Atomsk's Sanakan Profile picture
Dec 22, 2020 51 tweets 39 min read Read on X
1/

Many COVID-19 contrarians, including those behind the Great Barrington Declaration, *still* cite John Ioannidis' inaccurate estimate of SARS-CoV-2's fatality rate.

So let's go over how atrocious Ioannidis' paper is.



web.archive.org/web/2020111809… Image
2/

Background:

When a virus infects u, your body increases production of proteins known as antibodies, which are usually specific to that virus.

So measuring antibodies lets u estimate who was infected, and from that the infection fatality rate (IFR).

institutefordiseasemodeling.github.io/nCoV-public/an… Image
3/

Ioannidis uses antibody (a.k.a. seroprevalence) studies to estimate the number of people infected with the virus SARS-CoV-2. He then calculates IFR by dividing the number of COVID-19 deaths by the number of infected people.

Ioannidis does this badly:
medrxiv.org/content/10.110… Image
5/

Ioannidis' paper gives a median IFR estimate of 0.27%, which he corrects to 0.23%. That's a low outlier.

"[..] 0.79% (95% credible interval, 0.68–0.92%) [...], with a median range of 0.24–1.49%"
nature.com/articles/s4158…



web.archive.org/web/2020121700… Image
6/

Beware when folks cherry-pick Ioannidis' outlier of ~0.23% as if its credible.

Public Health Agency of Sweden:
"Globally, it is estimated that 0.5–1 percent of those who are infected with COVID-19 die"
web.archive.org/web/2020103000…



sciencedirect.com/science/articl… Image
7/

Also beware of people who try to mislead you into thinking the World Health Organization agrees with Ioanndis' low IFR estimate, or with his claims that SARS-CoV-2 has an IFR similar to that of seasonal influenza.



October 12:
who.int/publications/m… Image
8/

The points above have been made before. So what will this thread add?

Well, I'll go through each of the 61 studies Ioannidis cites to support his IFR estimate, + show they don't adequately support his estimate.

A numbered list of the studies:
web.archive.org/web/2020111809… ImageImage
9/

Antibody studies can use a *representative* sample of the population to accurately estimate the number of infections. Otherwise, one could over-estimate the number of infections + under-estimate IFR.

Scientists know how to get representative samples.

sciencedirect.com/science/articl… Image
11/

Ioannidis mostly cites studies that use non-representative sampling. That causes him to over-estimate seroprevalence + thus under-estimate IFR.

Studies with non-representative sampling may be useful for other purposes, but not for estimating population-wide IFR.
12/

For instance, blood donor studies:

- under-sample older people, a population more likely to die of COVID-19
- include people who go outside to donate blood, + are thus more likely to interact with people and get infected



link.springer.com/article/10.100… Image
13/

So one can exclude the following blood donor studies from Ioannidis' list of 61 studies in part 8/:

9 studies:
11, 14, 17, 29, 33, 35, 44, 46, 61



Image
14/

Studies of leftover samples from hospital visitors are non-representative. For instance:

- one can get infected at a hospital (nosocomial infection)
- some visit hospitals due to concern they're infected with SARS-CoV-2



link.springer.com/article/10.100… Image
15/

So one can exclude the following 'residual sera / hospital visitors' studies from Ioannidis' list of 61 studies in part 8/:

13 studies:
2, 9, 23, 27, 30, 31, 36, 39, 40, 42, 47, 59, 60

academic.oup.com/cid/advance-ar…

academic.oup.com/cid/advance-ar… Image
16/

Volunteers who hear antibody testing is occurring, but were not targeted for testing by random selection, may ask to be tested because they think they're infected (ex: they have symptoms, known prior exposure to an infected person, etc.).

uoflnews.com/post/uofltoday… Image
17/

A similar problem occurs for studies with non-randomized (non-probabilistic) sampling steps after initial randomization.

Besides studies in part 18/, many of the other studies Ioannidis cites use non-targeted volunteers.



link.springer.com/article/10.100… Image
18/

So one can exclude the following 'non-targeted volunteers / non-probabilistic step' studies from Ioannidis' list of 61 studies in part 8/:

10 studies:
12, 13, 15, 34, 38, 48, 50-52, 54

rapidreviewscovid19.mitpress.mit.edu/pub/p6tto8hl/r… Image
19/

People in schools, workplaces, shoppers, etc. are not necessarily representative of the general population. For instance, they're socially interacting in a closed setting, increasing their risk of infection.



