Coronavirus

[MXLRplus]

... We can't drive safely. ...

Everybody who has been in the bay area is well aware of mad skillz possessed by drivers. Kidding.

Tesla and the rest of mankind are working diligently on vehicle autonomy and safety systems; our cars are safer than they were just 5 years ago.

• But should they stop selling cars until we cut the fatality rate in 1/2?
• Traffic deaths are very light right now. Should we stay on Shelter-In-Place to keep car deaths down?
• Homicide is down. Should we stay on Shelter-In-Place to keep murder rates down.?
• Flu deaths are down. Should we stay on Shelter-In Place to suppress the flu?

I don't think some people realize the damage we've done already.

 

[EinSV]

These guys report about 43% asymptomatic.

Suppression of COVID-19 outbreak in the municipality of Vo, Italy : COVID19

The surveys were taken before and after the 14 day lockdown.

On the 21st of February 2020 a resident of the municipality of Vo, a small town near Padua, died of pneumonia due to SARS-CoV-2 infection. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI 0.8-1.8%). Notably, 43.2% (95% CI 32.2-54.7%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic. The mean serial interval was 6.9 days (95% CI 2.6-13.4). We found no statistically significant difference in the viral load (as measured by genome equivalents inferred from cycle threshold data) of symptomatic versus asymptomatic infections (p-values 0.6 and 0.2 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). Contact tracing of the newly infected cases and transmission chain reconstruction revealed that most new infections in the second survey were infected in the community before the lockdown or from asymptomatic infections living in the same household. This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection and their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics, the duration of viral load detectability and the efficacy of the implemented control measures.​

One interesting detail in the follow-up Vo study is that 67.7% of the PCR-positive individuals in the first round of testing were negative in the second round. The average time to clear the virus for these individuals was only 9.3 days according to the PCR test results. https://www.medrxiv.org/content/10.1101/2020.04.17.20053157v1.full.pdf

This very small window where virus was detected is consistent with other studies showing PCR has a very high rate of covid-19 false negatives, especially before symptom onset and then dropping off rapidly a few days after symptom onset. The Johns Hopkins study I posted recently is one example (chart and link below).

People have been using PCR results to estimate infection rate in a population, but the Vo study is yet another demonstration of why its very high rate of false negatives and short window for detecting virus makes it a very poor tool for that purpose.

https://www.medrxiv.org/content/10.1101/2020.04.07.20051474v1.full.pdf

 

[OPRCE]

No, compassionate use exemptions have been removed (the way they work is you have to apply for one for EACH patient you want to use it on, directly to the manufacturer). Gilead was being overwhelmed by these, so compassionate use was removed and the drug moved to an "off label" designation by the FDA so that physicians could obtain it from selected hospital (not retail) pharmacies for hospital only usage.

Your point, specifically that I was replying to (at least how I read it), was to suggest that Remdesivir be moved to a preventative / prophylactic usage model. That is never going to happen. It does not have a completely benign side-effect profile.

Right, thanks for the clarification.
For avoidance of doubt I probably should have said "It has been suggested as a potential prophylactic for frontline healthcare workers but I think it has not seen such use thus far."

 

[winfield100]

An Olympic Athlete disagrees with you:
Olympian Cameron van der Burgh Says COVID-19 Is 'By Far the Worst Virus'

Arguably, this would be one of the healthiest people in the world in terms of body conditioning, and for him to say that being sick with COVID-19 effectively drained what we as physicians call the "biological reserve" is noteworthy.

@bkp_duke @jbcarioca @SageBrush
Have you seen this study about ?single point mutations? in part of the sequence, specifically ?17? base pairs for tracing spreads. (These apparently don’t affect the infectious parts)
Genetic tracing 'barcode' is rapidly revealing COVID-19's journey and evolution

 

[bkp_duke]

@bkp_duke @jbcarioca @SageBrush
Have you seen this study about ?single point mutations? in part of the sequence, specifically ?17? base pairs for tracing spreads
Genetic tracing 'barcode' is rapidly revealing COVID-19's journey and evolution

View attachment 533902

Is that the RNA genetic drift of only a specific sequence, or are they sequencing the entire genome of the virus? If the entire genome, I'm not terribly surprised.

I would be more interested in:
1) the protein changes (just because there is a point DNA mutation doesn't mean it becomes a protein amino acid substitution - i.e. "silent" point mutations)
2) if there were protein changes, where on the proteins where they? Not all proteins show significant structural changes with a single amino-acid point change.

The protein changes are the key, and I don't see them elaborate on that in the article.

That info, however, does give a nice "finger print" for getting an idea of how things spread around.


EDIT - just saw this at the end of the article:
"We're seeing that the two parts of the virus that seem not to be mutating are the ones responsible for its entry into healthy cells and packaging its RNA," Rosen said. "Both of these are important targets for understanding the body's immune response, identifying antiviral therapeutics and designing vaccines."

