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research sensitivity, specificity

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Marc Bevand
2020-06-10 20:35:36 -07:00
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@@ -26,7 +26,8 @@ Ages 0 to 199: 2428102 infected, 27121 deaths, 1.117% IFR
``` ```
The average IFR for Spain is **1.117%**. However the true IFR may be higher due The average IFR for Spain is **1.117%**. However the true IFR may be higher due
to right-censoring and under-reporting of deaths. to right-censoring, under-reporting of deaths, or low specificity of the serological test;
or the true IFR may be lower due to low sensitivity of the serological test.
The Spanish serological study remains the largest published study available to The Spanish serological study remains the largest published study available to
this day. The age-stratified IFR was calculated from three sources: this day. The age-stratified IFR was calculated from three sources:
@@ -52,6 +53,24 @@ was only available for 20 585 deaths, and was missing for 6 536 deaths.
We assume that these 6 536 deaths were distributed proportionally—not equally—among age We assume that these 6 536 deaths were distributed proportionally—not equally—among age
brackets, which seems to be a reasonable assumption. brackets, which seems to be a reasonable assumption.
Regarding the specificity of the commercial test used (COVID-19 IgG Rapid Test
Cassette by Zhejiang Orient Gene Biotech Co Ltd) we found various claims, all
100% or close, so no significant false positives are expected:
* 100% claimed by the manufacturer ([serosurvey][sero], page 3)
* 100% measured by the Ministry of Health ([serosurvey][sero], page 3)
* 99.2% measured by a [third-party][hoffman]
However the sensitivity is more uncertain:
* 97% claimed by the manufacturer ([serosurvey][sero], page 3)
* 79% measured by the Ministry of Health ([serosurvey][sero], page 3)
* 93.1% measured by a [third-party][hoffman]
So a false negative rate anywhere from 3% to 21% could be possible, and we
think it is premature to adjust IFR calculations given the exact sensitivity is
not known.
# Applying the age-stratified IFR to other countries # Applying the age-stratified IFR to other countries
The script `calc_ifr.py` is also able to apply the age-stratified IFR to The script `calc_ifr.py` is also able to apply the age-stratified IFR to
@@ -75,3 +94,4 @@ health, etc, so this estimate should be interpreted with caution.
[daily]: https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/documentos/Actualizacion_120_COVID-19.pdf [daily]: https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/documentos/Actualizacion_120_COVID-19.pdf
[dailyalt]: https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/documentos/Actualizacion_109_COVID-19.pdf [dailyalt]: https://www.mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/documentos/Actualizacion_109_COVID-19.pdf
[wpop]: https://worldpopulationreview.com/countries/spain-population/ [wpop]: https://worldpopulationreview.com/countries/spain-population/
[hoffman]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178815/