COVID-19

[gerontocrat]

World data continues to climb - daily new cases & daily deaths (though as yet the daily deaths graph rises much more slowly than daily new cases ).

A daily new case rate of between 150 & 160k a week puts the monthly rate at between 4.5 & 4.8 million a month.

The data comes from https://www.worldometers.info/coronavirus/ - they are revising the data - usually in an upward direction which is a pain to keep up with.

[Archimid]

It seems comparable to NYC, but maybe I'm doing something wrong again:

Look at something like Lombardy

https://www.citypopulation.de/en/italy/admin/03__lombardia/

Also, absolute numbers and relative numbers matter for this sort of thing. There were 132 people older than 70 in ischgl. There are hundreds of thousands in NYC of a very different health status than people living on an alps resort town.

[blumenkraft]

[etienne]

edit2: Maybe the reason IFR is so low in this subset is because of demographics, local conditions, general population health, even though we are not supposed to look at those things. But still, the difference is really huge large. Of course, the 85% asymptomatic number and fewer children infected are interesting as well.

Well, Covid19 is a sickness where preconditions are important, and I believe that people in Ischgl have a better air and less stress than in Milano or NYC. I tried to find out what kind of Retirement Home there could be in Ischgl, but all information has been removed when searching on https://ischgl.riskommunal.net/

edit 1 : I found it http://www.stjosef-grins.at/, it is not on the territory of Ischgl.

[bbr2315]

edit2: Maybe the reason IFR is so low in this subset is because of demographics, local conditions, general population health, even though we are not supposed to look at those things. But still, the difference is really huge large. Of course, the 85% asymptomatic number and fewer children infected are interesting as well.

Well, Covid19 is a sickness where preconditions are important, and I believe that people in Ischgl have a better air and less stress than in Milano or NYC. I tried to find out what kind of Retirement Home there could be in Ischgl, but all information has been removed when searching on https://ischgl.riskommunal.net/

edit 1 : I found it http://www.stjosef-grins.at/, it is not on the territory of Ischgl.

Ischgi looks like what we would see in a typical rich, first-world community with excellent healthcare and a lack of a populace with substantial pre-existing conditions (besides age). I mean you are literally selecting for every favorable factor (wealth, outdoor physical activity with lots of sunlight / Vit D even for the elderly, HEALTH, healthcare).

In Manhattan, we have had 3,054 confirmed + probable deaths, we can extrapolate that to 3,500 total excess. That is approximately .21% IFR.

In The Bronx, we had 4.662 confirmed + probable deaths, we can extrapolate that to 5,600+ excess, for an IFR of .40%+.

I do not think the Bronx necessarily had 2x the infection rate of Manhattan although it was certainly higher. However, Manhattan is actually basically the American equivalent of Ischgi. It is the richest per capita county in the country. The male obesity rate is the second-lowest in the US behind San Francisco. ETC, ETC. The same cannot be said for The Bronx.

Now we look at rural Georgia and Mississippi etc where .3%+ IFRs are also now popping up. However these places do NOT have the healthcare of NYC and may very well be at the START of their pandemics with much higher mortality rates than Manhattan, Ischgi, or even The Bronx.

It seems COVID is a disease of exceeding inequality -- what disease isn't, really -- but this one in particular targets the elderly, the obese, the poor, the hypertensive, the diabetic, the rural. It has yet to really seep into the last category as of yet but I think this will turn out to have a death toll worse than Spanish Flu when it does (and much LIGHTER than Spanish Flu in places like Ischgi and Manhattan, hopefully).

We should remember a .1% IFR globally is 7.5 million deaths, .2% is 15 million, .3% is 22.5 million (or thereabouts). None of these figures are unlikely and they could even be exceeded. Containment in China has probably already failed and it will become obvious by October if not sooner that the entire NHEM is about to have a mass-death-ing event minus those areas with substantial immunity from the herald wave.

I think this actually legitimizes Trump's strategy, or lack thereof? It is also in the same vein of how Cuomo and DeBlasio's abject incompetence inoculated NYC against the virus' autumnal wave which if Spanish Flu was any indicator could be 2X+ deadlier (2% mortality vs 1%). None of the mitigation measures will work after the next 90 or so days and goodwill will be exhausted even in the "polite" European countries (we can except perhaps Taiwan, Aus, NZ, et al).

In a theoretical disease (that may now be reality) where approximately 40-45% of the population is infected before spread dies out and outbreaks become sporadic / go away, wave #1 has a mortality rate of 1% (spring / summer), wave #2 has a mortality rate of 2.5% (fall / winter), wave 3 has a mortality rate of 2% (early spring).

If you infect the entire pop in wave #1 to where wave #2 and #3 are reduced to sporadic cases, you also prevent the DOUBLING burden to the hospitals from the additional hospitalization from wave 2 and 3 which could further increase mortality (or perhaps this was also why mortality was so much higher in wave 2 of Spanish Flu?). Paradoxically, without vaccine and with containment measures unlikely to last 18 months, it then becomes most logical to infect the most people as early as possible (before wave #2) to avoid the highest death toll.

There is some possibility that those states most effective in containment for the moment will be worst-hit come October-March. Because if there is any pause in efforts before then.... it will not be good!

[be cause]

An almost stupid question ..
 ever since the first image of this coronavirus appeared in the British media it has been shown as rather pretty and multi-coloured .. any 3 year old would love a few in their Xmas stocking .. https://www.lungcancerresearchfoundation.org/wp-content/uploads/coronavirus.jpg

could such pretty pics have affected Boris and co.'s response ? Could such images have resulted in more death than if they had been dark , gray and forboding ? b.c.