Image
20/

So one can exclude the following 'workplaces / schools / shops' studies from Ioannidis' list of 61 studies in part 8/:

6 studies:
10, 16, 19, 20, 22, 58



ncbi.nlm.nih.gov/pmc/articles/P… Image
21/

So out of 61 studies Ioannidis cites in part 8/, only 23 have at least decently representative sampling:

1, 3-5, 7, 8, 18, 21, 24-26, 28, 32, 37, 41, 43, 45, 49, 53, 55-57

(note: part 13/ should include 10 studies, not 9, since paper #6 is also blood donor study).
22/

But papers 4, 5, 7, + 8 should be dropped from IFR calculations, since they sample regions included in paper 3.

That leaves 19 papers.

Sampling the same region multiple times unfairly skews the results, as per collinearity.



who.int/bulletin/onlin… Image
23/

Paper 18 should be dropped, since it implies only ~365 infections, which is much too small a number to derive a robust IFR estimate.

It's telling that Ioannidis tried to infer an IFR of 0.00% from that.

wwwnc.cdc.gov/eid/article/26… Image
24/

Re: "It's telling that Ioannidis tried to infer an IFR of 0.00% from that."

Ioannidis states it's risky to draw inferences from a sample size of less than 500... but doesn't let that stop him from using ~365 infections to infer a low IFR.

who.int/bulletin/onlin… Image
25/

Paper 37 (Karachi, Pakistan) should also be dropped, because Ioannidis uses an unsound method of getting the COVID-19 deaths he applies in his IFR calculation.

medrxiv.org/content/10.110…
aku.edu/news/Pages/New…



who.int/bulletin/onlin… Image
26/

That leaves 16 studies:
1, 3, 21, 24-26, 28, 32, 41, 43, 45, 49, 53, 55-57

(note: part 21/ should read say "only 22", not "only 23")

That's barely a quarter of the 61 studies Ioannidis said supported his IFR estimate. But at least the studies are now of better quality.
27/

Yet problems remain.

Take the example of paper 3 (for Brazil). Months ago when I first saw what Ioannidis did with paper 3, I lost any remaining confidence I had in the credibility of his paper and in his IFR work in general



who.int/bulletin/onlin… Image
28/

Paper 3 stated an IFR of ~1.0%.

If Ioannidis' paper was really a *systematic* review, then he would have used that IFR to start with, as he did for some other studies he cited.

Instead Ioannidis was non-systematic + biased.



medrxiv.org/content/10.110… Image
29/

To avoid paper 3's larger stated IFR, Ioannidis invented a new calculation based on his misinterpretation of figure 3 from the paper. In doing so, he contradicted paper 3 and used reasoning that makes no sense.



who.int/bulletin/onlin… Image
30/

Suppose a country of 10,001,000 people contains:
- city X: 10,000,000 people
- ten other towns: 100 people per town

Obviously, X predominately determines the country's IFR. But Ioannidis' method gives the same weight to X as to one of the towns. 🤦‍♂️

medrxiv.org/content/10.110… Image
31/

There are other IFR calculation issues. For example, Ioannidis gives an uncorrected IFR of 0.45% for paper 43 for Geneva (see image on the right side in part 8/).

But co-authors of paper 43 later used the paper's data to calculate an IFR of 0.64%:
thelancet.com/journals/lanin… Image
32/

Addressing those obvious issues for papers 3 and 43 leaves one with the following median IFR from the 16 studies in part 26/:

~0.5%

Similar median IFR @GidMK showed previously, but now with the removal of residual sera studies, collinearity, etc.

Image
33/

This median estimate of ~0.5% would likely go up once one corrected other issues with Ioannidis's paper.

