COVID-19 - Facts and Information Only Topic

[Hapless Bills Fan]

FDA authorizes first saliva test for diagnostic use under EUA from Rutgers University.  Will be available initially through hospitals and clinics associated with Rutgers:

https://www.nbcnewyork.com/news/national-international/us-clears-first-saliva-test-to-help-diagnose-new-virus/2372424/
https://www.rutgers.edu/news/new-rutgers-saliva-test-coronavirus-gets-fda-approval

 

This is huge, because anyone can collect a saliva sample from themselves.  The current regimen which requires a HCW to push a throat swab deep in your nasopharynx (no one can get it deep enough on their own).  The HCW must wear protective clothing since they're up-close-and-personal with your possibly virus containing schnoz, and proper isolation protocol requires a change of that clothing between tests to avoid potentially contaminating the next patient. 

 

In many places but especially right now the NYC area, the supply of protective gowns, masks, and special swabs limits the amount of testing performed.

It sounds as though the Rutgers group is going to try to work with large testing companies that have high throughput or rapid tests:
 

"Soon after the Rutgers-ADL team received notification from the FDA on Saturday, the White House’s COVID-19 testing task force called Brooks to offer congratulations and support and to ask about any specific hurdles to expanding testing and enabling other laboratories to benefit from the accomplishment.
 

Shortly after the White House call, the research team was contacted by chief executive officers of some of the world’s largest life sciences companies that are involved in COVID-19 testing.
 

“I have spoken with these companies’ leadership to not only share knowledge but to create opportunities for continuing to help innovate during this crisis,” Brooks said. “We will work closely with these new partners, the FDA and the White House task force to leverage everything Rutgers has to offer to not only help our community but also make a global impact.”

The University of Washington SCAN (Seattle Area Coronavirus Assessment Network) project has also been using at-home nasal swab testing under EUA for surveillance of covid-19 in the population.

 

15 hours ago, meazza said:

Wasn’t there already tests developed that didn’t require the swab? Abbott labs comes to mind.

 

As far as I know, the Abbott labs test just runs a nasal swab sample on its "ID Now" system, but if you have any links that's be great

 

7 hours ago, Nervous Guy said:

"The Abbott RealTime SARS-CoV-2 assay is a real-time (rt) reverse transcriptase (RT) polymerase chain reaction (PCR) test intended for the qualitative detection of nucleic acid from the SARS-CoV-2 in nasal swabs, self-collected at health care location or collected by a healthcare worker, nasopharyngeal (NP) and oropharyngeal (OP) swabs collected by a healthcare worker, from patients suspected of COVID-19 by their health care provider. "

 

https://www.molecular.abbott/us/en/products/infectious-disease/RealTime-SARS-CoV-2-Assay

 

Fair enough, but to my understanding, the FDA was not allowing nasal swabs with it here (in USA).  Nasopharangeal collected by a HCW or nothing was their view, with minor exceptions like the Seattle SCAN surveillance project.

 

The point is: allowing a saliva sample is big for testing scale up, assuming it works well.  (Even allowing a self-collected nasal swab would be big for testing scale up - again, assuming it works)

 

[Hapless Bills Fan]

Chinese study of covid-19 on items in hospital ward.  https://wwwnc.cdc.gov/eid/article/26/7/20-0885_article

 

Spoiler alert: a lot of covid-19 falls to the floor and gets tracked all over by shoes of staff working on covid-19 wards:
The rate of positivity was relatively high for floor swab samples (ICU 7/10, 70%; GW 2/13, 15.4%), perhaps because of gravity and air flow causing most virus droplets to float to the ground. In addition, as medical staff walk around the ward, the virus can be tracked all over the floor, as indicated by the 100% rate of positivity from the floor in the pharmacy, where there were no patients. Furthermore, half of the samples from the soles of the ICU medical staff shoes tested positive. Therefore, the soles of medical staff shoes might function as carriers

 

Also anything touched by staff hands:
The rate of positivity was also relatively high for the surface of the objects that were frequently touched by medical staff or patients (Tables 1, 2). The highest rates were for computer mice (ICU 6/8, 75%; GW 1/5, 20%), followed by trash cans (ICU 3/5, 60%; GW 0/8), sickbed handrails (ICU 6/14, 42.9%; GW 0/12), and doorknobs (GW 1/12, 8.3%). Sporadic positive results were obtained from sleeve cuffs and gloves of medical staff. These results suggest that medical staff should perform hand hygiene practices immediately after patient contact.

[Hapless Bills Fan]

6 hours ago, OldTimeAFLGuy said:

..Hap, how does your industry and similar scientific types deal with reports surfacing about multiple COVID-19 strains and mutations, with some purportedly more aggressive and more resistant than others?.....if this is the case, what do you folks concentrate on?......perhaps a BAD example, but the annual flu vaccine cannot cover ALL strains (not sure what the percentage is).....so do you concentrate on the more prevalent?......

 

The thing to understand about an RNA virus is that by its nature, it mutates constantly.  That's just the nature of the beast - RNA polymerase makes more errors than DNA polymerase (my shorthand is to say "RNA viruses are slobs").  That's the  way genomic epidemiology traces the virus around the world and figures out how long it's been circulating - by the mutations.  SARS-CoV2, the virus that causes covid-19 disease, has been tracked to mutate about 2x/month.   

Here's one of the tree maps produced by studying viral mutations:

 

Here's the Motherload:

https://nextstrain.org/ncov/global?f_country=USA

 

Here's a figure from a recent scientific paper that uses a phylogenetic tree of 160 of the 3957 genomes sequenced to date to identify 3 principle subtypes, A, B, and C.  The A and C subtypes are circulating in the Americas and Europe while the B subtype is more restricted to Asia (per paper).  Would their phylogenetic tree look less clear and show more subtypes if they included more than 5% of the current genomes?    The point is all the little dots (and all the little branches on the above trees) represent a different mutation, do you call them all strains?    ?‍♀️

 

Until/unless one identifies a functional difference (more virulent/ less virulent, more infectious/less infectious), it's clear as crystal mud.  Mutations that affect function are called "adaptive mutations" and so far we don't seem to be seeing them.

I don't know what is meant by "resistant" in this context.  One usually speaks of "resistant" in the context of resistance to therapeutic drugs, since we don't have drug therapies, hard to have resistance.

 

It's possible that the virus from some areas causes more severe disease but I don't think there's any clear evidence of that - difference in mortality seems so far more linked to demographics and presence of preexisting conditions like high blood pressure, diabetes, and so forth - as well as whether or not the hospitals are able to provide good care or are overwhelmed.  It's certainly possible but there hasn't been anything that's stuck out so far.

 

As far as vaccine development, there's a bit upthread of commentary from epidemiologist Trevor Bedford.  Fundamentally vaccines target the coat proteins - the spikey sticky-out bits.  Bedford points out that there are a handful of identified mutations in them.  So it would be necessary to ensure that antibodies against one coat protein cross-react against the variants of the coat protein.  This should be straightforward to test. 

 

If they don't cross-react, the usual strategy is to include different strains in the vaccine - Prevnar 13, the pneumoccocal conjugate vaccine, contains components to work against 13 different strains.  If that sounds like a much tougher development project, you're right.

A typical flu vaccine is trivalent (3 strains) or quadravalent (4 strains).  So if need be, a vaccine could encompass more than one strain of covid-19.

[Deranged Rhino]

 

[plenzmd1]

Maybe some hope for a therputic

 

https://www.usatoday.com/story/money/2020/04/17/remdesivir-coronavirus-drug-gilead-sciences-covid-19-treatment/5150793002/

[Edit: report on compassionate use of remdesevir outcomes in New England Journal of Medicine.  In contrast to some reports on other drugs, these were very sick people - 65% on ventilators or receiving ECMO.  Partial data read out from ongoing clinical trial in Chicago.]