<cleaned up link. kassy>

[blumenkraft]

I can't imagine anyone thinking the virus is less dangerous after seeing a vivid picture. But i learned to never judge others by my own standards. Also, humans are really weird. So...
¯\(º_°)/¯

[vox_mundi]

Texas Rolls Back Its Reopening a Day After Pausing Plans As Coronavirus Cases Rise
https://www.cnbc.com/amp/2020/06/26/texas-rolls-back-its-reopening-a-day-after-pausing-plans-as-coronavirus-cases-rise.html

Texas Gov. Greg Abbott announced Friday that he will roll back some of the state's reopening, only a day after he said he would place the state's restart plan on pause.

All bars and similar establishments that receive more than 51% of their gross receipts from the sale of alcoholic beverages are required to close at 12:00 p.m. Friday.

Texas reported a 79% increase in its weekly average of coronavirus cases on Thursday, averaging 4,757 daily new cases, according to a CNBC analysis of data compiled by Johns Hopkins University.

----------------------------------

Florida Governor Under Fire Over Claims State Is ‘Cooking the Books’ On Covid-19
https://amp.theguardian.com/us-news/2020/jun/26/florida-governor-ron-desantis-republican-coronavirus

Republican Florida governor Ron DeSantis’s faltering response to soaring new coronavirus numbers in his state is descending into acrimony, after an accusation his administration is “cooking the books” in an effort to hide the true impact of the devastating pandemic.

The claim from the state’s former leading Covid-19 data scientist comes as Florida smashed its own one-day record for new cases of the disease on Friday with 8,942, after two successive days above 5,000 – by far the highest figures since the pandemic began.

... So far this month, Florida has seen confirmed cases more than double from 56,000 to above 114,000, and set daily records on seven of the last 13 days. Meanwhile, the number of deaths among Florida residents has climbed to almost 3,400.

Rebekah Jones, who says she was fired from her job in charge of the state’s official Covid-19 database in May for refusing to manipulate its figures, claimed on social media to have evidence that employees at Florida’s department of health “have been instructed this week to change the numbers and begin slowly deleting deaths and cases so it looks like Florida is improving next week in the lead-up to July 4, like they’ve ‘made it over the hump’.”

https://twitter.com/GeoRebekah/status/1275539636803244032

“They’re only reporting all these cases now so they can restrict reporting next week to make everyone think it’s over,” she said.

DeSantis, a Donald Trump loyalist who has refused to slow Florida’s reopening or implement a statewide mask mandate, angrily dismissed the claim, calling a reporter from the Miami Herald who asked him about it “embarrassing”.

... A month after berating reporters whom he said “waxed poetically for weeks and weeks about how Florida was going to be just like New York,” that scenario has been realized, with New York joining New Jersey and Connecticut this week in ordering visitors from Florida – among other badly affected states – to quarantine.

Hospital systems around Florida are reporting steep drops in the availability in intensive care and other beds, even as the department of health changes how it records such figures.

https://www.sun-sentinel.com/coronavirus/fl-ne-coronavirus-florida-hospital-bed-capacities-tracker-20200403-tasn7rj2vncsjivrg75wb6gqkm-htmlstory.html

https://www.businessinsider.com/florida-scientist-state-stopped-tracking-icu-beds-ahead-july-4-2020-6

In Miami-Dade county this week, the positivity rate reached 27 percent, almost three times greater than the county’s average 14-day target of 10 percent.

Perhaps more wounding is veiled criticism from fellow elected Republicans.

Even Marco Rubio, Florida’s senior Republican US senator, weighed in. “Everyone should just wear a damn mask,” he said.

https://thehill.com/homenews/senate/504365-rubio-everyone-should-just-wear-a-damn-mask

... “Ron DeSantis has followed Donald Trump’s erratic leadership for three and a half months, and it clearly has not worked out for Floridians,” said Terrie Rizzo, chair of the Florida Democratic party. “Their eagerness to declare victory before the job was done has led us to this moment.”

-------------------------------------------

How Arizona ‘Lost Control of the Epidemic’
https://www.washingtonpost.com/health/how-arizona-lost-control-of-the-epidemic/2020/06/25/f692a5a8-b658-11ea-aca5-ebb63d27e1ff_story.html?outputType=amp

Arizona is facing more per capita cases than recorded by any country in Europe or even by hard-hit Brazil. Among states with at least 20 people hospitalized for covid-19, the disease caused by the coronavirus, no state has seen its rate of hospitalizations increase more rapidly since Memorial Day.

Maricopa County, which includes Phoenix, is recording as many as 2,000 cases a day, “eclipsing the New York City boroughs even on their worst days,” warned a Wednesday brief by disease trackers at Children’s Hospital of Philadelphia, which observed, “Arizona has lost control of the epidemic.”

https://policylab.chop.edu/blog/covid-19-outlook-ringing-alarm-bell-epicenters-waving-caution-flag-hotspots

This week, Arizona reported not just a record single-day increase in new cases — with Tuesday’s tally reaching 3,591 — but also record use of inpatient beds and ventilators for suspected and confirmed cases. Public health experts warn that hospitals could be stretched so thin they may have to begin triaging patients by mid-July.

Soon, the only option might be “crisis standards of care,” said Will Humble, a former director of the Arizona Department of Health Services. “If you’re in a bed, normally they’ll keep you for a few days, but they’re going to send you home with oxygen.”

Gov. Ducey, speaking to reporters Thursday, said hospitals are “likely to hit surge capacity very soon.”

“This virus is everywhere,” the governor said.

https://mobile.twitter.com/charlesornstein/status/1276336131961958408

... The mean age of Arizonans killed by covid-19 fell from 78 on April 27 to 69 on June 14, according to data processed by a modeling team made up of experts at Arizona State University and the University of Arizona. The average age of patients testing positive for the virus dropped from 51 on April 5 to 39 by mid-June. While older individuals are known to be at greater risk from the virus, Arizona has three times as many positive tests among people age 20 to 44 as it does in any other age bracket, according to state data.

... At virtually every stage of the state’s pandemic response, the interests of business have held sway, said Nathan Laufer, the founder of the Heart and Vascular Center of Arizona, a medical practice with locations in Phoenix and nearby counties, and a former director of the state medical association.

