• About

Sacred Cow Chips

Sacred Cow Chips

Tag Archives: Positivity Rate

Reformed Covid Reporting Might Quell the Omicron Panic

31 Friday Dec 2021

Posted by pnoetx in Coronavirus, Data Integrity

≈ Leave a comment

Tags

CARES Act, Covid-19, Delta Variant, Don Wolt, False Positives, Health and Human Services, HHS Protect, Jennifer Rubin, Monica Gandhi, Omicron Variant, PCR Test, Pediatric COVID, Phil Kerpen, Positivity Rate

That’s our Commander and Chief this week, posing in a mask on the beach in what is a phenomenal display of stupidity. More importantly, that kind of messaging contributes to the wholly unwarranted panic surrounding the Omicron variant of Covid-19. Panic, you say? Take a look at this admission from a New York health official. She says a recent alert on pediatric hospitalizations was driven by a desire to “motivate” parents to vaccinate their children. Yet Covid has never posed a significant risk to children. And take a look at what this insane physician posted. It’s fair to say he’s “catastrophizing”, an all too common psychological coping mechanism for alarmists.

The Omicrommon Cold

Given Omicron’s low apparent severity, it might be the variant that allows a return to normalcy. It’s perhaps the forefront of a more benign but endemic Covid, as it seems to be out-competing and displacing the far more dangerous Delta variant. In fact, Omicron infections are protective against Delta, probably for much longer than vaccines. The mild severity we’ve seen thus far is due in part to protection from vaccines and acquired immunity against breakthrough infections, but there’s more: there are plenty of non-breakthrough cases of Omicron, and most hospitalizations are among the unvaccinated. Yet we see this drastic decline in Florida’s ratio of ICU to hospital admissions (as well as a reduction in length of stay — not shown on chart). Similar patterns appear elsewhere. Omicron’s more rapid onset and course make it less likely that these patterns are caused by lags in the data.

Panic Begets Lockdowns

The frantic Omicron lunacy is driven partly by data on the number of new cases, which can be highly misleading as a guide to the real state of affairs. Testing is obviously necessary for diagnosis, but case totals as an emphasis of reporting have a way of feeding back to panic and destructive public policy: every wave brings surges in cases and the positivity rate prompting authoritarian measures with dubious benefits and significant harms (see here and here).

Flawed Case Data

In many respects, the data on Covid case totals have been flawed from the beginning, owing largely to regulators. At the outset in early 2020, there was a severe shortage in testing capacity due to the CDC’s delays in approving tests, as well as restrictions on testing by private labs. Many cases went undiagnosed, including a great many asymptomatic cases. The undercount of cases inflated the early case fatality rate (CFR). Subsequently, the FDA dithered in its reviews of low-cost, rapid, at-home tests. The latest revelation was the Administration’s decision in October to nix a large rollout of at-home tests. While the results of those tests are often unreported, they would have been helpful to individual decisions about seeking care and quarantining.

The PCR test finally distributed in March 2020 was often too sensitive, which the CDC has finally acknowledged, This is a flaw I’ve noted several times in the past. It led to false positives. Hospitals began testing all admitted patients, which was practical, and the hospitals were happy to do so given the financial rewards attendant to treating Covid patients under the CARES Act. However, it resulted in the counting of “incidental” Covid-positives: patients admitted with Covid, but not for Covid. That inflates apparent severity gleaned through measures like hospitalized cases, and it can distort counts of Covid fatalities and the CFR.

On balance, the bias caused by the test shortage at the start of the pandemic likely constrained total case counts, but the subsequent impact of testing practices is uncertain except for incidental hospitalized cases and the impact on counts of deaths.

Omicron Enlightenment

Omicron spreads rapidly, so the clamoring for tests by panicked consumers has resulted in another testing shortage, both for PCR tests and at-home tests at pharmacies. The shortage might not be relieved until the Omicron wave has crested, which could occur within a matter of a few weeks if the experience of South Africa and London are guides. In the meantime, another deleterious effect of the “case panic” is the crush of nervous individuals at emergency rooms presenting with relatively minor symptoms. Now more than ever, many of the cases identified at hospitals are incidental, particularly pediatric cases.

A thread by Monica Gandhi, and her recent article in the New York Times, makes the case that hospitalizations should be the primary focus of Covid reporting, rather than new cases. Quite apart from the inaccuracies of case counting and the mild symptoms experienced by most of those infected, Gandhi reasons that breakthrough infections so common with Omicron render case counts less relevant. That’s because high rates of vaccination (not to mention natural immunity from prior infections) reduce severity. Even Jennifer Rubin has taken this position, a complete reversal of her earlier case-count sanctimony.