[Hapless Bills Fan]

27 minutes ago, plenzmd1 said:

Hey @Hapless Bills Fan, help me out here if you will.

 

Testing aboard the Roosevelt implies about a 13% infected rate(600 out of 4800) , with 60% of those cases as of now being completely asymptomatic. I find that to be a good thing no? Implies many more may have had the infection, and if we can get massive anti body tests may help us fully open up sooner?

 

Am I looking at the wrong?

 

https://justthenews.com/politics-policy/coronavirus/uss-theodore-roosevelt-coronavirus-numbers-imply-higher-infection-rate

 

If 60% are fully asymptomatic, that would be a terrible thing as far as containment of the disease without really effective, thorough contact tracing and testing.

 

The ideal disease from a public health containment viewpoint, is one where people don't become infectious until they show symptoms, and when someone shows symptoms it knocks them flat so they stop running around making other people sick. 

 

As far as people being sick...let's say for example that 13% of the population of the US is infected right now (this is probably unrealistic, as an aircraft carrier is like the worst situation for spreading a contageous disease, and the population is selected to be young and healthy and less likely to show symptoms, but work with me). 

 

We are going to test everyone with an antibody test that has 95% specificity, meaning 95% of those tested are correctly identified as immune, and 5% have the test reacting to something else (a medication, antibodies to a different coronavirus, whatever).  This happens to be the reported specificity of the recent FDA-approved antibody test. 

 

Let's do some math.  13% of the US will test positive - 43 million people.

286 million people are negative.  But of those, 14 million will test positive even though they are not immune. 

57 million positive results, of which 43M are correct, and 14M are incorrect.

 

That means that if you or I are tested, and the test is positive, there's a 3 out of 4 chance that's a correct result, and a 1 in 4 chance that it's a false positive

There are also still 286 million susceptible people.

 

So I would say....probably not as good news as one might think. 

 

We still need to #testtraceisolate for actual success to contain the disease.

 

5 minutes ago, Gray Beard said:

Supposedly most young kids who get the virus are asymptomatic. Do you think the fact that the crew on a Navy ship consists largely of 20 year olds has something to do with the high percentage of asymptomatic cases?

 

as usual, thanks for your inputs, and I won’t be offended if you delete this comment.

 

I do think the age and the general health of the crew of a Navy ship has an influence on the number of asymptomatic cases.

Overall in the population S. Korea is now saying 20-25% asymptomatic - and they are doing a large amount of contact tracing and testing.

 

There are some studies that say higher though - Iceland I think tested everyone and says 50% asymptomatic.  I think one of the cruise ships was similar.

 

 

 

 

[Hapless Bills Fan]

On 4/13/2020 at 2:11 PM, Hapless Bills Fan said:

https://threadreaderapp.com/thread/1247609734896607232.html

 

Discussion by "my boi" virologist Trevor Bedford on estimating population prevalence of covid-19.  (I quote him a lot, because he kind of knows his stuff, and he puts it out there so that others can weigh in and correct if need be).

 

The "dream state" would be 50% of the population has actually had covid-19, in which case Jackpot! that's herd immunity.  Bottom line, Bedford doesn't think we're there, and here's why

 

Here's a report by the MRC estimating prevalence in Europe:

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-13-europe-npi-impact/ (summary)
https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-03-30-COVID19-Report-13.pdf (full thing)

 

Table from the above (note the error estimates):

 

Currently, the US has 560,891 cases of covid-19.

Bedford estimates

(note he uses the words "I guess", but the guess of a trained epidemiologist on his topic of expertise is not the same as my guess or your guess.  It would be more like the trained eye of a football scout estimating the foot speed of a prospect by eye vs. me doing it)

 

So Bedford's estimate would mean between 5.6M and 11.2M people in the US are actually infected: 1.7 - 3.4% of the population.

 

That's way short of what's needed for herd immunity.

 

Initial serology study of 3,000 people in Santa Clara, CA

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1

 

"The unadjusted prevalence of antibodies to SARS-CoV-2 in Santa Clara County was 1.5% (exact binomial 95CI 1.11-1.97%), and the population-weighted prevalence was 2.81% (95CI 2.24-3.37%). Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. "

 

Note that their estimate of population prevalence 2.5-4.2%  is not that far off Bedford's estimate 1.7-3.4% or the Imperial College estimates for most of Europe in the table above.

 

Again, this is far short of the ~50% of the population infected one needs for herd immunity.
 

18 hours ago, snafu said:

Are you looking at that in a nationwide sense?

What about *the* hotspot of NYC and surroundings?

Wouldnt that be better news for those folks, and not so much for areas of the country no so hard hit yet?

 

Nationwide sense.

Hotspot of NYC area: If you look at the Imperial College estimates for Spain and Italy, I would predict NYC would more closely resemble them with 10-15% estimate prevalence.   The Imperial College numbers give a huge range though (3.7% - 41%)

[Hapless Bills Fan]

6 minutes ago, snafu said:

Are you looking at that in a nationwide sense?

What about *the* hotspot of NYC and surroundings?

Wouldnt that be better news for those folks, and not so much for areas of the country no so hard hit yet?

 

Nationwide sense.

Hotspot of NYC area: If you look at the Imperial College estimates for Spain and Italy, I would predict NYC would more closely resemble them with 10-15% estimate prevalence.   The Imperial College numbers give a huge range though (3.7% - 41%)

[Magox]

20 minutes ago, Hapless Bills Fan said:

 

Initial serology study of 3,000 people in Santa Clara, CA

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1

 

"The unadjusted prevalence of antibodies to SARS-CoV-2 in Santa Clara County was 1.5% (exact binomial 95CI 1.11-1.97%), and the population-weighted prevalence was 2.81% (95CI 2.24-3.37%). Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. "

 

Note that their estimate of population prevalence 2.5-4.2%  is not that far off Bedford's estimate 1.7-3.4% or the Imperial College estimates for most of Europe in the table above.

 

Again, this is far short of the ~50% of the population infected one needs for herd immunity.

 

Correct, however If accurate it would show a mortality rate well below what was initially believed to be.  This would show somewhere between a .09% -.14% mortality rate which would be not that far off from the common flu.  But the Risk of lethality of the Virus wouldn’t any longer be so much the mortality rate but rather the rate of contagion which if this study is to be believed would be many multiples more than the flu.   And that would be the greater risk.

 

Of course this is just one small study but it does fall in line with the antibody study recently done in Germany.   I don’t believe the 25-50% asymptomatic assumptions that some of the health experts were stating will hold up.

[GottaRun]

Is this new or already responded to theory?  Not yet peer reviewed

https://www.mirror.co.uk/science/coronavirus-outbreak-started-september-british-21882200

 

"Researchers from the University of Cambridge have investigated the virus’ origin to calculate the likely date of the initial outbreak.

Their findings indicate that the outbreak in Wuhan occurred between September 13 and December 7.

Peter Forster, who led the study, said: “The virus may have mutated into its final ‘human-efficient’ form months ago, but stayed inside a bat or other animal or even human for several months without infecting other individuals.

“Then, it started infecting and spreading among humans between September 13 and December 7.”

 

"In the study, which is yet to be peer-reviewed, the researchers analysed coronavirus strains using a mathematical algorithm.

 

While the virus originated in bats, the scientists found hundreds of mutations between the original Sars-CoV-2 and the one first found in Wuhan.

Typically, a coronavirus usually acquires one mutation per month."

"According to the researchers, this indicates that the virus may have quietly been spreading in animals and humans for years, before reaching the form we see today.

