A million #COVID19 cases

A grim milestone.

5.1% aggregate death rate.

On my iPhone at 3:41 EDT. The U.S. now accounts for nearly one-fourth of global cases. That proportion will only increase, likely for several more weeks. Data source, Johns Hopkins.

UPDATE: 24 HOURS LATER

Fatality rate now 5.4%
___

A Boston physician writes in The New Yorker,

This disease is different from what we typically see, and its severity has unsettled even our most experienced doctors. One man arrived and had to be intubated immediately; his blood-oxygen level, thirty-eight per cent, was the lowest any of us had ever seen. (Greater than ninety-five per cent is normal; eighty per cent is alarming.) We have seen other patients with levels in the sixties or seventies. Another patient’s levels plummeted to below twenty per cent in the few seconds it took us to connect him to a ventilator. Not long ago, one of our physicians started wearing a new fitness tracker that purports to measure stress levels; when it recognizes high stress, it vibrates and displays messages, like “Relax” and “Take a break.” During a recent shift, it buzzed almost continuously…

APRIL 3RD UPDATE: A HOSPITALIST REFLECTS

For many patients, a diagnosis of covid-19 carries with it a deep unease associated with the worst of maladies. It is not pneumonia, or diabetes, or even a heart attack; it is H.I.V. and cancer. They’ve heard the gruesome statistics on the news—the high death rates, the rapid rise in cases, the dwindling supply of needed resources. And there are few symptoms as troubling for patients as shortness of breath. With the coronavirus, the anxiety of labored breathing is exacerbated by the fact that it must be suffered alone, without friends and family and with limited contact with doctors. Among the cruellest aspects of covid-19 is the intense isolation that it inflicts…

I am sympathetic to those concerned about the widespread economic and social disruption created by aggressive social distancing, and to the political and business leaders asking whether it’s all worth it. But I think that if they saw what I see—the fear, the tears, the gasping for air, the destruction of bodies and psyches wrought by the virus, the daily contortions that doctors, nurses, and hospitals must make to provide even basic care—they, too, would understand that social distancing is the only option. They would feel what I feel: that we cannot return to normal during a time when thousands of Americans, of all ages and backgrounds, cannot breathe, and there aren’t enough people or supplies to help them...

MEANWHILE, BACK IN THE WHITE HOUSE

Donald Trump takes repeated emphatic pains to disclaim any responsibility for his initially indifferent, dismissively negligent reaction to the COVID19 pandemic: "It came from out of nowhere. No one could have foreseen it."

Right. Facts are inconvenient things.

Box 6: What Would the 1918 Influenza Pandemic Look Like Today?
In the worst pandemic in recorded history, the 1918 influenza pandemic, the novel virus infected approximately one-third of the global population over a period of 2 years, ultimately leading to 50 to 100 million deaths world-wide. One might imagine that the death rate would be lower today due to the advent of modern medical equipment and procedures that did not exist in 1918, but the global population is now approximately 4 times greater than in 1918. This growth, however, is disproportionately higher in low- and middle-income countries, often the ones with developing health systems. Many—predominantly in Africa, Southeast Asia, Latin America, and the Middle East—have experienced population growths of 1,000% or more since 1918. Crowded urban areas provide prime conditions for the spread of respiratory diseases, and urbanization is increasing globally, including the emergence of 47 “mega-cities” (populations over 10 million). By comparison, London was the world’s largest city in 1918, at approximately 5 million people. Additionally, global travel has increased by orders of magnitude compared to 1918. Even then, shipping and population movement (including World War I) played an important role in global spread of the disease, but today, humans can fly anywhere in the world in less than 1 incubation period, meaning that global transmission can be expected to be even faster.

In 1918, the global case fatality ratio is estimated to have been 2.5%, but it was considerably greater in low- and middle-income countries, with some estimates exceeding 10%. Today, some high-income countries would be expected to fare much better because of modern health care, but the case fatality in countries with limited access to healthcare could be as bad as or worse than 1918. Simple arithmetic would suggest the possibility of 100 to 400 million deaths if a 1918-like pandemic were to occur today, but unprepared or under-resourced health systems could further exacerbate disease transmission through nosocomial spread and an inability to promptly diagnose and render care, a particular concern for developing health systems. During the 2003 SARS epidemic, 72% and 55% of presumed and confirmed cases in Toronto and Taiwan, respectively, occurred as a result of healthcare transmission. A similar nosocomial outbreak in which healthcare facilities became amplifiers of the epidemic, this time of MERS, happened in South Korea in 2015. [Page 47 of 83]

Hat tip to Dr. Naomi Oreskes.
_____________

More to come...

Exponential Threat

A Trump re-election Super PAC has threatened SLAPP intimidation legal action and FCC license challenges to media airing this ad. Sue ME too. 

And sue The Guardian.

Everyone, pay it forward.
________

Novel Coronavirus pandemic screening assays: Laboratory QC issues.

