic Information Systems manager for the Florida Department of Health.

Researchers who saw the email reacted with shock and dismay, suggesting it could be evidence that the Gov. Ron De Santis' government was censoring information to support the case for re-opening Florida.

[hyksos]

https://covid-viz.herokuapp.com/

[TheVat]

Cool map, H.

Here's an analysis of excess deaths in the US, how it may reflect underreporting of all deaths caused by the pandemic...

https://medium.com/@surgofoundation/the ... dee8fac9b9

[BadgerJelly]

https://www.dw.com/en/world-food-progra ... a-53219305

[TheVat]

Yes, many situations that are always tenuous in low-income nations are now critical. How much sense does it make not to look at cost/benefit analysis when deciding on lockdowns for farmers and food-related workers? Especially in countries where the number of 70+ year olds that could be saved by a lockdown is quite small (as I talked about in other thread). It's insane to have millions starve in order to save a few thousand.

[From the other thread]

And there are some countries with low mortality numbers due to there being very few people over the age of 70 in the first place. And few people with serious genetic diseases who haven't already been weeded out by the simple lack of a modern healthcare system. And few people who are so well fed that obesity and metabolic syndromes are even on the radar. The European style lockdowns would make little sense there....

[Serpent]

Yes, many situations that are always tenuous in low-income nations are now critical. How much sense does it make not to look at cost/benefit analysis when deciding on lockdowns for farmers and food-related workers?

It doesn't exactly come under 'data', but it's here, so I'm asking here.
I do not understand how this works.
Are farmers prohibited from ploughing and seeding? If so, it makes no sense at all, since it's solitary outdoor work with no physical contacts.
The ground hasn't gone anywhere. The rain falls, or doesn't, as usual. The sun shines or doesn't.
The transport trucks between provinces and across the US border have not been stopped in Canada. Are they held up or turned back elsewhere?
Closing restaurants doesn't change the number of people who have to eat and need to buy food; it only changes the venues through which the food is normally distributed and that two or three layers of added value are removed.
I understand that meat-packing plants are super-conductors of the virus and need to be closed, but that's only bad news for obligate carnivores; everyone else could manage a few months on a meat-deprived diet.
So ---
What causes all this massive food shortage?

[zetreque]

Cool map, H.

Here's an analysis of excess deaths in the US, how it may reflect underreporting of all deaths caused by the pandemic...

https://medium.com/@surgofoundation/the ... dee8fac9b9

Or you can get a nice chart straight from the CDC.
https://www.cdc.gov/nchs/nvss/vsrr/covi ... deaths.htm

[TheVat]

Looks like Type A blood group may be more susceptible to severe effects of covid-19. And O group has some protection.

https://www.medrxiv.org/content/10.1101 ... 20114991v1

As usual, more studies are needed.

[toucana]

https://www.youtube.com/watch?v=wnmL8rIdMJA


Rebekah Jones, the former manager of Data & Surveillance Florida Department of Health who was abruptly fired a few weeks ago from her job of managing the Floridian online COVID-19 dashboard after she refused to falsify data, has been speaking to Lawrence O'Donnell of MSNBC about the experience of recreating the dashboard all on her own.

Q - What has been the state’s reaction to you basically doing this on your own ?
A - I don’t really think they are in a position to have a reaction any more after you know, they fired me for refusing to do something wrong, and then publicly defamed me, - and have since been quieter about it luckily - But I’m a private citizen now, it’s public information. There is no position that they can have on me doing this.

Q.- Your work has been praised by Dr. Deborah Birx and others, your credibility has been unquestioned. Has anyone in the state government said there was a reason to question your credibility about this ?
A - Yeah. There was a period where immediately after the news broke that I had been taken off the dashboard and fired after that .. umm… where I think a few government officials tried to accuse me of not being a scientist, or not having access to the data, or not having been the architect - But I rebuilt the whole thing within three days, so I think I’ve put that to bed.

[TheVat]

https://www.vox.com/21296067/coronaviru ... estaurants

Analysis of superspreaders. The article is longish, but the first half gives you the jist of it.

[toucana]

https://www.bbc.co.uk/news/world-us-canada-53088354

At the moment the positive case rate is just below 5% nationally, which is the level the World Health Organization recommends countries be at or below for 14 days before they ease restrictions on movement.
But about a third of states are above that level, as the chart below shows, and all of them have reopened to some extent over the last month.

[hyksos]

[TheVat]

And it's not just "we're testing more and more. "

The rate of hospitalizations is also rising, and ICU beds available decreasing, in those states. Those are better metrics for the pandemic's trend.

[edy420]

Just briefly skimmed through, but I didn't see any information on New Zealand..

Last week we had 0 cases. We successfully eradicated the spread of Covid 19. But..

Someone brought the virus into the country while visiting a dying relative. Now we have new cases again daily, today was 2.

We went on a 1 month lockdown. Everyone put in the hard work to social distance, stay at home, put all non-essential jobs on hold, and it payed off, because of our success. But now its all for nothing. We have to start all over again..

Just hearing talks of another lockdown..

[edy420]

We've managed to avoid another lockdown, with a total of 0 new cases over the last couple days. We still have 22 recovery cases, but hopefully we can get back to being Covid free in the next week or so...