Dr Forster said: “If I am pressed for an answer, I would say the original spread started more likely in southern China than in Wuhan.

“But proof can only come from analysing more bats, possibly other potential host animals, and preserved tissue samples in Chinese hospitals stored between September and December.

“This kind of research project would help us understand how the transmission happened, and help us prevent similar instances in the future.”

[Foxx]

43 minutes ago, Hapless Bills Fan said:

 

Initial serology study of 3,000 people in Santa Clara, CA

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1

 

"The unadjusted prevalence of antibodies to SARS-CoV-2 in Santa Clara County was 1.5% (exact binomial 95CI 1.11-1.97%), and the population-weighted prevalence was 2.81% (95CI 2.24-3.37%). Under the three scenarios for test performance characteristics, the population prevalence of COVID-19 in Santa Clara ranged from 2.49% (95CI 1.80-3.17%) to 4.16% (2.58-5.70%). These prevalence estimates represent a range between 48,000 and 81,000 people infected in Santa Clara County by early April, 50-85-fold more than the number of confirmed cases. "

 

Note that their estimate of population prevalence 2.5-4.2%  is not that far off Bedford's estimate 1.7-3.4% or the Imperial College estimates for most of Europe in the table above.

 

Again, this is far short of the ~50% of the population infected one needs for herd immunity.

and if the virus mutates enough, herd immunity is out the window, correct?

[Hapless Bills Fan]

1 minute ago, Foxx said:

and if the virus mutates enough, herd immunity is out the window, correct?

 

Yes, but....

If outbreaks are occurring regularly during mutation, usually people retain enough immunity to keep the disease from being as serious, and to keep the transmission somewhat in check. 

 

With the observed mutation rate, the estimates I've seen are that a vaccine developed (similarly herd immunity) is expected to be good for several years.

[OldTimeAFLGuy]

1 minute ago, Hapless Bills Fan said:

 

Yes, but....

If outbreaks are occurring regularly during mutation, usually people retain enough immunity to keep the disease from being as serious, and to keep the transmission somewhat in check. 

 

With the observed mutation rate, the estimates I've seen are that a vaccine developed (similarly herd immunity) is expected to be good for several years.

 

...are the mutation rates similar to, below or above other similar viruses?..............

[Hapless Bills Fan]

2 minutes ago, OldTimeAFLGuy said:

 

...are the mutation rates similar to, below or above other similar viruses?..............

 

As I understand it, a couple orders of magnitudes less than influenza.  Similar to other coronaviruses (common cold).

Apparently coronaviruses have some proofreading capability in their RNA polymerase, which influenza viruses lack.

Or so I've been told.

[Foxx]

4 minutes ago, Hapless Bills Fan said:

 

Yes, but....

If outbreaks are occurring regularly during mutation, usually people retain enough immunity to keep the disease from being as serious, and to keep the transmission somewhat in check. 

 

With the observed mutation rate, the estimates I've seen are that a vaccine developed (similarly herd immunity) is expected to be good for several years.

i understand.

 

because the standard flu mutates greatly, this is why a new flu vaccine is developed each and every year, to cover the expected dominate strain for that year. also, while it is generally thought that this particular coronavirus, COVID - 19 is slow to mutate, it is still possible for an unexpected wild leap, as can happen with any virus. 

[OldTimeAFLGuy]

9 minutes ago, Hapless Bills Fan said:

 

As I understand it, a couple orders of magnitudes less than influenza.  Similar to other coronaviruses (common cold).

Apparently coronaviruses have some proofreading capability in their RNA polymerase, which influenza viruses lack.

Or so I've been told.

...thank you ..

11 minutes ago, Hapless Bills Fan said:

 

As I understand it, a couple orders of magnitudes less than influenza.  Similar to other coronaviruses (common cold).

Apparently coronaviruses have some proofreading capability in their RNA polymerase, which influenza viruses lack.

Or so I've been told.

 

...so then despite being less, this is far more destructive, contagious and/or potentially fatal versus influenza mutations, especially with no vaccines yet, albeit one that addresses a nominal percentage of strains as in our regular flu seasons?.....

[Hapless Bills Fan]

1 hour ago, OldTimeAFLGuy said:

...thank you ..

 

...so then despite being less, this is far more destructive, contagious and/or potentially fatal versus influenza mutations, especially with no vaccines yet, albeit one that addresses a nominal percentage of strains as in our regular flu seasons?.....

 

Well, the mutation rate of the virus really doesn't have to do with how infectious it is (how easily it spreads), its morbidity (how many people it makes ill) or its mortality (how many people it kills). 

 

 

 

 

[plenzmd1]

hmm, 30% infection rate in this random study..granted in a highly dense location...i know @Hapless Bills Fan has explained why this may not be a good thing...but to me means mobidity rate is way less than we think..and we are closer to getting that herd immunity. Hapless, what number is considered "herd immunity"? Thanks

 

https://www.bostonglobe.com/2020/04/17/business/nearly-third-200-blood-samples-taken-chelsea-show-exposure-coronavirus/

 

33 minutes ago, Hapless Bills Fan said:

 

The number for "herd immunity" depends on the basic reproduction number, R0.  For R0=2, it's roughly 50%.  For R0=3, it's 60%. 

Early estimates for covid-19 R0 were 2.0-2.4 - I am searching for revised estimates based upon increasing learnings about # of asymptomatic patients.  It may be higher!

 

30% of folks walking around on the street, EXCLUDING anyone who had already tested positive by RT-PCR, is scary. 

Chelsea is a very densely populated area.  It's largely immigrants - 65% Latino - and many of them work in positions (health related fields) where they're considered essential and continuing to go to work (nursing home aides, cleaners in hospitals, stockers in grocery stores, that kind of thing) ?  I would assume those who were out walking about were disproportionately those who had to go someplace, like, to work........

 

Bear in mind that as the story points out, having a positive antibody response does not mean you are cured of the disease...many of these people may still be infectious.   

I don't understand why they did this: "To get Chelsea residents to participate in the study ― which included a questionnaire that was available in English, Spanish, and Portuguese — investigators allowed them to remain anonymous. But that meant none of the participants received the results of the blood tests."

 

Did the people really not WANT to know their results?  Or was this done because it was easier for the researchers?

[Hapless Bills Fan]

1 hour ago, plenzmd1 said:

hmm, 30% infection rate in this random study..granted in a highly dense location...i know @Hapless Bills Fan has explained why this may not be a good thing...but to me means mobidity rate is way less than we think..and we are closer to getting that herd immunity. Hapless, what number is considered "herd immunity"? Thanks

 

https://www.bostonglobe.com/2020/04/17/business/nearly-third-200-blood-samples-taken-chelsea-show-exposure-coronavirus/

 

 

So here's another one saying "Whoaoa, this may be way more prevalent!"
https://www.boston25news.com/news/cdc-reviewing-stunning-universal-testing-results-boston-homeless-shelter/Z253TFBO6RG4HCUAARBO4YWO64/?fbclid=IwAR0uHANXzsg28A2ireFpmH-36ZXvX8DUljGcYsGugMJjpYE_hXo8BjyHn2g
 

The Centers for Disease Control and Prevention is now “actively looking into” results from universal COVID-19 testing at Pine Street Inn homeless shelter.

The broad-scale testing took place at the shelter in Boston’s South End a week and a half ago because of a small cluster of cases there (per this link, 1 person + tracing others) Of the 397 people tested, 146 people tested positive. Not a single one had any symptoms.

That's 36% not symptomatic at the time of test. (the testing was performed in response to a known positive test; some of those tested may develop symptoms, just as some of the 30% positive antibody tests walking around Chelsea might have or might develop symptoms,  There's also the reported false positive 10% with the Biomedomics test used.