“It’s fine to be pro-business, but you have to be pro-citizen first,” Laufer said. The governor, in belatedly handing local authorities more control, is “playing catch-up,” he added, “but it’s too little, too late.”

Some residents noted that the Republican governor was following his party’s standard-bearer. “Hindsight’s 20/20" ... “I think he was a little slow. But he’s a conservative man and he wanted to do what Trump said.”

... “I have to see somebody sick, directly related to me or close to me, in order for it to become like reality,” said Joshua Kwiatkowski, strolling this week at an open-air shopping center in Tempe, Ariz. “So it hasn’t really, I guess, sank in.”

... A chart displaying the number of new cases, which did not show the 14-day decline recommended by White House guidelines, “really doesn’t tell you much,” Ducey said at his May 4 news conference.

That evening, the state ended its partnership with the university modeling team whose projections plainly showed a rising caseload in Arizona. It was resumed following an outcry.

Two days later, top health officials acknowledged having changed the testing count to include viral tests confirming an infection and serology tests determining the presence of coronavirus antibodies — a move with the potential to artificially lower the positivity rate touted by Ducey at his May 4 briefing.

“This is a good trajectory for Arizona,” he affirmed at the time.

... Limited resources have also hampered the ability of the hardest-hit counties to conduct thorough contact tracing. Maricopa County shifted in the early weeks of the pandemic to what it called a “mediated” approach in which all sickened people are interviewed but are then made responsible for notifying their own contacts.

A spokesman for the county health department, Ron Coleman, confirmed this week the limited approach is still in use, even as cases soar.

[Archimid]

. Containment in China has probably already failed and it will become obvious by October if not sooner that the entire NHEM is about to have a mass-death-ing event minus those areas with substantial immunity from the herald wave.

Mass-death will happen in any area that follows Trump's advice (die for the economy). Places with the discipline to distance and mask will not suffer mass death. They haven't so far and they won't if they stick to science. The only way they suffer mass death is if they listen to Trump et al.

I think this actually legitimizes Trump's strategy, or lack thereof?

I've heard of Monday morning quarterbacks but never heard of Saturday evening quarterbacks. You think Trump strategy is justified because more people die upfront and at some point in the future places that didn't listen to trump will falter in their resolve?

I doubt it. Places that listened to Trump will keep showing us more deaths. BY the time herd immunity is reached treatments will be so good that IFR will be < 0.1% and vaccines will be here anyway.

[vox_mundi]

[nanning]

(Short warning, sorry for being off-topic)

That is really bad link you posted, be cause. Please be careful, posting bad links means other people that click on it will have their privacy compromised as well.

<snip>
<cleaned up link so removed quoted version. kassy>

This is the direct link to that image:
    https://www.lungcancerresearchfoundation.org/wp-content/uploads/coronavirus.jpg

Perhaps you were reading this document via Google?
    https://www.lungcancerresearchfoundation.org/lung-cancer-groups-issue-statement-on-coronavirus/

Browsing via Google is giving them all your behaviour and lists of interests and online contacts. Allways use the addressbar for browsing or use a safer search engine such as duckduckgo.com. To get out of the Google and Facebook etc 'bubbles', you should check the links before you click on them or post them here.

[wili]

We run from  our horrors, but the horror inevitably follows us...

[El Cid]

The Ischgl report, a few points:

- IFR was 0,25% which is lower than elsewhere but as others have pointed out they had all the positives: great healthcare, good, fresh air, lots of sunshine, wealthy population probably outdoors a lot, etc. I also wonder what the average age in Ischgl is, but did not find anything about that
- Still, even 0,25% is much, much more than the flu
- 42% had antibodies. This by itself refutes Neven's idea that 5 times as many have come into contact with the virus than those having antibodies
- Lots of children seemingly do come into contact with the virus without developing antibodies, so Ischgl probably has herd immunity. - Likely 40% antibody positives is enough for herd immunity instead of 50-70% as previously thought

[Neven]

The official narrative rests on many assumptions, but the biggest assumption of all is that SARS-CoV-2 suddenly popped up in November 2019 on a wet market in Wuhan. Many anecdotes counter this narrative, and now science is catching up. Here's another crap story:

Coronavirus traces found in March 2019 sewage sample, Spanish study shows

MADRID (Reuters) - Spanish virologists have found traces of the novel coronavirus in a sample of Barcelona waste water collected in March 2019, nine months before the COVID-19 disease was identified in China, the University of Barcelona said on Friday.

The discovery of virus genome presence so early in Spain, if confirmed, would imply the disease may have appeared much earlier than the scientific community thought.

The University of Barcelona team, who had been testing waste water since mid-April this year to identify potential new outbreaks, decided to also run tests on older samples.

They first found the virus was present in Barcelona on Jan. 15, 2020, 41 days before the first case was officially reported there.

Then they ran tests on samples taken between January 2018 and December 2019 and found the presence of the virus genome in one of them, collected on March 12, 2019.

“The levels of SARS-CoV-2 were low but were positive,” research leader Albert Bosch was quoted as saying by the university.

The research has been submitted for a peer review.

Read rest here.

[pietkuip]

The official narrative rests on many assumptions, but the biggest assumption of all is that SARS-CoV-2 suddenly popped up in November 2019 on a wet market in Wuhan. Many anecdotes counter this narrative, and now science is catching up.

Already in December someone in Svärdsjö in the province of Dalarna in Sweden got sick. The symptoms were not recognized then. But they looked at the lung x-rays again and the covid anti-body test was positive.
https://www.svt.se/nyheter/lokalt/dalarna/antikroppstest-och-rontgenbilder-hor-lakaren-om-extremt-tidig-corona-i-dalarna

This was a person who had not traveled, in a somewhat remote corner of the country.