APRIL 1ST UPDATE: I typically post 2-3 times a week, and Lord knows there are plenty of topics of interest and importance to move on to, but this Covid-19 pandemic issue is blotting out the sun these days. Per this "testing" topic below, there is now worrisome "crisis response theater" political pressure to waive FDA certification / regulatory standards to "get more test kits out there quickly." Bad idea. Accuracy matters.

I will be looking into your and your competitors' lab QA performance (e.g., @LABCORP). Do you publish your #coronavirus RT-PCR screening assays false positive/negative rates? https://t.co/H7zcyAWRuh

— Bobby Gladd (@BobbyGvegas) March 16, 2020

Yeah, right. I'm sure I'll get responses. Of course.

I first alluded to my technical concerns here. Accruing Hopkins real-time pandemic data here.

CLINICAL ASSAYS

You pee in a cup. You have a blood draw. You submit to having your nose or throat swabbed. You spit up some sputum into s vial, provide a stool sample. You undergo a biopsy, provide a hair sample, or blow into the breathalyzer. These specimens are then "tested" for their possible qualitative or quantitative "results" of pressing diagnostic (and subsequent treatment options) import.

If you assume the findings to be uniformly "accurate," you would be wrong. Not exactly news, yet repeatedly glossed over amid the throes of the crisis du jour.

The upshots of (always present) lab error risks have varying consequences. Some of them potentially quite adverse.

Note: should you accurately test "negative" for this virus, the result only holds for the date and time the specimen was collected. You could become infected with the pathogen at any time thereafter and subsequently be a "positive."

SOME DISCUSSION KEYWORDS OF INTEREST

Prevalence, Incidence, R0 ("R-naught"), Etiology, Sensitivity, Specificity, PPV, NPV, Bayesian Priors, Accuracy, Precision, False Positives, False Negatives, Cross-Reactivity, Coefficient of Variation (CV), Spikes, Blanks, Replicates, Matrices, Blinds, Reference Standards, Reagents, Chain of Custody, Cross-Contamination, Screening Test, Confirmation Test, Aliquot, Qualitative, Quantitative, Hockey Stick Curve, de minimus, LLD, RT-PCR (Real Time Polymerase Chain Reaction), CLIA...

That's enough for openers. Again, see my prior remarks.

THE RT-PCR ASSAY (now used to process coronavirus swab "test kits")

Pay attention to the workflow and technology used. This is not a litmus paper test. It's a DNA "amplification" assay (specifically RNA). It requires time, adequately trained lab workers, and QA-validated equipment and supplies.

UPDATE: from Scientific American on COVID19 testing.

Per The Daily Beast:

On New Year’s Eve, Chinese officials notified the World Health Organization that a new type of viral pneumonia was circulating in the city of Wuhan. Less than two weeks later, virologists published the entire genetic sequence of a new type of coronavirus from the same family of viruses that caused the SARS and MERS outbreaks.

That blueprint, or genome, provided an effective means of identifying the infectious agent, now officially called SARS-2-CoV, or the 2019 novel coronavirus. Within two weeks of the release of that critical information, another team, led by researchers in Berlin, published a diagnostic method. The test offered one means by which labs could collect throat or nasal swabs and screen for new cases of COVID-19, as the disease caused by the virus is called, based on isolating and amplifying a genetic signature specific to it.

The race was on as the WHO adopted the German-developed tests and distributed it to dozens of countries. But China, the United States, and several other countries developed their own ways to screen for a modern plague that has since infected over 200,000 people worldwide, including 6,500 people in all 50 states, causing at least 107 U.S. deaths...

So, right off the bat you're gonna need new "genetic signature" "reference standards" comprised of known quantities of the novel pathogen. Without these "controls" you have no way to determine the relative precision and accuracy of patient specimen outcomes (and the concomitant false positive and false negative error rates).

Again:

No clinical test is immune from error (particularly qualitative yes/no screening measures--especially newly rush-developed and deployed assays). And, error rates vary from worker to worker and lab to lab. Vigilant, consistently documented lab QC is neither easy nor cheap (pdf). Without it, you're flying blind.

Some other considerations: the quality (incl expiration dates) of the "reagent" chemicals used in specimen processing; the training and experience levels of the line lab staff; calibration of the analytical instruments, the specimen workload (sample overload raises a number of exigent risks, including workflow corner-cutting and fatigue errors, and elevated likelihood of cross-contamination).

I repeat:

WHAT DOES THE CDC SAY ABOUT THIS NEW COVID-19 TESTING?

Not much. Certainly not anything quantitatively specific pertaining to QC.

CDC has developed a new laboratory test kit for use in testing patient specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. The test kit is called the “Centers for Disease Control and Prevention (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel.” It is intended for use with the Applied Biosystems 7500 Fast DX Real-Time PCR Instrument with SDS 1.4 software. This test is intended for use with upper and lower respiratory specimens collected from persons who meet CDC criteria for COVID-19 testing. CDC’s test kit is intended for use by laboratories designated by CDC as qualified, and in the United States, certified under the Clinical Laboratory Improvement Amendments (CLIA) to perform high complexity tests.