But yes, plenzmd1, to your point - the original ~15% seriously (hospital needed) ill and ~3-5% critically ill" estimates were derived from situations where only people reporting symptoms (and sometimes only a subset of them) were being tested and the early estimates were 1-2% truly asymptomatic, so if 20-30% of people are truly asymptomatic, the morbidity estimates would most certainly drop.

 

If my back-of-the-envelope is correct, 25% asymptomatic (say) would mean the true "seriously ill" % would be more like 11%, the true "critically ill" % would be more like 2-4%.  35% asymptomatic would mean the true "seriously ill" % would be more like 10%, true "critically ill" % would be more like 2-3%.

[Edit: it was pointed out to me I should add, if 40-60% of the population contracts the disease almost all at once, those would still be huge, hospital-capacity overwhelming numbers - 40% infection and 10% seriously would mean 13 million people seriously ill, 40% infection and 3% critically would mean 3.9 million critically ill]

Very very interested to see how further antibody testing results play out (along with everyone else)

 

 

 

 

[Hapless Bills Fan]

On 4/14/2020 at 6:42 PM, Limeaid said:

Wyoming reports first death, last of the 50 states.

https://www.usatoday.com/story/news/nation/2020/04/13/coronavirus-wyoming-first-death-last-state-mark-gordon/2987542001/

 

 

I'll tag this on here.  I believe it's been suggested that Wyoming may be one of the first states to re-open.  It's had 1 death caused by covid-19:  last state for that

Has just over 300 total cases.

https://www.washingtonpost.com/nation/2020/04/17/wyoming-coronavirus-parties/

 

a group of protesters showed up at the state capitol building Wednesday to demand that Gov. Mark Gordon (R) release a plan to reopen the economy, believing the covid-19 curve had been sufficiently flattened, as the Wyoming Tribune Eagle reported.

 

But Gordon said this week that it was too soon to lift restrictions. Since Wyoming was late to the outbreak compared to other states, he said, it will probably be late to its peak, too.

“If we ease up and fail to adhere to the guidance currently in place, if we think that this will turn off like a switch, we may not be ready to relax any restrictions,” he said. “If anyone thinks that simply easing restrictions currently in place will lead to an immediate return to normal, they need to think again."

Example of the frustrations:  They're trying to contain several flaring outbreaks, including an outbreak at a psychiatric hospital "Wyoming Behavioral Institute"

Mayor Steve Freel of Casper, Wyo had just watched a Facebook video of a party that took place over the weekend showing partygoers “flat-out thumbing their noses” at public health guidelines, he said. And what’s worse: The party was attended by a health-care worker with a pending coronavirus test. The health-care worker’s roommate, an employee at the Wyoming Behavioral Institute — home to one of the largest clusters of cases in Wyoming — had tested positive for the virus last Friday. So, because of evident exposure, the unidentified health-care worker then sought a covid-19 test on that same day.  But despite a self-quarantine recommendation, the worker decided to go to a party on Friday night, Freel said. On Saturday, the worker went to another party.  And finally, on Monday, Freel said the health-care worker got the test results back: positive for coronavirus.

So now, Public health officials were left scrambling to locate all the partygoers to get them in isolation as quickly as possible.

The governor's point is while they're dealing with rich folks jetting into Jackson Hole and three large clusters of cases that are spreading into the community (see HCW story above), Public Health officials realize they are vulnerable to a flare-up, despite the overall low case count:
 

"Mark Dowell, the county’s health officer, said Wednesday that the low number of statewide and county cases is likely deceiving, warning that it may be “easy to think it’s not that big a deal when it hasn’t destroyed your community.” But signs of community transmission are growing, as officials monitor at least three large clusters of coronavirus cases statewide. “We have not flattened any curve at all,” Dowell said."

I personally think the same is true of many areas with low case counts.  If they are dealing with isolated cases, the chances are very high that there is unrecognized community spread both giving rise to those cases and resulting from them.  If they are dealing with a known infection cluster or two, all it takes is one or two ijits flouting social distancing to propagate that cluster into the community, and if there aren't any distancing restrictions in place to contain the spread, off we go.

This story has at its root, a clear ijit - what maroon gets a covid-19 test because of a known positive roomie, then decides it's a smart notion to attend 2 parties while they wait for the result? but the point is, the spread could have as easily occurred through someone who shopped or ate in a restaurant or waited for a bus with the roomie before he was known positive.  That's the root public health problem with a disease which is NBD for many of the people who contract it.

 

[Hapless Bills Fan]

Vaccines.  I've seen a couple misleading headlines, so let's "bite the snake" and try to share understanding of the landscape.

https://www.nature.com/articles/d41573-020-00073-5

 

This figure does a pretty good job of explaining where some of the 115 vaccine candidates currently in development are:

This table does a pretty good job of summarizing the candidates that are actually in clinical trials to date. 

Some of it may read like gibberish, let me try to break it down simply:

-there is an "old school" of vaccine development, where either the virus itself is grown up then inactivated, or viral proteins are produced, purified, and chemically attached to "carrier" proteins.  Either option is mixed with an adjuvant, a chemical that helps boost immune response.  There's a lot of pharma development work at each step, but it's "tried and true"; pretty much every vaccine we have today uses one of these two options.

-there is a "new school" of vaccine development where RNA or DNA encoding a viral protein is packaged up and injected.  The idea is your body will use the injected RNA or DNA as a template and make the protein.  The protein will then be exposed on the surface of an antigen presenting cell (part of your immune system) and your body will have an immune response.  This is exciting technology because it requires much less development time, but it's far less proven.  I think there's a successful Zika virus vaccine for horses, and that's about it, despite a number of candidates being trialed.

-that's oversimplified, there are other players such as viral vectors serving as "delivery trucks" for the protein

 

You'll note that this table says the vaccines are all in "Phase I" clinical trials.  "Phase I" is a small study, designed to show safety in fit volunteers.  With a vaccine, it has the added benefit of being able to assess whether the vaccine has achieved an immune response, but it's not until the vaccine is proven safe and administered to a larger group which better matches the population to be vaccinated (elders, people who have health conditions, etc) and then that population is monitored for a while to see if a lasting immune response is produced, that we learn something.

 

There are a couple of vaccine candidates that are not described in the above article.  One is University of Oxford
http://www.ox.ac.uk/news/2020-03-27-oxford-covid-19-vaccine-programme-opens-clinical-trial-recruitment

https://techcrunch.com/2020/04/17/university-of-oxford-coronavirus-vaccine-trial-aims-to-have-500-people-in-testing-by-mid-may/

This is an adenovirus vaccine vector expressing a viral protein and serving as a "delivery truck"
 

In China, CanSino Biologicals seems to be working with something similar:
http://www.cansinotech.com/homes/article/show/56/153.html

Recently, there's been a lot of noise in the media from the Oxford group saying they could have a vaccine "available for general use by the fall".  I think what that means is, in the final stage of clinical studies - Phase III - and being manufactured.  But I think what people reading that think is that they'll be able to go to their doctor or pharmacist and roll up their sleeves, and that seems rather far-fetched even if they do steps in parallel and go ahead with building the large-scale manufacturing capacity at risk right now.  The human immune system just takes time to respond - sometimes takes a couple of doses - then it takes time to see if there will be an immune response and time to see if it lasts.  Then there are safety studies, looking at adverse events in the vaccinated population and carefully comparing them with unvaccinated controls.