[Archimid]

but the biggest assumption of all is that SARS-CoV-2 suddenly popped up in November 2019 on a wet market in Wuhan

The origins of the virus are irrelevant to fight it. The origins of the virus may be the biggest assumption from the perspective of mass media or historians, but from an epidemiology and healthcare perspective, the origins are barely relevant. ( except to the super detailed expert developing cures and understanding based on genetics and other specific markers.)

[gerontocrat]

but the biggest assumption of all is that SARS-CoV-2 suddenly popped up in November 2019 on a wet market in Wuhan

The origins of the virus are irrelevant to fight it. The origins of the virus may be the biggest assumption from the perspective of mass media or historians, but from an epidemiology and healthcare perspective, the origins are barely relevant. ( except to the super detailed expert developing cures and understanding based on genetics and other specific markers.)

And of somewhat more immediate concern is what is happening now..

World & the USA both at record levels of new cases (using 7 day trailing average for a clearer view). But both the World and USA deaths data not yet showing the sort of increase to be expected very soon. (graphs attached)

The UK graph is also attached, which given the recent UK news reports on mass abandonment of social distancing, suggests the UK is more likely to join the USA & World trends.

I also attach the Italy graph to show where we would like to be by now.

[Yuha]

There's several reasons why the number of deaths in US is not yet rising the way the number of infections is:

• Deaths come with a delay.
• Some (but certainly not all) of the increase in cases is due to increased testing.
• Doctors have more experience and know better what treatments work in the critical cases. Besides preventing some deaths, this may also delay death further in other cases.
• Nursing homes, hospitals etc. are better prepared to protect their vulnerable residents/patients.
• While the young and healthy are eager to return to normality, the elderly and other risk groups are continuing to self isolate, practice social distancing etc.
• It's possible that some states are cooking the books. Perhaps not actually forging the records but controlling the way statistics are collected and reported.

[Archimid]

+1 Yuha

Increased testing lowers the CFR because of statistical artifacts. But in addition to statistics, the actual IFR is lowered by early detection and awareness.  Early detection allows for improved treatment and more time for medications to work at lower dosage.

[Neven]

Already in December someone in Svärdsjö in the province of Dalarna in Sweden got sick. The symptoms were not recognized then. But they looked at the lung x-rays again and the covid anti-body test was positive.
https://www.svt.se/nyheter/lokalt/dalarna/antikroppstest-och-rontgenbilder-hor-lakaren-om-extremt-tidig-corona-i-dalarna

This was a person who had not traveled, in a somewhat remote corner of the country.

Yes, thanks for repeating this. I wanted to quote it before.

This is highly interesting, and there are many more such anecdotes.

The origins of the virus are irrelevant to fight it.

I'm not referring to the origin, but to chronology. If the virus was around for many months before November 2019, and in several places around the world, this makes a significant difference to modelling and policy. In the interview with professor Sunetra Gupta I posted a few weeks ago, this aspect of timing/chronology was one of the themes discussed.

From The Guardian three weeks ago:

The worst case, adopted by government, was that left unchecked, the virus was so dangerous the epidemic could claim 500,000 lives. The best case, set out by Gupta, is not currently borne out by scientific data – but she insists it is an important consideration and counterbalance.

Gupta’s model showed that if the virus had arrived in Britain a month earlier than thought – in December rather than January – it might have spread far wider than anyone appreciated, and infected half the population. If that was the case, the risk of dying would be a fraction of the 1% it is generally believed to be, and infections would soon wane through “herd immunity” – achieved when more than two-thirds have acquired immunity to the virus.

[etienne]

Having the virus around for a longer time doesn't make it less problematic, because some mutation must have happened that makes it much more contagious. The main difference is concerning heard immunity, but antibodies tests don't show much prevalence. The other difference could be political, but I'm not sure that it makes such a difference.

[kassy]

From the link in #7213:

Then they ran tests on samples taken between January 2018 and December 2019 and found the presence of the virus genome in one of them, collected on March 12, 2019.

Since they found it only once they should retest it thoroughly. If i had to bet i would still go for false positive/not related.

[blumenkraft]

I would go for cross-contamination.

[kassy]

From the testers? Retest should show that too...and that should be the thing you rule out before publishing this find.

[blumenkraft]

Exactly. Even more if the finding is so extraordinary.

[Archimid]

If the virus was around for many months before November 2019, and in several places around the world, this makes a significant difference to modeling and policy.

Even if I trusted this environmental sample,  it would be perfectly normal for the virus to be around long before November 2019, in trace amounts. The chances for local small epidemics to have occurred and nobody noticing is also there.

But why it didn't break out into a pandemic then and it does now?

I like to understand it in terms of probability. The probability of a person passing the virus is a function of :

1. The carrier's physiology
2. The strain of the virus
3. The stage of the disease
4. The speed and direction of the airflow out of a person's orifices.
5. The capacity of the environment to sustain the virus
6. The availability of susceptible people
7. The susceptible's physiology


Each one of those elements set limits on the spread of a virus. 2 may have something to do with the initial spread behavior or the quoted article. But even if we were talking about the Wuhan strain, it would be perfectly normal for it to be found elsewhere. I believe 5 and 6 are the most likely culprits for the low level of infection not becoming a pandemic sooner.

As for 5, I think it is likely that during summer and early fall the outside was not a favorable environment for viral survival, significantly decreasing the probability of infection.

I think 6 is the primary factor to explain the lag. That one tiny virii that first left the bat had the highest available pool potential victims. That is true, but it is also true that a virus as a collective has an extremely small pool of actual susceptible individuals when the number of infected is very small. The pool of actual susceptibles increases as the pool of potential susceptibles decreases.

So TLDR: The virus didn't explode earlier because it needed critical mass.

[etienne]

So TLDR: The virus didn't explode earlier because it needed critical mass.

I can't agree with that critical mass explanation. The virus evolves, and one specific change was needed for it to become more contagious.

