Evaluation of diagnostic test procedures for SARS-CoV-2 using latent class models: comparison of antigen test kits and sampling for PCR testing based on Danish national data registries

TL;DR

This study estimates the real-world sensitivity and specificity of SARS-CoV-2 PCR and antigen tests using latent class models on Danish national data, revealing high specificity but lower sensitivity for antigen tests.

Contribution

It introduces a method to evaluate test performance without assuming PCR as a gold standard, providing real-world estimates from large-scale national data.

Findings

Both tests have >99.7% specificity.

PCR sensitivity estimated at 95.7%.

Antigen test sensitivity estimated at 53.8%.

Abstract

Antigen test kits have been used extensively as a screening tool during the worldwide pandemic of coronavirus (SARS-CoV-2). While it is generally expected that taking samples for analysis with PCR testing gives more reliable results than using antigen test kits, the overall sensitivity and specificity of the two protocols in the field have not yet been estimated without assuming that the PCR test constitutes a gold standard. We use latent class models to estimate the in situ performance of both PCR and antigen testing, using data from the Danish national registries. The results are based on 240,000 paired tests results sub-selected from the 55 million test results that were obtained in Denmark during the period from February 2021 until June 2021. We found that the specificity of both tests is very high in our data sample (>99.7%), while the sensitivity of PCR sampling was estimated to be 95.7% (95% CI: 92.8-98.4%) and that of the antigen test kits used in Denmark over the study period was estimated at 53.8% (95% CI: 49.8-57.9%). Our findings can be used as supplementary information for consideration when implementing serial testing strategies that employ a confirmatory PCR sample following a positive result from an antigen test kit, such as the policy used in Denmark. We note that while this strategy reduces the number of false positives associated with antigen test screening, it also increases the false negatives. We demonstrate that the balance of trading false positives for false negatives only favours the use of serial testing when the expected true prevalence is low. Our results contain substantial uncertainty in the estimates for sensitivity due to the relatively small number of positive test results over this period: validation of our findings in a population with higher prevalence would therefore be highly relevant for future work.