Incidental Infections

Phil Kerpen’s reaction to Gandhi’s article was on point, however:

“Unless HHS Protect adds a primary [diagnosis] column, hospital census isn’t much more useful than cases.”

HHS Protect refers to the Health and Human Services public data hub. Without knowing whether Covid is the primary diagnosis at admission, we have no way of knowing whether the case is incidental. If Covid is the primary reason for admission, the infection is likely to be fairly severe. It is more useful to know both the number of patients hospitalized for Covid and tge number hospitalized for other conditions (incidentally with Covid). The distinction has been extremely important to those interpreting data from South Africa, where a high proportion of incidental admissions was a tip-off that Omicron is less severe than earlier variants.

The absence of such coding is similar to the confusion caused by the CDC’s decision early in pandemic to issue new guidance on the completion of death certificates when Covid is present or even suspected. A special exception was created at that time requiring all deaths involving primary or incidental Covid infections to be ruled as Covid deaths. This represented another terrible corruption of the data.

Summary

Earlier variants of Covid were extremely dangerous to the elderly, obese, and the immune-compromised. Yet public health authorities seemed to take every opportunity to mismanage the pandemic, including contradictory messaging and decisions that compromised the usefulness of data on the pandemic. But here we are with Omicron, which might well be the variant that spells the end of the deadly Covid waves, and the focus is still squarely on case counts, vaccine mandates, useless masking requirements, and President Brandon wearing a mask on the beach!

Case counts should certainly be available, as Gandhi goes to great lengths to emphasize. However, other metrics like hospitalizations are more reliable indicators of the current wave’s severity, especially if paired with information on primary diagnoses. Fortunately, there has been a very recent shift of interest to that kind of focus because the superior information content of reports from countries like South Africa and Denmark is too obvious. As Don Wolt marvels:

“Behold the sudden interest by the public health establishment in the “With/From” COVID distinction. While long an important & troubling issue for many who sought to understand the true impact of the virus, it was, until very recently, actively ignored by Fauci & crew.”

That change in emphasis would reduce the current sense of panic, partly by making it more difficult for the media to purvey scare stories and for authorities to justify draconian non-pharmaceutical interventions. It’s no exaggeration to say that anything that might keep the authoritarians at bay should be a public health priority.

False Positives, False Cases, False Deaths

14 Monday Sep 2020

Posted by pnoetx in Coronavirus, Pandemic

≈ Leave a comment

Tags

Andrew N. Cohen, Antibodies, Bruce Kessel, Coronavirus, COVID Deaths, Covid-19, False Negatives, False Positives, Infectious vs Infected, Michael G. Milgroom, NFL, PCR Tests, Positivity Rate, Rapid Tests, Seroprevalence, T-Cells, University of Arizona

The tremendous increase in testing for COVID-19 (C19) this summer was associated with an increase in cases. Most of these tests were so-called PCR tests with samples collected via deep nasal swabs. More testing did not fully explain the increased case load, but false positives (FPs) still accounted for a substantial share. That’s especially true in light of the decline in positivity rates, which reflected a decline in the actual prevalence of active infections. FPs also account for a substantial share of the deaths attributed to COVID, which are obviously cases of false attribution. If a test for C19 is positive, it will be listed on the death certificate.  

COVID Case Inflation

The exaggeration of confirmed cases due to FPs is more substantial as the prevalence of active infection declines. That’s because the share of true positives in the tested population declines, while the share of false positives must rise due to the greater share of uninfected individuals in the population.

Now, as the contagion is waning in former hot spots, there is a danger that FPs create the impression of persistence in the case counts. That’s costly not just for those incorrectly diagnosed, but also in terms of medical resources, for communities subject to excessive public intervention, such as inappropriate lockdowns, and in terms of the fear promoted by these inaccuracies.

FPs are extremely disruptive when testing is relied upon in critical situations such as health care staffing, or even among sports teams. For example, at the University of Arizona, out of 25 positive tests on September 3, only 10 were confirmed as positives in later tests. The NFL has also had its share of false positives. 