On Monday, February 3, 2020, CDC submitted an Emergency Use Authorization (EUA) package to the U.S. Food and Drug Administration (FDA) in order to expedite FDA permitted use of the CDC diagnostic panel in the United States. The EUA process enables FDA to consider and authorize the use of unapproved, but potentially life-saving medical or diagnostic products during a public health emergency. The U.S. Secretary of Health and Human Services declared the SARS-CoV-2 virus a U.S. public health emergency on Friday, January 31, 2020. FDA issued the EUA on February 4, 2020. IRR began distribution of the test kits to states, but shortly thereafter performance issues were identified related to a problem in the manufacturing of one of the reagents which led to laboratories not being able to verify the test performance. CDC is remanufacturing the reagents with more robust quality control measures. New tests will be distributed once this issue has been addressed. CDC continues to perform initial and confirmatory testing.

I'd be wanting particulars addressing "robust quality control measures." Not that I'm likely to get much in response.

Below, different surveillance topic, same concerns.

If you remain asymptomatic (and don't meet CDC pre-screening criteria such as traced-contact or high prevalence area recent travel), you don't want to be screened for COVID-19. Think about the upshot of being a false positive. You could well be forcibly quarantined away from home on your own dime.

But, to be fair, I am by no means oblivious to plausible pushback, e.g., what if there is a significant sub-stratum of those who never evince clinical symptoms yet are nonetheless truly infected and (even if transiently) contagious: i.e., "vectors," asymptomatic "carriers?" How will we reliably estimate that prevalence?

One last observation here for now. There are thousands of other types of routine clinical lab tests in process every day, many of them of pressing importance, and all in need of uniform QC for effective dx accuracy and precision.

UPDATE: MORE TERMS

"R-naught"

Degrees of contagion exponentiality. For a different context see my 2006 post "Each one reach two."

Erratum: Psychiatric disease vectors.

UPDATE

This Is How We Can Beat the Coronavirus
Mitigation can buy us time, but only suppression can get us to where we need to be.

While many watched the coronavirus spread across the globe with disinterest for months, in the last week, most of us have finally realized it will disrupt our way of life. A recent analysis from Imperial College is now making some Americans, including many experts, panic. The report projects that 2.2 million people could die in the United States. But the analysis also provides reason for hope—suggesting a path forward to avoid the worst outcomes…

Very interesting article by two nationally esteemed clinician / scholars. Read all of it. They recommend mass screenings, for mandatory "suppression." My QA/QC concerns remain. I'm open to rebuttal.

MARCH 21 UPDATE

Serious long-read from The Atlantic.

The in-depth case for mass screening.

Some relevant words curiously not to be found in the article: Sensitivity, Specificity, Prevalence, QC, Quality Control, PPV, NPV, Error, Accuracy, Precision.

100% (or, "good enough, albeit unknown") testing reliability assumed, in light of the exigency.

ISSUES OF FRAUD

Coronavirus (COVID-19) Update: FDA Alerts Consumers About Unauthorized Fraudulent COVID-19 Test Kits

Yeah, that direct-to-consumer BS stuff is so predictable.

Much less well-known to the public is what we call Dry Labbing.

During my lab QC days in Oak Ridge in the 1980s, one of our commercial competitor facilities finally got busted after a year of "dry labbing"--discarding incoming EPA specimens, simply faking and reporting "results," and sending the invoices.  

More recently, anyone recall Theranos?

UPDATE

An excellent New Yorker article:

Why Widespread Coronavirus Testing Isn’t Coming Anytime Soon
By Robert P. Baird
March 24, 2020

…The clinical lab director expressed concern that granting regulatory authority to the states means that “we are now in the Wild West of laboratory regulation. It’s really a let-the-buyer-beware world. Essentially, apart from the F.D.A.’s E.U.A. process, there is very limited regulation of the quality, accuracy, and specificity of diagnostic tests for covid-19, and I think that’s a dangerous situation.” Bartkus, in Minnesota, said, “I will tell you, there is pressure to get these tests out: from the public, from the laboratories, from the politicians. It is a challenge to do that in a scientific and equitable way when you have no expertise in authorizing other labs to do testing.”

Read all of it. Goes beyond the scope of my concerns here, but, yeah.

MORE GREAT JOURNALISM

Everyone should read this comprehensive piece by Ed Yong:

How the Pandemic Will End
The U.S. may end up with the worst COVID-19 outbreak in the industrialized world. This is how it’s going to play out.

…the second pressing need: a massive rollout of COVID-19 tests. Those tests have been slow to arrive because of five separate shortages: of masks to protect people administering the tests; of nasopharyngeal swabs for collecting viral samples; of extraction kits for pulling the virus’s genetic material out of the samples; of chemical reagents that are part of those kits; and of trained people who can give the tests. Many of these shortages are, again, due to strained supply chains. The U.S. relies on three manufacturers for extraction reagents, providing redundancy in case any of them fails—but all of them failed in the face of unprecedented global demand…

Just a little snip bearing on my part of the "testing" topic.

UPDATE

Epidemic population screening test issues are just the tip of the iceberg. Click the title. Read all of it.