 

This is a blog, but a pretty good job summarizing what's going on by pharma researcher Derek Lowe:

https://blogs.sciencemag.org/pipeline/archives/2020/04/15/coronavirus-vaccine-prospects

 

Two points Lowe makes:
"some things cannot be accelerated by any means known to humanity. The last point above, how long immunity lasts, is a big question for both people naturally infected by SARS-Cov2 and for those given a vaccine, and unfortunately there is no way to answer that one other than time, which is in short supply these days. The field provides many examples of vaccines whose protection has not held up as well as expected as the years went on. ....... we may end up with a first-round vaccine that doesn’t last as long as it might, but will provide enough immunity to do the job and provide cover for us to collect more data on an optimized candidate."
 

"that takes us to the second question for any new therapy: safety, and its balance with efficacy. This is an especially fraught question with any therapy that’s targeting the immune response, because the downsides are gigantic: a runaway immune reaction can disable someone for life or even kill them within minutes where they stand......

you can’t avoid the problem: the huge person-to-person variation in everyone’s immune system means that these severe events can never be ruled out at some low level if you’re dosing enough people.  Now you see the exact bind that vaccine development has always been in, because the whole point is to treat millions, even billions of people who are not currently sick, to protect them against disease while not doing more harm along the way by setting off the body’s fiercest and most alarming biological responses."

 

 

 

 

 

[ChevyVanMiller]

Sweden’s approach should be very interesting to study against what most of the rest of the world has done. In essence, they have stayed open, just encouraging the elderly to quarantine. To date, they have appreciable numbers of higher cases of Covoid commensurate with their population.

 

The officials there believe that the herd immunity that they will realize will make their gambit pay off. The WHO believes that they will experience a catastrophic increase in cases over the next few weeks. The results will certainly bolster one strategy or the other.

 

https://www.cnn.com/2020/04/10/europe/sweden-lockdown-turmp-intl/index.html

[OldTimeAFLGuy]

..looks like the Rochester NY division of Ortho Clinical Diagnostics had their antibody testing procedure approved by FDA/USDA.....

 

FDA approves test at Rochester lab for identifying coronavirus antibodies

By Jorge Fitz-Gibbon-NY Post

 

The US Food and Drug Administration has approved a coronavirus antibody test developed in a Rochester lab that could help scientists learn more about acquired immunity to the bug, according to a new report.

 

The test, developed by New Jersey-based Ortho Clinical Diagnostics at its upstate New York facility, allows researchers to help identify antibodies in the blood of patients who have been infected by COVID-19 and eventually recovered, NBC affiliate WHEC-TV in Rochester reported Wednesday.

 

“The test can help us understand acquired immunity,” the company said on its website.

 

https://nypost.com/2020/04/15/fda-approves-test-for-identifying-coronavirus-antibodies/

[mod edit: I went all over the links on their website looking for critical information: what does ortho claim the sensitivity and selectivity are for their test?  This matters.  If anyone knows, please LMK and I'll add.  A previously FDA approved test is 93% sensitivity (how many exposed people are correctly ID'd) and 95% selectivity (how many people who were not actually exposed get a negative test).  If 5% of the population is exposed and the whole population is tested, this would mean 50% of the people who get a positive test, have a false positive.]

[Hapless Bills Fan]

 

Plainly put.  Ask the labs to identify what they need.  Make a list.  Fill the list. 

 

This is a straightforward logistics and supply problem that is probably being repeated in every state in this country - the sort of thing that national public health resources were set up to overcome, the sort of thing the Defense Logistics Agency is supposed to be very good at.

[meazza]

https://www.latimes.com/california/story/2020-04-20/coronavirus-serology-testing-la-county
 

7 minutes ago, Hapless Bills Fan said:

 

So there's some good news/bad news here about this serology testing report in LA county.

 

The good news is that the LA study actually had a sample of people selected by a market research firm to be representative, not self-selected on Facebook and extrapolated to the whole county as was done in Santa Clara county.

 

The bad news is that it's a very small sample - you have to scroll down through the article to learn that the sample size was only 863 people.

 

News I don't know what to make of: the test used both by the Stanford study and this LA study is sold by Premier Biotech as described in the article, but Premier says it is made by a company called Hangzhou Biotest Biotech, imported from China, and not authorized for use by the FDA.   It is allowed to be used for research purposes under current US policy.  They claim they have validated the test and it has a 99.5% specificity (eg false positives 0.5% of the time).  Quality control etc are questions - some imported Chinese antibody tests that were used in Europe were found to have extremely variable QC.

 

OK, let's go back to those 863 people.  The result announced is 2.8-5.6% positives, meaning 24-48 people.  It would be helpful if the article mentioned the actual number of positives they obtained.  EDIT: OK I found USC's press release.  4.1%, or 35 people.  Hangzhou's stated specificity means expect 4 false positives; a real-world rate 98.1% sensitivity (the lower bound in the Stanford paper) would mean expect 17 false positives amoung 863 people. 

 

Bear this in mind when interpreting various antibody study results to come.

 

Extrapolating this small sample size to 220,000 or 440,000 residents of LA is a pretty big stretch because of the false positive question.  The take-home point is: we're talking about 3-6% of the population being immune, even in a significant outbreak area -  not 30% or 40% or 60%.

This is actually a pretty good match for the Imperial College model predicting prevelence in Europe, and not a bad match for the epidemiologist estimate that there are 10-20 more people infected than we're detecting - which would be about 160,000 people.

 

[Punching Bag]

Along with tax deadline and Treasury stimulus check here is another change due to COVID-19

 

While some will be dealing with medical bills others will be dealing with surplus in the medical flex accounts due to doctors, dentist, etc appointments being cancelled:

 

Quote

CARES Act

The Coronavirus Aid, Relief, and Economic Security Act (CARES Act) was recently signed into law. The Act brings an exciting change as it allows over-the-counter (OTC) drugs and medicines without a prescription (Rx) along with menstrual care products purchased on or after January 1, 2020 to be eligible for health savings account (HSA), flexible spending account (FSA), and health reimbursement arrangement (HRA) reimbursement.¹

 

[meazza]

4 hours ago, meazza said:

https://www.latimes.com/california/story/2020-04-20/coronavirus-serology-testing-la-county
 

 

But it also is positive news with regards to the mortality rate as it will be way lower than 1% even though the contagion rate is much higher.

[Hapless Bills Fan]

18 hours ago, meazza said:

But it also is positive news with regards to the mortality rate as it will be way lower than 1% even though the contagion rate is much higher.

 

I don't think that is at all clear yet.  It's very clear that the death rate will be far lower than the 4.5% case fatality rate LA is currently rocking, but I don't think anyone thought it would be that high.  It's not so clear when there's a larger sample size and more is known about the test, it's going to be "way lower than 1%".  It may be 0.5-1%. 

 

S. Korea, which has done extensive contact tracing and testing, is currently running about 2% on the case fatality rate. 

 

Issues with the study:

-It's extrapolating from 863 people, for one thing.  That's a pretty small number to extrapolate to 10 million people.

-Uncertainty in the test specificity (98% as Stanford gives as their lower bound with the same test? 99.5% as the mfr says? less?) mean uncertainty in the actual number of positives - 35 positives, of which 2 to 17 may be false positives (the higher number is 2% of 863).  In real life, 95% specificity would not be a shocker.

-Substantial number of hospitalized, seriously ill people of uncertain outcome

-All disease outbreaks tend to under-count relevant deaths at first - people who weren't tested and died, or died at home, or in a nursing home.  When the seasonal mortality is examined, there may be a shift.

 

From the article itself:

Paul Simon, chief science officer for Los Angeles County’s public health department, noted that the county was averaging 50 deaths from coronavirus a day, eclipsing cardiac disease as the top killer.  “If this mortality were to continue for the whole year — we hope it doesn’t, but if it did — COVID would be the leading cause of death in Los Angeles County,” Simon said.