This doesn't surprise me, as mutations in those key areas would inactivate the virus and prevent it from spreading (i.e. a non-advantageous mutation).

 

[bpsmits]

So, how is Sweden doing?

Let's compare them to a handful of other countries - countries of Western Europe of similar size (Belgium, Netherlands, Switzerland, Austria, Portugal), as well as their Scadinavian neighbors (Denmark, Finland, Norway).

Total cases:

Belgium: 37,183
Netherlands: 31,589
Switzerland: 27,404
Portugal: 19,685
Austria: 14,671
Sweden: 13,822
Denmark: 7,242
Norway: 7,069
Finland: 3,681

Cases / million population:

Belgium: 3,208
Switzerland: 3,166
USA: 2,232 (for context)
Portugal: 1,931
Netherlands: 1,844
Austria: 1,629
Sweden: 1,369
Norway: 1,298
Denmark: 1,250
Finland: 664

We can see that Sweden, despite having somewhat relaxed measures, has not exploded in cases as some have predicted. Primary schools remain open. Shopping centers remain open. For now.

Are they doing great? Not exactly. Are they doing horribly? No
Somewhere in the middle. Which I would consider a success since they did not incur near the cost as most other countries.

Of course, the final chapter has not yet been written. They could still see numbers "take off". We will see.

The density of the population will have something to do with it:

Population per km2

Belgium: 379
Switzerland: 201
Portugal: 112
Netherlands: 413
Austria: 105
Sweden: 22
Norway: 17
Denmark: 135
Finland: 16

 

[EinSV]

Typo fixed (too late to edit):

This very small window where virus was detected is consistent with other studies showing PCR has a very high rate of covid-19 false negatives, especially before symptom onset and then increasing rapidly a few days after symptom onset. The Johns Hopkins study I posted recently is one example (chart and link below).

 

[EinSV]

ICYMI-- another report on antibody testing, this one from an Austrian town:

"A comprehensive test using rapid antibody tests unearths astonishing results in Ortisei these days. Almost 49 percent of the 456 St. Ulrichers tested have antibodies against Covid-19 .... That is almost 50 times the number in the official medical statistics."
(per Google translate)

https://www.stol.it/artikel/chronik/flaechendeckende-tests-in-st-ulrich

 

[OPRCE]

So, how is Sweden doing?

Let's compare them to a handful of other countries - countries of Western Europe of similar size (Belgium, Netherlands, Switzerland, Austria, Portugal), as well as their Scadinavian neighbors (Denmark, Finland, Norway).

Total cases:

Belgium: 37,183
Netherlands: 31,589
Switzerland: 27,404
Portugal: 19,685
Austria: 14,671
Sweden: 13,822
Denmark: 7,242
Norway: 7,069
Finland: 3,681

Cases / million population:

Belgium: 3,208
Switzerland: 3,166
USA: 2,232 (for context)
Portugal: 1,931
Netherlands: 1,844
Austria: 1,629
Sweden: 1,369
Norway: 1,298
Denmark: 1,250
Finland: 664

We can see that Sweden, despite having somewhat relaxed measures, has not exploded in cases as some have predicted. Primary schools remain open. Shopping centers remain open. For now.

Are they doing great? Not exactly. Are they doing horribly? No
Somewhere in the middle. Which I would consider a success since they did not incur near the cost as most other countries.

Of course, the final chapter has not yet been written. They could still see numbers "take off". We will see.

Taking three European countries with similar populations (~10M) for comparison:

Country..........Confmd.....Dead.....Recovd.....Tests/Mpop......rawCFR......ResolvedCFR...CaseGrowth...DeathGrowth
Sweden...........13’822......1’511............550.............7'387..............10.93%.........73.31%.............4.59%..............7.93%
Austria............14’671.........443.......14'671...........19'902................3.02%...........4.16%..............0.52%..............2.78%
Switzerland....27’404.......1’368.......17'100...........25'566................4.99%...........7.41%.............1.20%..............3.09%

It seems clear that, due to considerably less testing, Swedish cases are being detected later, typically when the patient presents to hospital with severe pneumonia, at which point the death rate is a terrifying 73.3%. Coupled with the very lax social distancing to date, this would also mean undetected community spread is likely much more prevalent, thus a sharply increasing case-load and belated, more persistent lockdown can be expected.

By contrast the latter two countries are well over the hump, the major difference between them being that Austria closed its border to Italy 2..3 days before Switzerland, and did so tighter.

Overall it is looking like Sweden's experiment will prove to be a spectacular failure and false economy.

[data from COVID19INFO.live and Worldometer]

 

[EVNow]

I’m repeating the cause for the high number of fatalities in Belgium: we count suspect deaths as covid-19 victims, while other countries only count confirmed cases.