...The word “epidemiology” is derived from “epi” and “demos”—“above the people.” It is the science of aggregation, the science of the many. Yet it works most effectively when it moves in step with medicine, the science of the one. On the morning I visited the Shitala shrine in Kolkata, the goddess of bygone population-decimating epidemics was also serving as the personal goddess of a mother who had brought a child with a weeklong fever. To win the Kampf against covid-19, it’s essential to trace the course of the virus as it moves through populations. But it’s equally essential to measure its course within a single patient. The one becomes the many. Count both; both count.

 Siddhartha ROCKS!

AND, THERE'S MORE

From Bats to Human Lungs, the Evolution of a Coronavirus

For thousands of years, a parasite with no name lived happily among horseshoe bats in southern China. The bats had evolved to the point that they did not notice; they went about their nightly flights unbothered. One day, the parasite—an ancestor of the coronavirus, sars-CoV-2—had an opportunity to expand its realm. Perhaps it was a pangolin, the scaly anteater, an endangered species that is a victim of incessant wildlife trafficking and sold, often secretly, in live-animal markets throughout Southeast Asia and China. Or not. The genetic pathway remains unclear. But to survive in a new species, whatever it was, the virus had to mutate dramatically. It might even have taken a segment of a different coronavirus strain that already inhabited its new host, and morphed into a hybrid—a better, stronger version of itself, a pathogenic Everyman capable of thriving in diverse species. More recently, the coronavirus found a new species: ours. Perhaps a weary traveller rubbed his eyes, or scratched his nose, or was anxiously, unconsciously, biting his fingernails. One tiny, invisible blob of virus. One human face. And here we are, battling a global pandemic.

The world’s confirmed cases (those with a positive lab test for covid-19, the disease caused by sars-CoV-2) doubled in seven days, from nearly two hundred and thirteen thousand, on March 19th, to four hundred and sixty-seven thousand, on March 26th. Nearly twenty-one thousand people have died. The United States now has more confirmed cases than any country on earth, with more than eighty thousand on March 26th. These numbers are a fraction of the real, unknown total in this country and around the world, and the numbers will keep going up. Scientists behind a new study, published earlier this month in the journal Science, have found that for every confirmed case there are likely five to ten more people in the community with an undetected infection. This will likely remain the case. “The testing is not near adequate,” one of the study’s authors, Jeffrey Shaman, an environmental-health sciences professor at Columbia University, said…

ANOTHER, WAPO:

Three months into the pandemic, here is what we know about the coronavirus

CNN BREAKING NEWS

Can we trust that they have performed and submitted adequate QA?

APRIL 1ST UPDATE

The Atlantic. Excellent. Read all of it carefully.

Among other adverse possibilities, an incentive for "Dry Labbing."
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More to come...

#COVID19: Our National Emergency declares a National Emergency

Trump holding a Friday the 13th White House Rose Garden Presser starting at 3:30 pm. The "National Emergency" Devils will be in the details. I hope the media will do their jobs and be on the vigilant lookout for the inevitable Trump Swamp grift.

Developing story. Stay tuned.

Random stuff: Today I played my last day of pickup hoops for now at the Towson BYKOTA Senior Center. They've been ordered to close indefinitely by the Maryland Governor. The Towson YMCA I recently joined has closed indefinitely. The 2020 Baltimore Science Fair I've been involved with has been canceled. The nation is rapidly shutting down. NY Governor Cuomo warned today that we may be looking at a nationally massive 6-9 months' disruption. Many small businesses will quite likely fail.

News reports tonight show widespread panic shopping. I've not added to the problem, which could leave me SOL.

In light of all the imprecise Presser blather about coronavirus "testing," I will soon update my prior riff on lab QA. Myriad issues remain glossed over.

Weeks ago, the global mortality rate of COVID19 confirmed cases was 3.4%. Trump dismissively insisted that it was much lower than that, and would decline even further.

It is now slightly more than 3.7%, according to Hopkins data.

UPDATE

 

This is the scene at O’Hare airport. The traveler who took the photo said it’s a 6-hour wait for bags then on to customs for 2-4 more of waiting in shoulder-to-shoulder crowds. Police are handing out water and disinfectant wipes. @fly2ohare #ord #coronavirus #COVID19 pic.twitter.com/UTx9E0nj1s

— Brooke Geiger McDonald (@BrookeGMcDonald) March 15, 2020

SUNDAY MARCH 15

The paper goods shelves at my local Giant supermarket mid-day. The breads shelves were picked clean as well. Eggs were also all gone from the refrig dairy aisle, and elsewhere canned and dry goods were disappearing rapidly.

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More to come...

"Immunologically Naive Species" + Donald Trump = PANDUMBIC

Trump-hating WHO formally declares a global Pandemic

Trump and Pence are all outraged and butthurt because no one takes them seriously.

res ipsa loquitur

UPDATES

The global COVID19 mortality rate is increasing as the number of confirmed cases mounts. According to the latest Hopkins data, it's at 3.6%, up from 3.4%. Some assumed that as the denominator grew, the fatality rate would sharply decrease. Nope, not yet.