 

The media and various "see it's not so bad!" sters are interpreting these studies that way, and the Stanford study explicitly tried to make that argument

But it's a big stretch at this point for reasons above.

 

8 hours ago, meazza said:

I see your points.  I’m being cautiously optimistic that the study is positive news since I’ve heard from a couple of podcasts that there have been other places such as in the Netherlands and in Germany where similar results were obtained.

 

I guess being cooped at home can make someone impatient.

 

A point to bear in mind is whatever the actual death rate may turn out to be when all the evidence is in...this is a disease that has overwhelmed the health care system if allowed to propagate unchecked.  It did so in Wuhan, China...it did so in Italy.....it did so in Spain...it did so in NYC....it may be doing so in Sapporo and Tokyo if we believe the BBC report

 

I see a lot on Twitter etc "see, the death rate is over exaggerated so we can open back up!". 

A lower death rate doesn't prevent overloaded hospitals and intensive cares if neither containment or mitigation measures are in place...a larger number of asymptomatic cases running about actually increases the difficulty of keeping the disease in check since one can't rely on feeling ill or fevers to keep folks home.

 

 

[Hapless Bills Fan]

Good news for people taking high blood pressure medications.  Fundamentally: while high blood pressure appears to be associated with poor outcomes from covid-19, taking medication to TREAT high blood pressure may be associated with lower risk of all-cause mortality. 

 

As noted up-thread, there is actually an ongoing clinical trial of at least one blood pressure med as a potential covid-19 therapeutic.

 

https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.120.317134

Association of Inpatient Use of Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers with Mortality Among Patients With Hypertension Hospitalized With COVID-19

Conclusions: Among hospitalized COVID-19 patients with hypertension, inpatient use of ACEI/ARB was associated with lower risk of all-cause mortality compared with ACEI/ARB non-users. While study interpretation needs to consider the potential for residual confounders, it is unlikely that in-hospital use of ACEI/ARB was associated with an increased mortality risk.

[Hapless Bills Fan]

Retrospective study on outcomes from 368 veterans treated for covid-19 at VA hospitals through April 11:

1) standard of care

2) hydroxychloroquine

3) hydroxychloroquine + azythromycin

 

Clinical endpoints clear and relevant:

1) death

2) need for mechanical ventilation

"Retrospective" means the study authors combed through the medical records of veterans already treated.  It's not the "gold standard", a formal double-blinded clinical trial, where the protocol is to try as hard as possible to randomize assignment to treatment or placebo group, and where the HCW caring for the patients don't know who is getting what.  It's been shown over and over again that in open-label studies, there can be effects that aren't due to the drugs. 

Still, it's not evidence of benefit for hydroxychloroquine with or without azythromycin.

From AP article about the study:
About 28% who were given hydroxychloroquine plus usual care died, versus 11% of those getting routine care alone. About 22% of those getting the drug plus azithromycin died too, but the difference between that group and usual care was not considered large enough to rule out other factors that could have affected survival.

Hydroxychloroquine made no difference in the need for a breathing machine, either.

[edit: there was a % difference, but their data crunching looking for confounding factors said not significant]

 

Researchers did not track side effects, but noted a hint that hydroxychloroquine might have damaged other organs. The drug has long been known to have potentially serious side effects, including altering the heartbeat in a way that could lead to sudden death.

Article from Forbes:
These findings highlight the importance of awaiting the results of ongoing prospective, randomized, controlled studies before widespread adoption of these drugs,” the researchers wrote.
 

Preprint of the article itself, if you roll that way:

https://www.medrxiv.org/.../2020.04.16.20065920v1.full.pdf

[Simon]

 

Thought this was an interesting interview with some thoughtful takeaways:

 

Michael Osterholm

 

Hap, feel free to relocate this if you think it's more appropriate for the other thread.

 

[I see no lies, but I do ask folks who want to discuss it to click on the time stamp in the upper left corner, copy the link you obtain, and carry it over to the discussion thread]
 

Excerpt with one of the best explanations of the testing problem.  It's just not about the phone numbers and addresses for labs!

For example, everybody wants to do widescale coronavirus testing today. Talking heads without any experience in testing declare, "We'll test millions of people each week, and then we'll know who is infected and can follow up." Very few people realize that the testing community in this country can't do that. We don't have adequate international manufacturing capacity and supply chains for reagents, the chemicals needed to run these tests.

The reagent capability -- meaning securing those chemicals that are key for running many of these tests, whether you're testing for virus or antibody -- before the pandemic was more or less, adequately supported by a "garden hose of production." Then Covid-19 came along and the Asian countries, specifically China, demanded a major increase in reagent supplies.
 

Finally, the whole world caught the pandemic, and now there are billions of people who need to be tested. We need a firehose to meet that demand but we can't build reagent manufacturing facilities overnight. I urge that whatever we do going forward has to be based on reality. We're not going to test your way out of this thing when we don't have tests.
 

(...) So, we're going to have this reagent issue for some time to come, and we must understand that and come up with a plan based on reality.
 

BERGEN: What is the role of the reagents in these tests?
 

OSTERHOLM: Reagents in the test are like the gasoline in a car. For example, if you take a nasal swab from a possible Covid-19 case, you have to extract specific material out of that swab. So, if you don't have the chemical reagent to do that, you can't run the test. You just can't have a swab and walk into a lab and say, "Test this." For each test, there are chemicals required to run it, and it varies by which kind of test you're talking about.

He doesn't mention, but a follow-on point: this is EXACTLY the sort of thing a NATIONWIDE public health response and national acts like the Defense Production Act were designed to address: Identify national needs (like the need for nasal swabs, or for test reagents, or for the chemicals needed to manufacture test reagents) and put national industry to work manufacturing what is needed.  As a nation, we have the planning and logistics skills to accomplish this, given the national mandate.  We also have a lot of unemployed or underemployed workers with good "people skills" who could be re-deployed as contact tracers, quarantine assistants, etc.

 

 

 

[BuffaLoko]

On 4/6/2020 at 3:51 PM, Hapless Bills Fan said:

Really good explanation from virologist Peter Kolchinsky of why covid-19 is a harder beast to fight than SARS was.

 

https://threadreaderapp.com/thread/1246975275021348865.html?fbclid=IwAR0fbXN74tI4gmZETIgRhNSuuk5KCEh3X0lG90w0Rnf9bjNx0IdoFvqOclE

 

"Well, the ACE2 doorknob that SARS-1 & SARS-2 use is present on a variety of cells, including those in our lungs & throat. SARS-1 would enter a person via a droplet in the air (from cough) & quickly start infecting lung cells, causing severe damage person could really feel (i.e. become symptomatic). In other words, SARS-1 quickly made its presence known. In some patients, SARS-1 would go into the upper airways to replicate from where it could spread to others with a cough (or just breathing). But b/c SARS-1 patients got very sick from all the virus replicating in their lungs, they were quarantined before others got close enough to get sneezed or coughed on.

 

SARS-2, on the other hand, takes up residence in the throat cells first, which doesn’t cause significant symptoms. The person can remain asymptomatic or might not think they have anything worse than a cold. And from that person’s throat it can readily spread to others. Over the course of a week, in some patients, it will move into the lung neighborhood and replicate just as SARS-1 would, causing severe symptoms, by which point the person is quarantined, but no matter since it had successfully spread."