Some of these issues include:

- under-estimated COVID-19 deaths via right-censoring



thelancet.com/journals/lanin…

link.springer.com/article/10.100… Image
35/

- over-estimating seroprevalence for papers 21, 28, 49 (Gangelt, Guilan, Los Angeles), and papers 56 + 57 under-estimating seroprevalence by a smaller proportion



Image
36/

Take-home messages:

- Ioannidis predominately uses studies with non-representative sampling
- excluding the most non-representative studies doubles his IFR to ~0.5%
- correcting his other mistakes would most likely increase his stated IFR even more

37/

Re: "doubles [Ioannidis'] IFR to ~0.5%"

Ironic.



"Ioannidis told viewers that the virus has an “infection fatality rate that is in the same ballpark as seasonal influenza.”"
buzzfeednews.com/article/stepha…


who.int/publications/m… Image
38/

The difference between an IFR of ~0.6% and IFR of ~0.2% is 3X less COVID-19 deaths (with the same number of infections).

Ex: the USA now has ~320,000 reported COVID-19 deaths. IFR 3X lower would be ~213,000 more people alive



Image
39/

Alongside parts 5/ and 6/:
"[IFR in a typical low-income country:] 0.23% (0.14-0.42 [...]) [...].
[In a typical high income country:] 1.15% (0.78-1.79 [...])"
web.archive.org/web/2020110103…

From May, before move evidence on IFR:
[mdpi.com/2076-393X/8/2/…]
sciencedirect.com/science/articl… Image
40/

There are other oddities that individually wouldn't mean much, but taken together show Ioannidis is biased towards showing a lower IFR.

For example, he uses an 0.09% IFR for paper 26 in part 8/, when his source gives a higher value:

medrxiv.org/content/10.110… Image
41/

Similarly, Ioannidis gives an IFR on 0.28% for paper 21 in part 8/, even though his cited source gives a higher IFR.

In any event, his source likely under-estimates IFR by at least a factor of 4.




medrxiv.org/content/10.110… Image
42/

Ioannidis uses PCR results for paper 56, even though PCR-positive antibody-test-negative people would be less likely to die in time to be included in his IFR.

That allows him to reduce paper's 56's IFR from 1.67% to 0.91%.



medrxiv.org/content/10.110… Image
43/

And Ioannidis reports a 1.16% IFR for paper 45 from part 8/ (for England, without excluding nursing home deaths), while the source he cites gives an IFR of 1.43%.



medrxiv.org/content/10.110… Image
44/

Jay Bhattacharya uses Ioannidis' age-specific result to influence governments:

"For people 70 and over, the infection survival rate is 95%. For people under 70, it is 99.95%"
web.archive.org/web/2020120920…

^^^That doesn't hold up.



link.springer.com/article/10.100… Image
45/

Paper 37 has three phases of testing, occurring one after the other. Ioannidis knew of phases 1 and 2.

He left out phase 1, + gave phase 2 an IFR of 0.08%.




An update today rebuts that:

medrxiv.org/content/10.110… Image
47/

But population-wide IFR tends to be higher in:
- older countries
- places with a greater proportion of infections in older people

Accounting for that reveals an age-specific IFR higher than in Ioannidis' paper (see part 44/)



nejm.org/doi/suppl/10.1… Image
48/

The WHO publishing Ioannidis' paper in their journal doesn't mean they agree with him (ex: a journal can have 2 papers that contradict each other)

WHO officials endorse an IFR estimate >2X larger than Ioannidis' (see part 7/)


who.int/bulletin/discl… Image
49/

Below is a thread that uses the same method to analyze 4 other seroprevalence-based multi-country IFR estimates:

50/

The population fatality rate, or PFR (i.e. COVID-19 deaths per capita), should be less than IFR, since you can't have more people infected than actually exist.

Yet in at least 3 instances, Ioannidis gives 'corrected' IFRs that are less than PFR.