ANOTHER WILD NYSE DAY

BREAKING:

WASHINGTON (Reuters) - The White House has ordered federal health officials to treat top-level coronavirus meetings as classified, an unusual step that has restricted information and hampered the U.S. government’s response to the contagion, according to four Trump administration officials...

_____________#Pandumbic

More to come...

HIMSS20 and SXSW bug out. Is COVID-19 a "Force Majeure?"

 
Ouch. Wonder if they're insured, and if Force Majeure indemnity comes into play?

HIMSS is a roughly $100 million a year "non-profit" business (501c6), according to their latest available IRS 990. The annual conference is the Really Big Show in terms of their yearly gross revenue. This stand-down was a real shot below the waterline. One of many to come across the world economy and societies.

I am the ASQ 2020 Baltimore Science Fair volunteer lead. It may well have to be canceled or postponed.

I was fortunate to get press comps to cover the HIMSS events for a half-dozen years, ending in 2016. Great fun.

They had no choice here but to cancel. It was increasingly problematic.

Now Trump won't get to hold his little taxpayer-funded MAGA Rally "Keynote" on Monday. Small silver lining.

UPDATE

Hopkins COVID-19 link

Buckle up, folks.

UPDATE: ANOTHER ONE BITES THE DUST

ON DECK

Joyce White Vance is a well-known law professor at Alabama and former federal prosecutor. She's a frequent MSNBC panel contributor. I dig her, but she's way out of her lane here.

I cut my white-collar teeth in a forensic-level radioanalytical / mixed-waste lab (pdf) in Oak Ridge in the '80s, serving as a technical programmer and quality control (QC) analyst.

From January of 1986 through about May of 1991 I served under a series of personal services contracts with a laboratory owned by a major environmental engineering and remediation firm. We performed environmental and health physics support analyses for clients with radiation and mixed waste contamination and exposure problems (mixed waste is that which is composed of conventional chemical toxins and radionuclides). Since much of our work involved litigation support, we were trained to—and continually reminded of the need to—perform to forensic standards (i.e., to a quality level sufficient for our analytical results to stand up as viable evidence in court).

It was my job to develop, install, and maintain custom, procedure-specific software for use by the technicians in calculating radionuclide concentrations and dose exposures. I also worked on statistical quality control applications, applied research toward development of analytical correction factors, and helped write and subsequently administer our Software Quality Assurance procedure. While at this complex I worked amid much of the very same analytical technology (e.g., High Performance Liquid Chromatography, Gas Chromatography/Mass Spectrometry) also employed by drug testing labs, as much of our specimen workload consisted of urine samples suspected of contamination. I also learned just how difficult it can be to substantiate analytical results. We underwent frequent adversarial lab audits that would be the envy of a Spanish Inquisitor. I have been audited right down to my rounding algorithms…

Alluded to this work in my 1998 grad thesis. to wit:

 
While I am long since out to pasture, a lot of this standard QA/QC process knowledge is durable.

"Mass testing" for coronavirus is not "logical, sensible, & doable."

I'm reviewing the CDC tech specs and guidelines at the moment.

Stay tuned.

For now, consider a couple of items.

Lots to unpack there.

 

From another of my rants, this time on "Total Information Awareness."

While the relative "accuracy" (sensitivity & specificity) levels of many clinical methods that estimate disease probabilities (or any type of  experimental assay with anterior empirical underpinnings using Bayesian statistical methods [see below] ) are tolerably well-defined (and uniformly well below 99.9%), those pertaining to a TIA program are wholly speculative at this point, and will not clarify for years (if ever). One daunting limitation will come in the form of pervasively inaccurate and/or incomplete data pouring in from the myriad public and private sources. Another will owe to the relative recency and transience of the phenomenon. As Robert Levy of the Cato Institute observes: "Never mind that Pentagon computer scientists believe that terrorists could easily avoid detection, leaving bureaucrats with about 200 million dossiers on totally innocent Americans — instant access to e-mail, web surfing, and phone records, credit-card and banking transactions, prescription-drug purchases, travel data, and court records." (see www.nationalreview.com/comment/comment-levy112602.asp) I could not agree more. While the innocent will more or less simply go on with their customary daily life transactions, our terrorist enemies will undoubtedly take evasive measures. What shall we do? Outlaw, among other things, all anonymous cash transactions? If we don't (and we cannot) the very utility of a TIA database will be fatally compromised at the outset.

Given that no test is infallible, there are inescapable trade-offs in terms of relative false-positive/false negative levels associated with any assessment. For example, where routine workplace drug tests are concerned, labs seek to limit false positives (and the lawsuits they spawn), while they are far less troubled by false negatives (recreational drug users who slip through the screenings). With respect to terrorism, on the other hand, authorities will necessarily fret principally over false negatives -- actual terrorists who go undetected. Should you wrongly end up on a Homeland Security "No-Fly List" or be uselessly visited by a couple of FBI agents in the wake of a false positive TIA "hit", you will likely be met with bureaucratic indifference at best should you protest. At worst, you could be wrongly arrested, have your assets seized, lose your job, or otherwise have your reputation ruined.