We have the new numbers for Luxembourg, it's going quite up. The irony is that schools should restart like before COVID 19 this Monday, right now only half of the pupils are coming with a weekly change so that the groups didn't mix. The reason to go forward is that contamination seems to happen mainly during the free time, not at work, while shopping...

[Neven]

But why it didn't break out into a pandemic then and it does now?

Excellent question!

[vox_mundi]

Your chasing a laboratory error.

-------------------------

Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases
https://www.medrxiv.org/content/10.1101/2020.06.13.20129627v1

https://www.medrxiv.org/content/10.1101/2020.06.13.20129627v1.full.pdf

Abstract
SARS-CoV-2 was detected in Barcelona sewage long before the declaration of the first COVID-19 case, indicating that the infection was present in the population before the first imported case was reported. Sentinel surveillance of SARS-CoV-2 in wastewater would enable adoption of immediate measures in the event of future COVID-19 waves.

-------------------------------------

What the author said:

#SARSCoV2 virus genome was detected in samples of waste water in Barcelona, collected in March 12, 2019. These results suggest the infection was present before knowing about any case of COVID-19 in any part of the world.
https://mobile.twitter.com/FLAHAULT/status/1276518123034808321

----------------------

What virologists who actually perform the test said:

------------------------

Prof Francois Balloux
@BallouxFrancois
Director @UGI_at_UCL (Univ
 College London Genetics Institute)

There has been a claim that #SARSCoV2 has been in circulation in Barcelona in March 2019. This is remarkably implausible. All the genomic evidence available (~100k genomes) points to an origin of the virus around November 2019 in China (e.g. below). (1/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732776918724609


https://europepmc.org/article/MED/32387564

There is some uncertainty when the virus arrived in Europe. The first confirmed #COVID19 cases in Europe date back to December 2019. Coronavirus RNA was also detected in wastewater from December 2019 in Milan and Turin, but not before. (2/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732778948833280

The evidence for #SARSCoV2 being in circulation in Barcelona in March 20019 is shaky. The detection method (RT-PCR) can be error-prone. The methods are poorly explained in the preprint and the study lacks any negative control. (3/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732781373030400

The work does not include any attempt to confirm that the RNA detected by the RT-PCR is from #SARSCoV2 rather than some other coronavirus in circulation. Such confirmation is essential and would have been fast, easy and cheap to do through (partial) genome sequencing. (4/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732785164722176

In short, the study does not seem to have been carefully and competently performed. It lacks the required minimal controls, validation and confirmation steps. This is most likely a case of sample mix-up or contamination. (5/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732786536259585

#SARSCoV2 being in circulation in March 2019 is an exceptionally strong claim as it would change everything we know about the pandemic. It feels highly irresponsible to have released such a preliminary preprint based on sloppy, incomplete and questionable evidence. (6/6)
https://mobile.twitter.com/BallouxFrancois/status/1276732787865911297

--------------------------

- qPCR based on IP2/IP4 not reliable & cross contaminated.

- No neg controls included in the study

- No #SARSCoV2 genome sequenced & phylogenetic analysis performed to assess it was truly a #SARSCoV2

In short they have likely amplified another #coronavirus
https://mobile.twitter.com/GaetanBurgio/status/1276648127458467840

-------------

They are using a PCR target shown to have Toss-of-a-coin specificity and their amplifications are right on bordereline. This is another example of importance of peer review am afraid   This is not true!
https://mobile.twitter.com/alanmcn1/status/1276639926453501953

--------------------------

It might be a precursor of SARS-CoV-2. RdRp is conservative across different corona viruses.
https://mobile.twitter.com/jaywang06138467/status/1276701175270735873

Only sequencing the amplicons will tell

-----------------------------------

PCR false positive results are rare. However, they do occur. Though the analytical specificity of these tests is usually 100%, the clinical specificity is less, due to contamination (a significant problem for NAT procedures) and/or human error in the handling of samples or data (very hard to eliminate entirely).  These false positive results will have substantial-to-large effects when prevalence is low (Andrew Cohen, personal communication).

Novel real-time RT-PCR assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase, spike and nucleocapsid genes of SARS-CoV-2 may help to improve the laboratory diagnosis of COVID-19. Compared to the reported RdRp-P2 (IP2/IP4) assay which is used in most European laboratories, these assays do not cross-react with SARS-CoV in cell culture and may be more sensitive and specific.

https://jcm.asm.org/content/58/5/e00310-20

https://covidreference.com/diagnosis

------------------------------------

Statistics 101

The Effects of a Small Sample Size Limitation

Determining the veracity of a parameter or hypothesis as it applies to a large population can be impractical or impossible for a number of reasons, so it's common to determine it for a smaller group, called a sample. A sample size that is too small reduces the power of the study and increases the margin of error, which can render the study meaningless. Researchers may be compelled to limit the sampling size for economic and other reasons. To ensure meaningful results, they usually adjust sample size based on the required confidence level and margin of error, as well as on the expected deviation among individual results.

Small Sample Size Decreases Statistical Power

The power of a study is its ability to detect an effect when there is one to be detected. This depends on the size of the effect because large effects are easier to notice and increase the power of the study.

The power of the study is also a gauge of its ability to avoid Type II errors. A Type II error occurs when the results confirm the hypothesis on which the study was based when, in fact, an alternative hypothesis is true. A sample size that is too small increases the likelihood of a Type II error skewing the results, which decreases the power of the study.

https://en.m.wikipedia.org/wiki/Type_I_and_type_II_errors

------------------------------

[kassy]

This story is interesting (even though it does not help the big picture).

Patient 91: How Vietnam saved a British pilot and kept a clean Covid-19 sheet

"If I'd been almost anywhere else on the planet, I'd be dead. They would have flicked the switch after 30 days," says Stephen Cameron from his hospital bed.

The 42-year-old Scottish pilot spent 68 days on a ventilator, thought to be a longer stretch of time than any patient in the UK. He did so not in a hospital in his hometown of Motherwell, but in Vietnam's sprawling and hectic Ho Chi Minh City, with no close friends or family for thousands of miles.