51/

Re: "Ioannidis gives 'corrected' IFRs that are less than PFR"

For the paper #'s in part 8/, with IFR listed before PFR:

#6
0.11% , 0.19%
transparencia.registrocivil.org.br/especial-covid

#46
0.07% , 0.15%
coronavirus.data.gov.uk/details/deaths…

#50
0.00% , 0.04%
coronavirus.jhu.edu/us-map

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Atomsk's Sanakan

Atomsk's Sanakan Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @AtomsksSanakan

Dec 9
@luckytran Bhattacharya' NIH nomination for 2025 is reminiscent of Scott Pruitt's EPA nomination for 2017:

Position a contrarian ideologue whose views contradict published evidence + expert assessments.

x.com/_johnbye/statu…
x.com/pjavidan/statu…

cnbc.com/2017/03/09/sco… Image
@luckytran In which Bhattacharya does the intellectual equivalent of claiming vaccine denialists are being unfairly persecuted because Andrew Wakefield's blog told him so

🤢

x.com/AlastairMcA30/…

x.com/AliNeitzelMD/s…
x.com/AtomsksSanakan… Image
@luckytran x.com/AtomsksSanakan…
x.com/AtomsksSanakan…

Bhattacharya, November 2020:

"What they're doing is focused protection, and you can see the result. The infection rates are going up in Sweden, but the death rates are not."
edhub.ama-assn.org/jn-learning/vi…

ourworldindata.org/explorers/covi… Image
Read 5 tweets
Nov 18
@luckytran No, 'focused protection' did not lead to herd immunity within 6 months in Florida.

"Florida, which adopted a focused-protection approach"
spiked-online.com/2021/08/02/the…

x.com/GidMK/status/1…

x.com/AtomsksSanakan…
x.com/AtomsksSanakan…

gbdeclaration.org/frequently-ask… Image
@luckytran When your main non-lockdown example... has a lockdown.

"announced a ban on public events of more than eight people"
web.archive.org/web/2020120111…

"upper secondary schools are again closing"
thelocal.se/20201203/swede…

x.com/DrKatrin_Rabie…

Bhattacharya:
gbdeclaration.org/frequently-ask… Image
Read 5 tweets
Nov 17
@luckytran Re: "Bhattacharya has spread disinformation on COVID"

You may want to support this claim, if you haven't already.

There are plenty of examples of him spreading misinformation.

For instance: on masking

x.com/AtomsksSanakan…
x.com/RobertoCast212…

jamanetwork.com/journals/jamap… Image
@luckytran Promoting obvious disinformation about China's COVID-19 policy.

x.com/ResidingCynic/…
x.com/doritmi/status…

web.archive.org/web/2022010218… Image
@luckytran Saying a majority of Indians had "natural immunity" when the real number was ~25%, weeks before India suffered a large COVID-19 wave

x.com/GYamey/status/…
x.com/AtomsksSanakan… Image
Read 28 tweets
Feb 23
71/J

I recently got a copy of Dr. Judith Curry's book without buying it myself.

Looking over it confirmed to me that it's largely misinformation.

I'll illustrate that by assessing its claims on COVID-19.

x.com/AtomsksSanakan…

"11.3.1 COVID-19"
amazon.com/Climate-Uncert… Image
72/J

To reiterate: Curry draws parallels between COVID-19 + climate change.

But some of the sources she cites suggest an ideologically convenient narrative misinformed her.

That becomes clearer when assessing her claims.

x.com/AtomsksSanakan…
x.com/AtomsksSanakan… Image
73/J

No mention of the misinformation she + other contrarians promoted, and which conflicted with knowledge advances by experts.

(8/J - 12/J, 32J - 36/J, 44/J, 45/J, 63/J, etc.)

x.com/AtomsksSanakan…
x.com/AtomsksSanakan…
x.com/AtomsksSanakan…
x.com/AtomsksSanakan… Image
Read 47 tweets
Feb 17
1/J

Dr. Judith Curry recommends people read at least the 45-page preview of her new book.

I did.

It's bad enough I wouldn't recommend buying the book.
It's largely contrarian conspiracist misinformation.




amazon.com/Climate-Uncert…
Image
Read 72 tweets
Aug 30, 2023
PapersOfTheDay

"Executive Summary to the Royal Society report “COVID-19: examining the effectiveness of non-pharmaceutical interventions”"


"Effectiveness of face masks for reducing transmission of SARS-CoV-2: [...]"
royalsocietypublishing.org/doi/10.1098/rs…
royalsocietypublishing.org/doi/10.1098/rs…
Jefferson + Heneghan don't like the papers.

Makes sense they wouldn't given their track record, especially Jefferson on the Cochrane mask review he led.







brownstone.org/articles/royal…



cochrane.org/news/statement…
Image
Read 5 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us!

:(