For now, suffice it to assert that, if you are asymptomatic for COVID-19, you don't want to risk the severe personal upshot of turning up false positive.

CDC SCREENING CRITERIA

Criteria to Guide Evaluation of PUI (Patient Under Investigation) for COVID-19

"…Clinicians should use their judgment to determine if a patient has signs and symptoms compatible with COVID-19 and whether the patient should be tested. Decisions on which patients receive testing should be based on the local epidemiology of COVID-19, as well as the clinical course of illness. Most patients with confirmed COVID-19 have developed fever1 and/or symptoms of acute respiratory illness (e.g., cough, difficulty breathing). Clinicians are strongly encouraged to test for other causes of respiratory illness, including infections such as influenza.

Epidemiologic factors that may help guide decisions on whether to test include: any persons, including healthcare workers, who have had close contact with a laboratory-confirmed COVID-19 patient within 14 days of symptom onset, or a history of travel from affected geographic areas within 14 days of symptom onset…

Close contact is defined as—

a) being within approximately 6 feet (2 meters) of a COVID-19 case for a prolonged period of time; close contact can occur while caring for, living with, visiting, or sharing a healthcare waiting area or room with a COVID-19 case
– or –
b) having direct contact with infectious secretions of a COVID-19 case (e.g., being coughed on)

If such contact occurs while not wearing recommended personal protective equipment or PPE (e.g., gowns, gloves, NIOSH-certified disposable N95 respirator, eye protection), criteria for PUI consideration are met…"

Couple of quick observations here. First, the CDC guidelines are episodically updated, so they are (inescapably) in flux. Second, (inter-subjective albeit informed) "clinical judgment" will have to contend with mostly uninformed "political judgment" (read alarmist pandering).

So, right at the outset we have potential for individual and population results variability--the enemy of assay accuracy. More shortly.

SPECIMEN COLLECTION

Specimen Type and Priority
For initial diagnostic testing for COVID-19, CDC recommends collecting and testing upper respiratory (nasopharyngeal AND oropharyngeal swabs), and lower respiratory (sputum, if possible) for those patients with productive coughs. Induction of sputum is not recommended. Specimens should be collected as soon as possible once a PUI is identified, regardless of the time of symptom onset…

Earlier there was a reference to "serum" (blood samples), but that is not now on the CDC page. I'd be wanting to see stratified data minimally on relative sensitivity and specificity for both upper respiratory specimen types and the lower respiratory (sputum). Probably as yet to soon to get solid numbers there.

Consistency of specimen collection and handling will also be very important. For one thing, the risks of cross-contamination during collection, handling/shipment, and at the lab bench will require constant mitigation vigilance.

What of the manufacturing QA documentation of the test kits themselves? 'eh? After all, Trump never met a regulatory standard he didn't want to eliminate.

Once we get to the actual test kit production analyses (pdf), all the myriad QC risks (and documentation requirements) that apply to lab work generally most certainly apply here. These are not Playskool chemistry kit litmus paper tests.

A FINAL THOUGHT FOR NOW

These CDC tests are "qualitative," yielding simply either "positive" or "negative" findings. No quantitative estimate of "severity," i.e. "viral load." By contrast, if you test "positive" for illegal drugs via a workplace EMIT screen, it must be confirmed by a more accurate quantitative GC/MS lab technology. Warranted, in light of the adverse consequences of a positive finding.

Well, should you test positive on a COVID19 screen, you will be remanded to quarantine custody. absent any further confirmatory clinical assays. And probably on your own dime. What are you gonna do, sue?

Calls among antsy politicians are increasing for (vaguely specified) "mass testing." Bad idea.

Epidemic mortality rates are properly derived as "deaths / confirmed cases." You can disingenuously deflate the apparent rate by summarily changing the denominator to "PUIs tested" in the wake of mandating indiscriminate mass testing without pre-screening judgment criteria. Don't tell Trump.

ERRATUM: THE OAF OF OFFICE

President Trump at the CDC, prattling on in his 2020 re-election campaign "KAG" cap, and humbling praising himself for his scientific public health acumen (inherited from his late "great super genius" MIT physics professor uncle).

Here's Trump rambling at length about how smart he is and how well he understands public health pic.twitter.com/1Co6MaRkzl

— Aaron Rupar (@atrupar) March 6, 2020

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More to come...

President Trump to address "interoperability, innovation and digital health" at HIMSS20

Right. Seriously?

Let's get real, OK?

Another taxpayer-paid MAGA2020 Rally, co-opting HIMSS in Orlando. After which he will attend a Seminole County high-dollar donor re-election fundraiser dinner.

Trump's appearance will be the first time a sitting president has appeared at the event. His HIMSS20 speech is currently scheduled for Monday, March 9, at 4 p.m. in the Valencia Ballroom of the Orange County Convention Center.

HIMSS is getting willingly played. I seriously doubt Donald Trump can even pronounce "interoperability." interoperababble
SPEAKING OF PRESIDENTS

Protect yourself and your community from coronavirus with common sense precautions: wash your hands, stay home when sick and listen to the @CDCgov and local health authorities. Save the masks for health care workers. Let’s stay calm, listen to the experts, and follow the science.