Cameron, the last Covid-19 patient in an intensive care unit in Vietnam, has been the sickest doctors have had to deal with during the outbreak.

The country, home to 95 million people, has seen only a few hundred confirmed cases, single-digit ICU admissions and not a single recorded death. So rare was a case of Cameron's severity in Vietnam, every minute detail of his recovery was reported in national newspapers and on TV news bulletins.

He's now known nationwide as Patient 91, the moniker given to him by public health officials when he fell ill in March.

continues on:

https://www.bbc.com/news/world-asia-53196009

[blumenkraft]

Crazy thought, but is this virus making people stupid? Is being a covidiot a symptom of the illness?

How Covid-19 can damage the brain

Link >> https://www.bbc.com/future/article/20200622-the-long-term-effects-of-covid-19-infection

[blumenkraft]

Parties — not protests — are causing spikes in coronavirus

Link >> https://www.mprnews.org/story/2020/06/24/npr-what-contact-tracing-may-tell-about-cluster-spread-of-the-coronavirus

[Neven]

Crazy thought, but is this virus making people stupid? Is being a covidiot a symptom of the illness?

All people are stupid. The only difference between people is that some know this and others don't.

[Archimid]

I can't agree with that critical mass explanation. The virus evolves, and one specific change was needed for it to become more contagious.

Let me put it this way. Sars like mutations like C19 happen all the time, all over the world. Mutations always occur inside a host but almost never get passed on. Sometimes new strains pass on and the same checks are performed. Most new strains die very quickly.

 But sometimes extraordinary events happen and chains of infection are created. Once enough chains of infection are created the process becomes self-sustaining. That is when the virus can take hold and show it's full R.

[vox_mundi]

U.S. Coronavirus Cases Surge By More Than 45,000 As States Roll Back Reopenings
https://www.cnbc.com/amp/2020/06/27/us-coronavirus-cases-surge-by-more-than-45000-as-states-roll-back-reopenings.html



There were 45,255 additional Covid-19 cases reported across the nation on Friday, bringing the total to more than 2.46 million cases, according to Johns Hopkins University data.

As of Friday, the U.S. seven-day average of new cases increased more than 41% compared with a week ago.

Deaths caused by Covid-19 lag behind other data points such as hospitalizations, which lag confirmed infections as the disease can take weeks to fully develop in a person.

Hospitalizations due to Covid-19 were growing in 14 states as of Friday, according to a CNBC analysis of Covid Tracking Project data.

As of Friday, Texas reported a 57% increase in hospitalizations, based on a seven-day average, compared with one week ago. It's average number of daily cases grew by nearly 70%, according to John Hopkins data.

... Harris County, which includes Houston, moved to its highest Covid-19 threat level, signalling a “severe and uncontrolled” outbreak.

“The harsh truth is that our current infection rate is on pace to overwhelm our hospitals in the very near future,” Lina Hidalgo, the county judge, said at a press conference on Friday. “We opened too quickly.”

https://abc13.com/stay-home-work-safe-order-lina-hidalgo-coronavirus-texas-reopen/6270984/

As of Friday, Arizona reported a 36% increase in hospitalizations, based on a seven-day average, compared with one week ago. It's average number of daily cases grew by more than 42%, according to John Hopkins data.

Today, AZ hospitals statewide are filling up with patients, some critically ill. The state had more than 66,000 confirmed cases as of Friday, up from just over 20,000 on June 1. Thousands more are being reported each day, and 1,535 people have died.

More than 2,400 people are hospitalized with coronavirus this week, up from about 1,000 three weeks ago. More than 600 ICU beds were filled with virus patients this week, two-thirds of them on ventilators and sedated.

Arizona has just over 200 empty ICU beds, out of about 1,600 in the state. More are being added as hospitals brace for a flood of patients as newly infected people slowly get sicker. Traveling nurses are being hired from other states to back up overworked staff.

Some states, like Texas and Florida, have had to re-close some businesses while others, like Arizona, have put any further plans on pause.

Florida has broken its one-day record for new coronavirus infections for a second straight day with an additional 9,636 positive cases, the state’s department of health said on Saturday.

There were 76,129 tests conducted Friday, with a 12.7% positivity rate, officials said.

------------------------------

Meanwhile ...

Donald Trump’s motorcade has just arrived at Trump National Golf Club in Loudoun County, according to the White House press pool.

According to CNN senior congressional correspondent Manu Raju, this marks the 271st day he’s spent at one of his golf clubs and 363rd time at one of his properties in his presidency in the 1,254 days since taking office.

...  “a woman walking a small white dog nearby gave the motorcade a middle-finger salute”.

https://mobile.twitter.com/mkraju/status/1276885817378684928



------------------------------------

[Paddy]

Covid cases worldwide have passed 10 million, and deaths have passed 500 thousand: https://www.worldometers.info/coronavirus/

Probably Covid deaths will pass 1m before the end of the year, meaning exactly one punter will have got their prediction right, despite all the advances made with Remdesivir, dexamethasone, convalescent plasma, increased ITU capacity etc., since the daily worldwide death rate has been pretty constant around 5k per day for the last two months, and there are 187 days till the end of the year.

Given the rest of the 2020s are yet to come, and that this isn't covering the indirect deaths... but also that at some time in 2021 we should hopefully have a vaccine, I'd reckon either the 1m to 10m or the 10m to 100m bin is likely to be the correct one.

[blumenkraft]

Want to know if you have antibodies? Give blood. The Red Cross will test that for free.

Link >> http://redcross.org/

[blumenkraft]

All people are stupid.

If you think people are stupid now, wait for the time when IQ90 is the new IQ100. 

[be cause]

if Trump gets in again , middle finger salutes may attract the death penalty just bc .

[Archimid]

And online posting. But that is off topic here.