This is not true. Almost every country now counts "probable" covid cases as well. Infact China made this change in Feb ! CDC in US did just this week. Most of the deaths in Italy have been at home.

ps : Changes in US Data following new CDC guidelines on "Case" and "Death" definition (April 14, 2020) - Worldometer

 

[N5329K]

ICYMI-- another report on antibody testing, this one from an Austrian town:

"A comprehensive test using rapid antibody tests unearths astonishing results in Ortisei these days. Almost 49 percent of the 456 St. Ulrichers tested have antibodies against Covid-19 .... That is almost 50 times the number in the official medical statistics."
(per Google translate)

https://www.stol.it/artikel/chronik/flaechendeckende-tests-in-st-ulrich

That’s in line with Stanford’s Santa Clara study, too.
Robin

 

[OPRCE]

The density of the population will have something to do with it:

Population per km2

Belgium: 379
Switzerland: 201
Portugal: 112
Netherlands: 413
Austria: 105
Sweden: 22
Norway: 17
Denmark: 135
Finland: 16

Some 80% of Sweden consists of uninhabitable mountain terrain covered by IKEA-trees. Most of the population is packed into a lowland coastal strip from Gothenburg to Stockholm, where the density is probably close to the Denmark figure.

 

[traxila]

That’s in line with Stanford’s Santa Clara study, too.
Robin

Two studies showing ridiculous amounts of antibodies in population in CA and Austria. Homeless study in Boston showing half with antibodies and all with no symptoms. Does anyone know what the hell is going on?

 

[Oil4AsphaultOnly]

i know we're not supposed to treat people's lives lightly, but some people are like a cancer and present themselves prominently as evidence for eugenics: Protesters Demand End to Lockdowns Across U.S.: “Fire Fauci!”

i'm referring to Alex Jones, not the pro-choice woman.

They emperil us all, by embracing their ignorance OVER the advice of experts.

 

[EinSV]

That’s in line with Stanford’s Santa Clara study, too.
Robin

Governor Cuomo says New York will perform massive antibody testing over the next week, and I think we'll start seeing a flood of antibody test results from around the world over the next week or two. Should be very informative.

Andrew Cuomo on Twitter

 

[Daniel in SD]

What else might have killed him this year if it hadn't been coronavirus (which hopefully does NOT actually kill him - he is off life support so that is good but ECMO cost him his leg), do you think?

This is something people miss when they only look at deaths. The hospitalization rate for 45-64 years olds in NYC is 0.58% divide that by the percentage of 45-64 year olds you think have been infected to get the true hospitalization rate (probably greater than 3%). People shouldn't downplay the seriousness of infection for people who aren't "playing with house money" as @dqd88 puts it.

 

[EVNow]

I don't understand the play here. Is the federal government trying to prevent Dem governed states from getting necessary equipment for political reasons ?

Maryn McKenna on Twitter

The chief executive of a MA hospital, outbid for PPE by the feds multiple times, cut a deal, paid extra, hired the trucks — and then was interrogated by the FBI and had to get his Congressperson to intervene to keep DHS from heisting the shipment.​

 

[jerry33]

I don't understand the play here. Is the federal government trying to prevent Dem governed states from getting necessary equipment for political reasons ?

Maryn McKenna on Twitter

The chief executive of a MA hospital, outbid for PPE by the feds multiple times, cut a deal, paid extra, hired the trucks — and then was interrogated by the FBI and had to get his Congressperson to intervene to keep DHS from heisting the shipment.​

It's called creating a fascist state. And they're doing pretty well at it.

 

[NikolaACDC]

i know we're not supposed to treat people's lives lightly, but some people are like a cancer and present themselves prominently as evidence for eugenics: Protesters Demand End to Lockdowns Across U.S.: “Fire Fauci!”

i'm referring to Alex Jones, not the pro-choice woman.

They emperil us all, by embracing their ignorance OVER the advice of experts.

For Alex Jones - and a lot of others - it's not ignorance. They make a lot of money with it.

 

[Daniel in SD]

ICYMI-- another report on antibody testing, this one from an Austrian town:

"A comprehensive test using rapid antibody tests unearths astonishing results in Ortisei these days. Almost 49 percent of the 456 St. Ulrichers tested have antibodies against Covid-19 .... That is almost 50 times the number in the official medical statistics."
(per Google translate)

https://www.stol.it/artikel/chronik/flaechendeckende-tests-in-st-ulrich

Maybe I'm missing something but google translate says two thirds of the people who tested positive had symptoms?
"The nationwide tests started last Tuesday. In the meantime - as of Friday evening - 456 St. Ulricher were tested, and almost half have antibodies. More than 2 thirds of those tested are between 20 and 59 years old. And an important detail on the side: Almost a third said they had no symptoms."
Obviously if you test people who have symptoms in a COVID-19 hot spot you're going to get a lot of positive results. This doesn't sound like a random sample at all.