— Barack Obama (@BarackObama) March 4, 2020

Indeed. Follow the science.

The dangerously flip ignorant recklessness is breathktaking.

UPDATE

BREAKING: #HIMSS2020 canceled. Coronavirus halts the conference where Trump was scheduled to speak. https://t.co/LIWwl6SwJS

— Erica Teichert (@eteichert) March 5, 2020

Following recent reports from the WHO and the CDC, it is clearly necessary to cancel #HIMSS20. More information and the official HIMSS statement are available here: https://t.co/vv5u6eO1d4.

— HIMSS (@HIMSS) March 5, 2020

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More to come...

Laurene Powell Jobs

“There’s been a significant breakdown in Americans’ ability to speak to one another and to hear one another. That’s become much worse in the last three years, where there’s been full license given to the otherization of our neighbor.” -- Laurene Powell Jobs

My wife just alerted me to the NY Times interview with Laurene Powell Jobs. My fabulous new grandson Calvin's fabulous Momma Eileen posted the above video on FB this morning.

"I'm Calvin, and I approved this message."

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I am reminded of another fine book in my stash that I cited a few years back, of some topical relevance to the foregoing:

TRIBALISM 
The most straightforward cause of strife on the new pastures is tribalism, the (often unapologetic) favoring of in-group members over out-group members. This is going to be a very short section, because there’s little doubt that humans have tribalistic tendencies that promote conflict. Insofar as there is a debate about our tribalistic tendencies, it’s not about whether we have them, but about why. In my view, the evidence strongly suggests that we have innate tribalistic tendencies. Once again, anthropological reports indicate that in-group favoritism and ethnocentrism are human universals. Young children identify and favor in-group members based on linguistic cues. Reaction-time tests (IATs) reveal widespread negative associations with out-group members in adults, children, and even monkeys. People readily favor in-group members over out-group members, even when the groups are arbitrarily defined and temporary. People readily replace racial classification schemes with alternative coalitional classification schemes, but they don’t do the same for classification by gender, as predicted by evolutionary accounts of human coalitional psychology. And there is a neurotransmitter, oxytocin, that makes people selectively favor in-group members. Finally, all biological accounts of the evolution of cooperation with non-kin involve favoring one’s cooperation partners (most or all of whom belong to one’s group) over others. Indeed, some mathematical models indicate that altruism within groups could not have evolved without hostility between groups.

In short, we appear to be tribalistic by nature, and, in any case, we are certainly tribalistic. This is bound to cause problems— though by no means insurmountable problems— when human groups attempt to live together. 

COOPERATION, ON WHAT TERMS? 
Tribalism makes it hard for groups to get along, but group-level selfishness is not the only obstacle. Cross-cultural studies reveal that different human groups have strikingly different ideas about the appropriate terms of cooperation, about what people should and should not expect from one another...

Greene, Joshua (2013-10-31). Moral Tribes: Emotion, Reason, and the Gap Between Us and Them (pp. 78-79). Penguin Group US. Kindle Edition.

Also goes to recent topical interests of mine such as "Deliberation Science."

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More to come...

COVID-19 "Pandemic?" Wall Street freaks out.

Click the Hopkins Coronavirus graphic to enlarge. Defintely spreading worldwide. Update of my prior post.

Whatever the actual current and likely projected severity of the virus impact, the panicky economic upshot has been significant this week. We've quit checking our IRAs. Probably down "on paper" about $35k at this point. Glad we don't need to take any distributions right now. Ugh. Below, DJI year-over-year as of Feb 28th 2020..

Again, whatever the present clinical / epidemiological severity of COVID-19 and I am not a virologist), the supply chains' disruptions are indisputably exigent and worsening. Irrational?

How a Coronavirus Case in Korea Instantly Hit a Small Business in the US
Everyone is trying to figure out how to get around the sudden hurdles.

A small US company that specializes in exporting US frozen and refrigerated food products to Asia, including to South Korea, suddenly got hit by the coronavirus-spread-prevention machinery that is now screwing up businesses around the globe, according to an employee who doesn’t want to be named – and doesn’t want the company to be named – because they’re not authorized to discuss the matter.

The person said that one of their customers in Korea had ordered some frozen product. The US company — let’s call it Company X — in turn ordered it from its supplier in the US, and the supplier shipped it to Company X’s freight forwarder’s cold storage location at a California port. The freight forwarder was waiting for the instructions to place the product in a refrigerated container and ship it to Korea.

Meanwhile, Company X tried to get the letter of credit from its customer in Korea. It won’t ship the product without a letter of credit. With a letter of credit, the buyer’s bank guarantees that the seller gets paid the correct amount on time. It’s a fundamental tool in international trade.

But the person then got an email from the Korean counterpart who explained that there was no letter of credit, that he tried to go to the bank to obtain the letter of credit, as he normally does, but that he couldn’t leave the office building to go to the bank because someone in the building had tested positive for the coronavirus. That was the first email…

Buckle up, folks. We're doin' a stockup CostCo run, making sure all of our meds supplies are adequate, and topping off the gas tanks.