[blumenkraft]

At the beginning of this pandemic, in the rather fringe right-wing Reddit subs, before they changed the tune after getting the "it's a hoax" memo, and before they realized they could use it to scapegoat China by calling it the Wuhan Virus, and before they realized it would destroy the Trump economy, they called the virus "airborne AIDS". Welp:

In a disturbing parallel to H.I.V., the coronavirus can cause a depletion of important immune cells, recent studies found

Link >> https://www.nytimes.com/2020/06/26/health/coronavirus-immune-system.html

[pietkuip]

At the beginning of this pandemic, in the rather fringe right-wing Reddit subs,

I am seeing right-wing stuff in Sweden and in the Netherlands. Both are similar in tone: politicians are stupid, experts are ignorant/arrogant, and then there are the conspiracy theorists.

Populist opposition.

They act like libertarians in the Netherlands, in Sweden they want an authoritarian approach.

Am I a conspiracy theorist when I guess that similar groups may be behind the anonymous accounts?

[The Walrus]

In the U.S., confirmed cases are about 30% higher than the spring peak.  By comparison,  testing is about three times higher, such that the positive test rate has decreased significantly.  Also, the death rate is down 80% from the spring peak.  Deaths and hospitalizations have fallen for 9 straight weeks.  Although the numbers are still above epidemic levels.

[bbr2315]

https://en.wikipedia.org/wiki/COVID-19_pandemic_in_the_Navajo_Nation

Navajo Nation apparently has highest TESTED per capita rate in US (pop: 173,667)

Cases: 7,320
Deaths: 350

If my math is correct that means about 35K have been infected UNLESS the mortality rate is super high here which it actually could be as that has historically been the case with native communities in the new continents & novel viral outbreaks.

If 20% of Navajo Nation has already been infected, the remainder of the outbreak there through summer could serve as another affirmation relative to the situation in NYC regarding how widespread the virus gets in relatively unmitigated spread before herd immunity helps its decline.

Their death toll has risen from 248 as of 6/1 to 350 as of 6/27, which would be... 14.3% infected at 6/1 (1% mort rate). With a few more days of June to go it looks like #s for both cases and deaths may have risen 50% this month (~21-22% infected by 7/1).

If Navajo Nation's death toll exceeds NYC's, it would have to reach 556. If it jumps 50% again in July, it will do that sometime in August. I do anticipate their outbreak will end by August or September at around 40-45% infected or about 2X today's numbers which would translate into a death toll of almost 700 or approximately .4% total pop IFR.

Also it is pretty bad that 35% of their deaths have been under 60...

[bbr2315]

In NY, apparently we only had 5 total deaths statewide yesterday which means probably even less in NYC, like 2-3. We are almost at zero.

The death figures for NYC zips are still slowly updating. Two more zipcodes have joined the one with an IFR of .661% in the .5%+ group.

[oren]

So? Do you expect Deaths and hospitalizations to continue falling?

[SteveMDFP]

So? Do you expect Deaths and hospitalizations to continue falling?

It's possible.  There's a plausible hypothesis as to why some respiratory viruses may become less virulent over time.  That is, those with more severe symptoms tend to get sequestered at home and in hospitals.  It's the less-symptomatic cases that then spread in communities and proliferate.  This creates strong evolutionary pressure that favors strains that are less pathogenic.  We *might* be seeing this in real time.  Or maybe what we're seeing is just a lag time between surge in cases and surge in deaths.  Or maybe we're seeing effects of incrementally improving treatment protocols.  Perhaps a combination of these factors.

Uncertainty abounds here.

[gandul]

So? Do you expect Deaths and hospitalizations to continue falling?

It's possible.  There's a plausible hypothesis as to why some respiratory viruses may become less virulent over time.  That is, those with more severe symptoms tend to get sequestered at home and in hospitals.  It's the less-symptomatic cases that then spread in communities and proliferate.  This creates strong evolutionary pressure that favors strains that are less pathogenic.  We *might* be seeing this in real time.  Or maybe what we're seeing is just a lag time between surge in cases and surge in deaths.  Or maybe we're seeing effects of incrementally improving treatment protocols.  Perhaps a combination of these factors.

Uncertainty abounds here.

Also, in some places, esp. big cities, many elderly people won’t get sick cause either they have already passed it or they did not survive it.

[vox_mundi]

Global Tally of Known Cases Passes 10 Million; Deaths exceed 500,000 https://www.nytimes.com/2020/06/28/world/coronavirus-updates.html

The global total of coronavirus cases passed 10 million on Sunday, according to a New York Times database, as countries around the world struggled to keep new infection rates from reaching runaway levels while simultaneously trying to emerge from painful lockdowns.

The number of confirmed infections, which took roughly 40 days to double after hitting five million in May, may be substantially underestimated, public health officials say. Data released last week by the Centers for Disease Control and Prevention indicated that the actual figures in many regions of the United States are probably 10 times as high as reported.

https://www.nytimes.com/2020/06/27/health/coronavirus-antibodies-asymptomatic.html

In April, roughly a month after the World Health Organization declared the coronavirus a pandemic, global virus deaths topped 100,000. That figure then climbed to 250,000 in early May and has nearly doubled in less than two months. More than a quarter of all known deaths have been in the United States.

... Unlike the US, Brazil, India and Russia, dozens of countries that took early steps to contain and track the pandemic have been able to control the virus within their borders. But experts fear that fatigue with lockdowns and social distancing has allowed the virus to spread with renewed intensity across many corners of the world.

----------------------------------

South Africa's Surge of Virus Cases Expected to Rise Rapidly
https://www.aljazeera.com/news/2020/06/global-coronavirus-death-toll-nears-500000-live-updates-200627234018796.html

South Africa's current surge of COVID-19 cases is expected to dramatically increase in the coming weeks and press the country's hospitals to the limit, the health minister said.

South Africa, a country of 57 million people, already has more than a third of the reported cases for all 54 countries in Africa, a continent of 1.3 billion people.