"So SARS-1 was a comparatively dumb virus. It went straight for the lungs, announced itself before it could spread to others, and so got social distanced into extinction. "

 

"But SAR-2, the one plaguing us now, is stealthier, spreading first before revealing itself (and causing harm).  What’s the take-away for all of us? It’s that beating this virus means social distancing & wearing masks even if we think we aren’t infected. Because we might be. The virus might be replicating in our throats without us knowing (that’s its evil plan!), so put up a roadblock. "
 

Nature publication about study this info is based upon: https://www.nature.com/articles/s41586-020-2196-x

 

The very best explanation I have read (so far) about the cause of high rate of transmission from asymptomatic persons! 

[plenzmd1]

K, i don't know how to read this article correctlytly, our fearless leader @Hapless Bills Fan will need to show me where the below conclusions are stated in the pre print( which i have now learned has not been peer reviewed..correct?)

 

https://www.medrxiv.org/content/10.1101/2020.04.05.20051540v1

 

Anyway, this is synopsis of what i saw on CNBC with their CEO.

 

BioBot small starup that can analyse wastewater and understand where ceratin thisgs are happening..finding where opiod use is heavy for instance. CEO mentioned developing countires are using their tech to spot out breaks of polio before sysmptoms present.

 

Today, she said they did a study of Wastewater on a portion of the Boston area on March 25 showed in an area with 2.3M people, there could be upwards of 115,000 infected. At that same time, there was 446 confirmed cases of the virus.

 

WOW

Edited April 23, 2020 by plenzmd1

[Justin C]

https://www.cnn.com/2020/04/22/us/california-deaths-earliest-in-us/index.html

 

California is contributing 2 deaths to Coronavirus on February 6 and 17, before the 1st reported death on February 29. So there might be some merit to the suggestions this has been around spreading since January.

[Hapless Bills Fan]

9 hours ago, plenzmd1 said:

K, i don't know how to read this article correctlytly, our fearless leader @Hapless Bills Fan will need to show me where the below conclusions are stated in the pre print( which i have not learned has not been peer reviewed..correct?)

 

https://www.medrxiv.org/content/10.1101/2020.04.05.20051540v1

 

Anyway, this is synopsis of what i saw on CNBC with their CEO.

 

BioBot small starup that can analyse wastewater and understand where ceratin thisgs are happening..finding where opiod use is heavy for instance. CEO mentioned developing countires are using their tech to spot out breaks of polio before sysmptoms present.

 

Today, she said they did a study of Wastewater on a portion of the Boston area on March 25 showed in an area with 2.3M people, there could be upwards of 115,000 infected. At that same time, there was 446 confirmed cases of the virus.

 

WOW

 

So somewhere upthread, I must have found a preliminary report.  It seems pretty iron-clad that they were able to detect SARS-coV2 in the wastewater.  They point out that more work needs to be done to determine the lower limit of detection.  It seems as though this could be pretty useful to help communities monitor when they might have an undetected epidemic beginning to grow; it's a lot more efficient to monitor wastewater than to test a statistically significant number of people.

 

I think CNBC went for the most sensational interpretation.  The actual study acknowledges a lot of uncertainty.  In their abstract:
"Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of March 25. The reason for the discrepancy is not yet clear, however, and until further experiments are complete, these data do not necessarily indicate that clinical estimates are incorrect."

 

The big uncertainty, which the authors acknowledge, is how much virus is actually shed in a patient's stool.  They cite two studies with a range of 0.6M - 30M genomes/ml.  That would correspond to a range of 0.1% to 5% infections at the time the samples were collected. 

 

At the time the samples were collected, the known, confirmed infections represented 0.02% of the Boston area population.  So the lower bound suggests the actual infections were at least 5x higher than the tested, confirmed infections at the time.  This is not a surprise; for various reasons, epidemiologists have been estimating that in many places actual infections are likely to be running 10-20x the number of tested, confirmed infections.  If an area is testing enough that <5% of their tests are positive AND a significant number of positive tests are asymptomatic, they may be identifying most of the infections.

 

Anyway, I think it's potentially a helpful strategy to fight the epidemic, but there are too many uncertainties in their calculations (and possibly too much variance in how much virus infected people actually shed in their poo) to be quantitative at this point. 

 

37 minutes ago, plenzmd1 said:

Thank you @Hapless Bills Fan, will need to reread a couple times to understand , damn you scientists way smarter than us who sling software for a living ?

 

Oh, Hell no, not at all, reading those kind of papers is a learned skill like anything else a chap practices.  At programming, I am strictly a "hunter-gatherer. When I have a programming problem, I hunt down and gather up what relevant code I can find and start cobbling it together.  Then I yell that the project will fall behind schedule unless we get a real programmer assigned to it ?

 

[Hapless Bills Fan]

This is actually a pretty readable, well-written article on the state of treating covid-19 - though it breaks down into philosophizing at the end.

(I'm looking for a better choice, if you've got one put it there)

 

https://www.theatlantic.com/health/archive/2020/04/coronavirus-immune-response/610228/

[PetermansRedemption]

Thought this was pretty interesting today. 

 

[Edit: Fox news link downrated  Look, this Fox News story doesn't even have the link to the study nor much data though it includes links to all of Fox News NYC and covid-19 coverage.  That's Total BS, sorry.  Fox News is notorious for allowing misrepresentations (They allowed Gregory Rigono false claims to be an "advisor" at Stanford University to tout 100% cure rate of tiny study that excluded all the outcomes that died or went to ICU, for example.  Stanford had to publicly come out and say "No, he's not, and we had no part in that "study").  I'll deconstruct the Fox News coverage further on.]

I'm trying to use quotes to make clear who wrote what, hope I succeeded:
 

14 minutes ago, Hapless Bills Fan said:

OK Here we go:

https://time.com/5825485/coronavirus-risk-factors/

"In the new study, published in the Journal of the American Medical Association (JAMA), researchers wanted to learn more about people who are hospitalized after contracting the novel coronavirus. "

 

Here's the study itself (which is linked within the Time article so that anyone curious can go right to the source

 

Time put together a helpful graphical presentation :

 

What does this mean?  It's been known from the initial data out of China that hypertension, diabetes, and heart disease are significant comorbidities for covid-19.  Obesity was not, but obesity is apparently not (yet) such a problem in China (5-6% obesity rates there), so this is added info.  It's also been known that the risk for death from covid-19 rises sharply with age. 

 

At a high level, I think it means we see what China saw, with the clear addition of obesity in NYC (which is not such a health problem in China)

In the US (per 2017-2018 data), 42.2% of adults are obese.  At first glance I would say, oh, obesity not over-represented but whups! they separated out obesity and morbid obesity, total 60.7%.  So yeah, 60.7% of covid-19 patients vs. 42.2% population, it's a risk factor.

 

In the US, 46% of adults have hypertension rising to at least 63% over age 60.  So 53.1% hypertension is probably? a risk factor above incidence in the general population?  hard to tell. 

In the US, diabetes affects 10.5% of the population but 26.8% of those 65 yrs and older.  So again, overrepresented at 31.7%.

 

I wish the authors would say what the most common multiple co-morbidities are -  I couldn't find that.   I'm going to guess hypertension, obesity and type II diabetes since they often go together. 

On the surface, for the 2,634 patients with outcomes, it's quite grim: 14% in ICU,  21% died (Fox News doesn't report this, but that's a lot of people who died without ICU treatment - what's the story there?)  .12% of the hospitalized placed on ventilators, and of those 12%, 88% of them died. 

 

The first big thing that leaps out at me from the Outcome data is that only 2,634 of the 5,700 patients had an outcome as of publication (died or recovered and were discharged)  For the majority of the patients, that means the outcome is still pending - they're still hospitalized, perhaps some are still on vents.  They may live and be discharged; they may be placed on a ventilator; they may die.  That may change the grim outcome, one of two ways (better, or grimmer).  But it highlights how prolonged the hospital treatment can be for covid-19 patients.