Lax Testing Standards

There is evidence that testing standards under CDC guidance are so broad that a large number of inactive, non-infectious cases are being flagged as positives (see the chart above for the intuition, as well as the graphic at the bottom of this post). The tests sometimes amount to a coin flip when it comes to evaluating positives; some of the positives might even come from non-novel coronaviruses such as the common cold! This paper by Andrew N. Cohen, Bruce Kessel, & Michael G. Milgroom – CKM) questions the guidance of public health authorities on testing more generally. From the abstract (my emphasis):

“Unlike previous epidemics, in addressing COVID-19 nearly all international health organizations and national health ministries have treated a single positive result from a PCR-based test as confirmation of infection, even in asymptomatic persons without any history of exposure. …  positive results in asymptomatic individuals that haven’t been confirmed by a second test should be considered suspect.”

False Positive Math

When I wrote about “The Scourge of False Positives” in July. I noted that a test specificity of 95% implies that 5% of uninfected individuals will falsely test positive. Unfortunately, that still produces a huge number of FPs when testing is broad. That’s NOT a good reason to avoid broad testing; it just means that positive tests should be confirmed by another test. (In this case, two tests with the same specificity reduce a 5% false positive rate to 0.25%. That’s why fast, cheap tests are necessary for confirmation.

Again, exaggerated case counts due to FP’s become more severe as a contagion wanes. That’s because FPs become an increasingly large share of positive test results and overstate the persistence of the virus. If active infections fall to 1% of 750,000 daily tests, or 7,500 true cases, the 5% specificity implies 37,125 FPs: true positives would be only 17% of positive cases. Much worse than a coin flip! And again, which cases are infectious?

How Bad Are FPs, Really?

This recent research, also authored by CKM, explains the reasons why FPs are usually an issue in the real world, despite the tests’ reportedly perfect reactivity to anything other than the virus’ genetic fragments. CKM find that the median FP rate in their sample of “tests of tests” was 2.3%. That means 23 out of every 1,000 uninfected people tested will test positive.

If that seems small to you, suppose the true prevalence of active infection in a population is 4%. If 1,000,000 people are tested and there are no false negatives (unlikely), then 40,000 infected people will be identified by the test. However, another 22,000 uninfected people will also test positive ((1,000,000 – 40,000 infected) x 0.023). That means the number of positive tests will be inflated by 55%. They’ll all receive some form of treatment or ordered into quarantine. Expanded Testing and FPs This summer, the volume of daily tests increased from about 150,000 a day in early April to more than 750,000 a day in July. That’s a 400% increase, but the true prevalence of active infection in the expanded test population during the summer was almost certainly lower than in the spring. Suppose active infections fell from 10% of the test population in the spring to 5% in the summer. That means the daily number of “true positives” would have risen from 15,000 to 35,000 in the expanded test population (and again I assume no false negatives for simplicity). The number of FPs, however, would have risen from 3,105 to 16,445. Therefore, FPs would have accounted for 40% of the increase in “confirmed” cases between spring and summer.

False COVID Deaths

FPs are also inflating COVID death counts. PCR tests are routinely given at hospital admission for any cause, and even after sudden death, especially as the availability of tests increased late in the spring. This subset of the tested population will certainly have its share of FPs. If such a patient dies, regardless of underlying cause, it might well be attributed to COVID-19 as it will still appear on the death certificate. The same has occurred in the case of traffic fatalities, suicides, and other sudden deaths.

Antibody Tests

The FP problem also plagues tests of seroprevalence, which determine whether an individual has had the virus or is cross-protected against the virus by antibodies acquired via non-novel coronavirus infections. The consequences of these antibody FPs can be serious as well, because it means a positive test might not ensure immunity. As the exposed share of the population increases, however, the FP share of antibody tests is diminished.

Conclusion

As long as testing is required, dealing with FPs (and false negatives, of course) requires repeated testing, as CKM state unequivocally. And the tests must be fast to be of any use. The current testing regime must be overhauled to prevent false positives from costly impositions on the lives of uninfected patients, consuming unnecessary medical resources, making unrealistic assessments of cases and deaths, and unnecessary suspensions of normal human social activity and liberty.

Follow Sacred Cow Chips on WordPress.com

Recent Posts

  • Interventionists Love You and Demand You Change, or Else
  • Let’s Suppress Fraudulent Votes
  • Fiscal Foolishness a Costly Salve For Midterm Jitters
  • Relax: Natural Variability Causes Heatwaves
  • The Vampiric Nature of “Stakeholder” Capitalism