Meanwhile, the President is off to South Carolina today to hold his latest MAGA Rally and brag some more about how great he is (UPDATE: And where he just called the COVID-19 outbreak severity a Democrat and media "hoax").

Wall Street continues its unprecedented vote of No Confidence in the lazy, bumbling Acting @POTUS @realDonaldTrump and his #PencePandemic. He should be re-impeached, for his existential incompetence. ... #COVID19 #coronavirus

— Bobby Gladd (@BobbyGvegas) February 28, 2020

No, I don't like him. Need one explain? Seriously?

Covid-19 Will Mark the End of Affluence Politics
The possibility of a global pandemic will reveal our inability to make and distribute the things people need—just in time for a presidential election.

On Tuesday, President Donald Trump dismissed concerns about Covid-19. As he put it, the virus is "under control" in the US and the “whole situation will start working out.” But according to Politico, Trump is privately voicing worries that the impact of the virus will undermine his chances of reelection. His panicked actions of late—including preventing an American from being treated in Alabama, at the request of a fearful Senator Richard Shelby—confirm that this virus is a political event of the first magnitude. While few in Washington have internalized it, the coronavirus is the biggest story in the world and is soon going to smash into our electoral politics in unpredictable ways.

…we will, in all likelihood, be locking down travel in some areas of the US for several weeks, as they did in China. People may be advised against gathering in large groups. It's not clear what any of this will mean for campaigning or primary voting, whether most of us will vote by mail or have our votes delayed.

Moreover, the coronavirus is going to introduce economic conditions with which few people in modern America are familiar: the prospect of shortages. After 25 years of offshoring and consolidation, we now rely on overseas production for just about everything. Now in the wake of the coronavirus, China has shut down much of its production; South Korea and Italy will shut down as well. Once the final imports from these countries have worked their way through the supply chains and hit our shores, it could be a while before we get more. This coronavirus will reveal, in other words, a crisis of production—and one that’s coming just in time for a presidential election.

Under the siren song of affluence, we began offshoring critical production capacity in the 1960s for geopolitical reasons. In 1971, economist Nicholas Kaldor noted that American financial policies were turning a "a nation of creative producers into a community of rentiers increasingly living on others, seeking gratification in ever more useless consumption, with all the debilitating effects of the bread and circuses of imperial Rome." Still, Bill Clinton and George Bush accelerated this trend throughout the 1990s and 2000s.

Affluence politics is not the politics of being wealthy, though, but rather the politics of not paying attention to what creates wealth in the first place. That is to say, it’s the politics of ignoring our ability to make and distribute the things people need. With the banking collapse in 2008, the election of Trump in 2016 and his mourning of empty factories, and now with Bernie Sanders dominating the early primaries, that era may at last be passing. A pandemic disease outbreak would only hasten this progression and force us back into the politics of production.

With potential shortages of goods, and restrictions on people’s movement, both parties are heading into unknown territory. It is likely Democrats will use this opportunity to further their case for Medicare for All. Pandemic surveillance and medical bureaucracies focused on billing do not mix well—stories about astronomical out-of-pocket costs for Covid-19 testing are already circulating. Republicans are likely to take a more xenophobic approach, emphasizing restrictions on foreigners and infected Americans. When it comes to managing shortages, however, both parties are split, just as they were in 1932, between their Wall Street factions that assume affluence and the less mature populist factions that seek assertive public power…

"Is there gas in the car? Yes, there's gas in the car..."

Erratum: I'm the local ASQ Volunteer Coordinator for the 2020 Baltimore Science Fair, 3 weeks out. Just emailed them to inquire as to whether they have a COVID-19 contingency plan.

UPDATE

Four Reasons Why the Coronavirus Is Such a Terrifying Economic Menace

The financial markets plunged into a state of abject panic this week, thanks to the novel coronavirus. As the rising number of COVID-19 cases fanned fears that a recession could be on the way, stocks fell at record speed. Investors also piled into government bonds, sending yields to new lows, a sign that the world’s money guys are desperate for safe bets as the possibility of a true pandemic becomes real.

Why is the coronavirus such a menacing economic threat?…

'eh?

Amazon blurb:

"Here is a volume that should be required reading for policy makers and health professionals." - Kirkus Reviews

After four decades of assuming that the conquest of all infectous diseases was imminent, people on all continents now find themselves besieged by AIDS, drug-resistant tuberculosis, cholera that defies chlorine water treatment, and exotic viruses that can kill in a matter of hours. 

Based on extensive interviews with leading experts in virology, molecular biology, disease ecology and medicine, as well as field research in sub-Saharan Africa, Western Europe, Central America and the United States, The Coming Plague takes readers from the savannas of eastern Bolivia to the rain forests of northern Zaire on a harrowing, fifty year journey through our battles with the microbes, and tells us what must be done to prevent the coming plague.

CODA

Wocka, wocka. I'm sure the brewer is not amused. Reports are that Corona beer sales are down 35%.
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More to come...