A Marm Kilpatrick Profile picture
Sep 29, 2020 5 tweets 2 min read Read on X
Specificity of antigen vs PCR-tests: data needed!
Many are understandably excited about the new rapid antigen tests. But there are a couple issues I haven't seen robust data on. Maybe you can help?
What is specificity of antigen tests vs PCR?
Thread
@michaelmina_lab
EUA (fda.gov/media/141570/d…) for BinaxNOW specificity (1-false +)=98.5% but:
- sample size is tiny (25 people submitting a total of 102 swabs from SYMPTOMATIC patients)
-95% CI (which should incorporate repeat testing & be analyzed as f(days since symptom onset) is: 92%-99.96%.
This means up to 8% (or more, if analysis done properly; totally unknown for asymptomatic people) of + antigen tests could be false +. If that's the case, these tests would be a disaster for screening people without reason to suspect they are infected (e.g. school kids).
EUAs often have tiny sample sizes, but millions of antigen tests have now been run. What is the real specificity (false +) w/ a reasonable sample size, how does it change vs days since symptom onset, & how does it compare to PCR specificity?
Speaking of which, what is specificity of PCR testing w/ 2 probes (e.g. CDC assay). I've again seen EUAs with tiny sample sizes often showing 100% specificity (on pre-pandemic samples), but haven't seen robust sample sizes. Can anyone help?

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More from @DiseaseEcology

Oct 29, 2022
How to mislead in science: hide raw data in supp material (SM).
Just had a dept-wide reading group of a recent Science paper on latitudinal/temperature trends in predation pressure (10.1126/science.abc4916). Paper claims simple clean patterns (fig) but where are the data???
Panel A (L) in main text. Raw data & regional analysis in SM. Paper makes simplistic & general claim: predation increases w/ Temp. But data tell v different story. Instead of clear increase in Bait Consumption w/ Temp, pattern is absent in 2/4 region, strong in 1/4, weak in 1/4.
Same for Fig 2B. Fig in main text (L) shows clean pattern. Actual data (R) show that pattern is mostly just in 1 type of animal (solitary tunicates) while other taxa show opposite pattern (Enc Bryozoans) or no pattern at all (most other taxa).
Read 14 tweets
Jun 23, 2022
COVID-19 vs Shark attack
There was a shark attack yesterday where I free dive frequently (abc7news.com/lovers-point-b…). A friend asked what's more dangerous, COVID-19 or swimming/free diving with sharks in the ocean?
Just for fun, here's a rough calculation.
tl;dr COVID-19 by a mile.
Chance of COVID-19 infection? Depends on many things: occupation, household size, behavior, exposure of household members etc. But in US roughly 60% of US has been exposed in last 2 years (webmd.com/lung/news/2022…). So crude estimate of yearly chance of infection 37%.
Chance of COVID-19 death given infection? Depends on age; for me, about 0.72%, pre-vaccination for the original SARS-CoV-2 variant.
So chance of infection & death ~1 in 375 pre-vaccination and 10-50x lower now (variant, vaccine doses, time since booster)
medrxiv.org/content/10.110… Image
Read 5 tweets
May 2, 2022
Why would Amazon workers vote against union & why aren't union dues progressive like taxes (i.e. lowest for lowest income)?
I've read several stories (nytimes.com/2022/05/02/tec…) about workers at 2nd Staten Island plant voting strongly against union but none of the articles say why.
Union dues would be $5/week for full time employees (amazonlaborunion.org), so if earning $15/hr, this is 0.33 hrs/week or 0.8% of salary which seems pretty cheap, & is even less than some large unions (e.g. Teamsters = 2.5 hr/mo or ~0.55hr/wk).
If union negotiated a 1% increase in pay that'd pay for union dues. That seems like a pretty low bar for a goal & doesn't include negotiating for better working conditions, etc. What are other reasons not to unionize or is it simply b/c of known cost & unknown benefits?
Read 5 tweets
Apr 19, 2022
Florida Manatees: doomed to extinction or actually doing pretty well?
A simple data analysis story.
Some of you may have seen this article in NYTimes 10d ago:
nytimes.com/2022/04/09/us/…
The article suggests Florida manatees are on their way out with quotes like this:
The perilous status of manatees is supported by claims like:
"In all of last year, 1,100 Florida manatees died, a record."
The article does acknowledge in some places manatees are doing better. But the overall tone is one of despair for a species on its way to extinction.
Read 15 tweets
Feb 8, 2022
#epitwitter
Need help w/ UK seroprevalence data
I recall previously seeing estimates of for SARS-CoV-2 infection for UK, but now I can only find estimates for exposure to spike protein which is infection OR vaccination (fig from
ons.gov.uk/peoplepopulati…)
but...
I want seroprevalence for infection so need data on antibodies to nucleocapsid protein or other non-spike protein. Does this exist?
I also can't find info on the response rate for survey. This page has response rates, but they are old (from July 2020) & they are very low (<15%). What is current response rate for serosurvey? ons.gov.uk/peoplepopulati…
Read 4 tweets
Feb 3, 2022
US COVID-19 deaths US >2000/day & continue to rise.
I can't help but wonder if focus on Omicron's mildness contributed to size of surge & deaths occurring now.
Difference in severity was small relative to higher infectiousness. Latter should have been singular focus of messaging.
Obviously it would have been far worse if omicron had been as severe as Delta. But focus on mildness of Omicron by scientists, media, government, CDC, etc. contributed to people being less safe than they should have & now thousands are dying/day & many more w/ long covid
Biggest failure, in my opinion, was lackluster efforts to roll out 3rd dose boosters, which played huge role in much smaller impact of Omicron on deaths in UK & elsewhere.
In US, many scientists argued against need for boosters, possibly b/c of global vaccine equity issues.
Read 7 tweets

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