True prevalence estimator using probabilistic programming

Copyright: Viktor Senderov and Savina Stoitsova, 2020 Email: [email protected] Licence: Apache Licence v2.0, 2020

This WebPPL script estimates true prevalence of something (e.g. a disease) based on a survey using a testing procedure whose specificity and sensitivity are known.

Web interface

Use directly in the web.

Manual usage

1. Open source code.
2. Paste source code in https://webppl.org.
3. Set sensitivity and specifity, as well as survey results by editting the INPUT section.
4. Run the script in your browser by clicking run.

Validation

The script has been validated against four epidemiological studies on Covid-19. Our performance is comparabale to the performance in the studies.

Study	Sensitivity (θ+)	Specificity (θ-)	Crude seropr.	Adj. seropr.(study)	Adj. seropr. (prevestim)	Ref
Santa Clara	0.828	0.995	1.5%	1.2%	1.18%	[1]
LA unweighted	0.827	0.995	4.06%	4.34%	4.27%	[2]
LA weighted	0.827	0.995	4.31%	4.65%	4.56%	[2]
Denmark	0.830	0.9954	1.8%	1.7%	1.631%	[3]
Gangelt IgA	1	0.912	18.5%	10.63%	11.86%	[4]
Gangelt IgG	0.909	0.991	13.6%	14.11%	14.03%	[4]

Motivation

See Stringhi et al. [5, supplementary information] for a generalization of this model.

References

1. Bendavid et al. (2020) COVID-19 Antibody Seroprevalence in Santa Clara County, California. https://doi.org/10.1101/2020.04.14.20062463.this

2. Sood et al. (2020) Seroprevalence of SARS-CoV-2–Specific Antibodies Among Adults in Los Angeles County, California, on April 10-11, 2020 https://jamanetwork.com/journals/jama/fullarticle/2766367?utm_campaign=articlePDF&utm_medium=articlePDFlink&utm_source=articlePDF&utm_content=jama.2020.8279

3. Erikstrup et al. (2020) Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors. preprint doi: https://doi.org/10.1101/2020.04.24.20075291

4. Streeck et al. (2020) Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event. https://doi.org/10.1101/2020.05.04.20090076

5. Stringhini et al. (2020). The Lancet. Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Geneva, Switzerland (SEROCoV-POP): a population-based study. https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(20)31304-0.pdf