 

What the authors want people and clinicians to take from this is if you contract covid-19: "We want patients with serious chronic disease to take a special precaution and to seek medical attention early, should they start showing signs and symptoms of being infected. That includes knowing that they’ve been exposed to someone who has this virus."

 

I'm actually a bit shocked by the mortality on ventilators.  If I recall correctly, China overall was something like 54% death rate for ventilated patients.  I'm concerned it may mean that the overwhelming number of patients meant that very sick people were being sent home instead of admitted, so that by the time patients returned and were admitted, it was kind of too late for the optimal outcome.

 

Last thing, here's an age range chart I threw together for hospital admits in NYC from the data link above.  It makes the case pretty clearly, I think, that just over 50% of all hospital admits are younger than 65 years of age.  Wouldn't we all love to know how the 45-64 yr range breaks down?

 

 

Fox News deconstruct:

 

4 hours ago, PetermansRedemption said:

Fox: https://www.foxnews.com/health/nearly-all-ny-coronavirus-patients-suffered-underlying-health-issue-study-finds

"A new study by a medical journal revealed that most of the people in New York City who were hospitalized due to coronavirus had one or more underlying health issues."

 

Hap sez: No, that is NOT what the study says.  Nowhere does it make that claim.  5,700 people is a fraction of those hospitalized in the NYC area.  Per this source, there have been 35,920.  So 5,700/35920 = 16%.  This hospital network self describes in the article as "the largest academic health system in New York".  Academic health systems (systems associated with medical schools) are sometimes called "tertiary care centers", meaning they typically get the sickest, most complicated cases that are referred from other hospitals.  So, we have to say "yes, there could be a selection for the sickest patients here".  Is the data from those 5,700 patients representative?  Maybe, maybe not - it's simply NOT a claim the study tries to make.

 

Quote

Health records from 5,700 patients hospitalized within the Northwell Health system -- which housed the most patients in the country throughout the pandemic -- showed that 94 percent of patients had more than one disease other than COVID-19, according to the Journal of the American Medical Association (JAMA).

 

Hap sez; The "94% more than one other disease" is correct. The "most patients in the country" is misleading - it makes it sound like this data is the majority of the covid-19 patients in the country.  Not even close, it's not even the majority in NYC!  It may be true that this hospital group has more patients compared to other hospital groups, but the wording is misleading.

 

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In addition, 42 percent of coronavirus patients who had body mass index (BMI) data on file suffered from obesity

 

Hap Sez: Again, technically true but misleading - it's actually 60.7% of covid-19 patients who suffer from obesity, because the authors separated obesity and morbid obesity (not coronavirus, that is also misleading, there are multiple coronaviruses known to infect humans).  I think this may be one of the biggest "news" in the article, because there just aren't that many obese people in China to know if it was a risk factor or not, and it clearly is. 

I don't need advanced statistics to say that 60.7% of covid-19 patients being obese overrepresents the 40.2% of US adults with obesity, while 42% (cited by Fox) vs 40.2% could just be random chance.  Basically, Fox is being careless here thus obscuring what may be one of the study's most important findings.

 

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The study also revealed that the overwhelming majority of patients who were on ventilators eventually died, and those who did more often had diabetes.  Data gathered from 2,634 patients who either died or were discharged from the hospital showed that 12 percent of them were placed on ventilators and of those who were, 88 percent of them died.

Hap sez: Once more: we have no idea what happened to the "majority of patients on ventilators" - they could still be on ventilators.  They correctly give the information that we only have outcomes for 316 patients on ventilators, of whom 278 died.  But there could be more patients who are still on ventilators, without an outcome - we don't know the outcomes for 3066 patients.  It's very careless writing at best.

Please, please please - if you choose to read Fox, please cross-check how that news is covered with another source than FOX.  At best, Fox is careless and misleading in how it presents data.  And that's if it's not outright allowing people to fabricate credentials and misrepresent stuff on-air.

 

[Sundancer]

https://www.nytimes.com/2020/04/23/nyregion/coronavirus-new-york-update.html?type=styln-live-updates&label=new york &index=1&action=click&module=Spotlight&pgtype=Homepage#link-1ac474b4

About 21 percent of people in New York City who were tested for coronavirus antibodies this week tested positive, Gov. Andrew M. Cuomo said on Thursday.

The surprising results come from a state program that randomly tested 3,000 supermarket customers across New York State. Nearly 14 percent of those tests came back positive, Mr. Cuomo said.
 

11 minutes ago, Hapless Bills Fan said:

 

Here's the link to the actual article about the test project

https://www.nytimes.com/2020/04/23/nyregion/coronavirus-antibodies-test-ny.html

 

Key quote:

In New York City, about 21 percent, or one of every five residents, tested positive for coronavirus antibodies during the state survey. The rate was 16.7 percent in Long Island, 11.7 percent in Westchester and Rockland Counties, and 3.6 percent in the rest of the state.

 

These results are, IMO, pretty aligned with the Imperial College predictions of 9-25% infection in Spain and Italy and 2-4% across most of Europe quoted upthread.  I think that NYC is more analogous to Spain or Italy (serious outbreaks) and Upstate more like Germany, etc

I'd like to see more about the study and about the test - a validated test will still have a false positive rate, and if the overall prevalence of infection is low, the false positives can be a significant % of the tests (again, explained in detail upthread).  For example, if the specificity is 99.5% - which is a durn good test - it means that in a group of 3000 tests, you will have 15 false positives.  Now if 21% of the population is testing positive, or 630 positives in 3000 tests, that's only ~2%  of your positive tests or no biggie.  But if 3.6% of the population is testing positive, or 108 positives in 3000 tests, that's 12%  (15/123) of your positives.

So 12 out of every 100 people you tell that they test positive, would have a false sense of security.

Here's the thing though, it's not uncommon for tests that are beauts in the lab (99.5% specificity) to have a bit higher false positive rate in the field due to cross-reacting with whatever - metabolites of the drugs the patient is taking, the fact that they had 4 coronavirus colds in the last 2 years, just "stuff".  So if the field specificity is 98%, and the prevelance is 3.6%, now you have 60 false positives in 3000 samples, and suddenly you're giving 36 out of 100 people the wrong gouge.

 

Just now, Limeaid said:

 

So would I. Like polls the key to the study is those chosen for test including locations.  The test is voluntary but unlike polls (like when they call me I give false answers) the results are not subjective other than who decides to volunteer for the test.  Was a good sample of supermarket and big box stores selected representing population?  I know as example in Washington DC there are very fewer supermarkets per people since many companies moved out after losses to riots.  

 

Edited April 23, 2020 by Hapless Bills Fan
merge responses

[ALF]

He was on a ventilator, fighting for his life. A stranger sent reinforcements

 

On the seventh night, they got some help: 11 ounces of gold-colored liquid from the veins of a stranger. A man who'd fought the same enemy and won.

 

 Because it's still an investigational treatment, the hospital needed permission from the FDA. They got it within hours. Now they just needed the plasma.

 

 He was looking for a plasma donor, because his friend was dying, and the donor had to meet all these requirements. A positive lab test for Covid-19. A compatible blood type. A full recovery from the disease, and so forth. He said he was looking for a needle in a haystack.

The man in Stuart texted him back: I'm your needle in the haystack.

 

https://www.cnn.com/2020/04/22/opinions/coronavirus-plasma-donor/index.html

[Hapless Bills Fan]

Good article about drug development strategies for covid-19.  Nothing "imminent breakthrough" but explains the strategies being used to search through known molecules for potential treatments:

https://www.scientificamerican.com/article/three-ways-to-make-coronavirus-drugs-in-a-hurry/