More than 4,300 people have been hospitalised out of South Africa's 138,000 confirmed cases, Health Minister Zwelini Mkhize said in a statement. He warned this number is expected to rise quickly.

“We are seeing a rapid rise in the cumulative number of positive COVID-19 cases indicating that, as we had expected, we are approaching a surge during the ... months of July and August,” Mkhize said in a statement.

“It is anticipated that while every province will unfortunately witness an increase in their numbers, areas where there is high economic activity will experience an exponential rise,” said Mkhize, saying that the cities of Johannesburg, Cape Town and Durban will see the biggest increases.

----------------------------------

Half a Million In Lockdown as Beijing Fights New Virus Cluster
https://www.aljazeera.com/news/2020/06/global-coronavirus-death-toll-nears-500000-live-updates-200627234018796.html

China imposed a strict lockdown on nearly half a million people near the capital to contain a new outbreak on Sunday, as authorities warned it was soon to "relax" over the new cluster of cases.

After China largely brought the coronavirus under control, hundreds were infected in Beijing and cases emerged in neighbouring Hebei province.

Health officials said Sunday that Anxin county - about 150 kilometres (90 miles) from Beijing - will be "fully enclosed and controlled", the same measures imposed at the height of the pandemic in the city of Wuhan.

----------------------------------

'Window Is Closing' for US to Get Coronavirus Under Control, Trump's HHS Secretary Warns
https://amp.cnn.com/cnn/2020/06/28/politics/hhs-alex-azar-coronavirus-rise-in-cases-cnntv/index.html

Health and Human Services Secretary Alex Azar warned Sunday that the "window is closing" for the United States to get the coronavirus pandemic under control, as confirmed cases are surging in a majority of the country and some states are dealing with record numbers of hospitalizations.

"Things are very different from two months ago... So it is a very different situation, but this is a very, very serious situation and the window is closing for us to take action and get this under control," Azar told CNN's Jake Tapper on "State of the Union."

... The top health official's message differs from that of President Donald Trump, who seems ready to move on from the still-raging pandemic, and Vice President Mike Pence.

At a Friday press briefing by the White House's coronavirus task force, the first in nearly two months, Pence declared that the US had "flattened the curve," painting a rosy picture at odds with reality.

... Even as residents in some states have been turned away from testing sites that have reached capacity, Mr. Pence falsely said that anyone who wanted to be tested for the coronavirus could be tested.

https://www.nytimes.com/2020/06/26/us/politics/trump-coronavirus.html

President Trump first made this claim in March, and top health experts have repeatedly contradicted this. Testing sites in several states, including Texas, Florida and Arizona, have been overrun.

https://twitter.com/TFizzle18/status/1276926709628129281

https://twitter.com/HoustonHealth/status/1276908422290706433

https://twitter.com/FloridaPIOs/status/1276931781053362176

https://twitter.com/FloridaPIOs/status/1276860127744835584

https://www.nytimes.com/2020/06/25/upshot/virus-testing-shortfall-arizona.html

Nationwide, coronavirus cases have risen 65 percent over the past two weeks.  Thirty-six states are reporting a rise in positive coronavirus cases, and only two are reporting a decline in cases compared to last week.

On Friday, the US reported the highest number of new cases in a single day, with at least 40,173 new infections. The previous daily high was reported on Thursday.



----------------------------------

CDC: ... The overall percentage of respiratory specimens testing positive for SARS-CoV-2 increased from week 24 (6.5%) to week 25 (7.6%) nationally, driven by increases in seven regions.

https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html

-----------------------------------

Positivity Rates Are Climbing In Hard-hit States
https://www.nytimes.com/2020/06/28/world/coronavirus-updates.html

Gov. Greg Abbott said the virus had taken a “swift and dangerous turn” in Texas, noting that the percentage of coronavirus tests coming back positive had risen to 13 percent from 4 percent in a month.

In Los Angeles County, officials said on Saturday that the positivity rate there had risen to 9 percent; two weeks ago it was averaging 5.8 percent.

Arizona’s positivity rates have been climbing steadily since early May and have been averaging above 20 percent for a week, according to figures compiled by Johns Hopkins University.

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

... What’s most significant about positivity rates is which way they are moving, and up is not good. It’s a strong suggestion that the pandemic is gaining strength — and that rapidly rising case counts are not merely the result of having performed more tests, as President Trump and Vice President Pence have argued recently. If wider testing were all there was to it, positivity rates ought to be flat or falling, not rising.

-----------------------------------

Outbreaks From Restaurants Grow As More U.S. States Permit Indoor Dining.
https://www.nytimes.com/2020/06/28/world/coronavirus-updates.html

... As more restaurants and bars open for indoor dining, hard-to-trace outbreaks are prompting warnings from public health officials in several states.

In Michigan, more than 85 cases were linked to Harper’s Restaurant and Brewpub in East Lansing. In Alaska, the Seward Alehouse closed and encouraged customers to get tested after an employee contracted the virus.

And in Kansas, cases were linked to the Wild Horse Saloon in Topeka and a bar called the Hawk in Lawrence. Sonia Jordan of Lawrence-Douglas County Public Health said her department released details of the Hawk outbreak because “we are not confident in being able to identify everyone who was there.”

... At least 100 cases were tied to the Tigerland nightlife district in Baton Rouge, La.

The rapid identification of restaurant clusters contrasts with the continuing uncertainty about infections stemming from protests against racially biased policing, which have been held in more than 2,000 U.S. cities since the death of George Floyd in police custody on May 25. The Times has reached out to dozens of cities that have had large protests, finding some small case groupings but no major clusters.

Thus far, the effort has found about 50 infections connected to protests, including members of the National Guard in Nebraska, Minnesota and Washington, D.C.

----------------------------------

[gandul]

So the conclusion is that the US spike is more due to demonstratIons, or to hasty reopening, or both, together with the usual US factors (not wanting to lose the job, not wanting to go the doc to avoid a bill, not having papers).