Archives

  • August 2022
  • July 2022
  • June 2022
  • May 2022
  • April 2022
  • March 2022
  • February 2022
  • January 2022
  • December 2021
  • November 2021
  • October 2021
  • September 2021
  • August 2021
  • July 2021
  • June 2021
  • May 2021
  • April 2021
  • March 2021
  • February 2021
  • January 2021
  • December 2020
  • November 2020
  • October 2020
  • September 2020
  • August 2020
  • July 2020
  • June 2020
  • May 2020
  • April 2020
  • March 2020
  • February 2020
  • January 2020
  • December 2019
  • November 2019
  • October 2019
  • September 2019
  • August 2019
  • July 2019
  • June 2019
  • May 2019
  • April 2019
  • March 2019
  • February 2019
  • January 2019
  • December 2018
  • November 2018
  • October 2018
  • September 2018
  • August 2018
  • July 2018
  • June 2018
  • May 2018
  • April 2018
  • March 2018
  • February 2018
  • January 2018
  • December 2017
  • November 2017
  • October 2017
  • September 2017
  • August 2017
  • July 2017
  • June 2017
  • May 2017
  • April 2017
  • March 2017
  • February 2017
  • January 2017
  • December 2016
  • November 2016
  • October 2016
  • September 2016
  • August 2016
  • July 2016
  • June 2016
  • May 2016
  • April 2016
  • March 2016
  • February 2016
  • January 2016
  • December 2015
  • November 2015
  • October 2015
  • September 2015
  • August 2015
  • July 2015
  • June 2015
  • May 2015
  • April 2015
  • March 2015
  • February 2015
  • January 2015
  • December 2014
  • November 2014
  • October 2014
  • September 2014
  • August 2014
  • July 2014
  • June 2014
  • May 2014
  • April 2014
  • March 2014

Blogs I Follow

  • Passive Income Kickstart
  • OnlyFinance.net
  • TLC Cholesterol
  • Nintil
  • kendunning.net
  • DCWhispers.com
  • Hoong-Wai in the UK
  • Marginal REVOLUTION
  • CBS St. Louis
  • Watts Up With That?
  • Aussie Nationalist Blog
  • American Elephants
  • The View from Alexandria
  • The Gymnasium
  • A Force for Good
  • ARLIN REPORT...................walking this path together
  • Notes On Liberty
  • troymo
  • SUNDAY BLOG Stephanie Sievers
  • Miss Lou Acquiring Lore
  • Your Well Wisher Program
  • Objectivism In Depth
  • RobotEnomics
  • Orderstatistic
  • Paradigm Library

Blog at WordPress.com.

Passive Income Kickstart

OnlyFinance.net

Financial Matters!

TLC Cholesterol

Nintil

To estimate, compare, distinguish, discuss, and trace to its principal sources everything

kendunning.net

The future is ours to create.

DCWhispers.com

Hoong-Wai in the UK

A Commonwealth immigrant's perspective on the UK's public arena.

Marginal REVOLUTION

Small Steps Toward A Much Better World

CBS St. Louis

News, Sports, Weather, Traffic and St. Louis' Top Spots

Watts Up With That?

The world's most viewed site on global warming and climate change

Aussie Nationalist Blog

Commentary from a Paleoconservative and Nationalist perspective

American Elephants

Defending Life, Liberty and the Pursuit of Happiness

The View from Alexandria

In advanced civilizations the period loosely called Alexandrian is usually associated with flexible morals, perfunctory religion, populist standards and cosmopolitan tastes, feminism, exotic cults, and the rapid turnover of high and low fads---in short, a falling away (which is all that decadence means) from the strictness of traditional rules, embodied in character and inforced from within. -- Jacques Barzun

The Gymnasium

A place for reason, politics, economics, and faith steeped in the classical liberal tradition

A Force for Good

How economics, morality, and markets combine

ARLIN REPORT...................walking this path together

PERSPECTIVE FROM AN AGING SENIOR CITIZEN

Notes On Liberty

Spontaneous thoughts on a humble creed

troymo

SUNDAY BLOG Stephanie Sievers

Escaping the everyday life with photographs from my travels

Miss Lou Acquiring Lore

Gallery of Life...

Your Well Wisher Program

Attempt to solve commonly known problems…

Objectivism In Depth

Exploring Ayn Rand's revolutionary philosophy.

RobotEnomics

(A)n (I)ntelligent Future

Orderstatistic

Economics, chess and anything else on my mind.

Paradigm Library

OODA Looping

  • Follow Following
    • Sacred Cow Chips
    • Join 120 other followers
    • Already have a WordPress.com account? Log in now.
    • Sacred Cow Chips
    • Customize
    • Follow Following
    • Sign up
    • Log in
    • Report this content
    • View site in Reader
    • Manage subscriptions
    • Collapse this bar
 

Loading Comments...