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Review
. 2020 Dec;25(50):2000568.
doi: 10.2807/1560-7917.ES.2020.25.50.2000568.

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Paul S Wikramaratna  1   2 , Robert S Paton  1   3 , Mahan Ghafari  3 , José Lourenço  3
Affiliations
Review

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Paul S Wikramaratna et al. Euro Surveill. 2020 Dec.

Abstract

BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; accuracy; testing.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Impact of time post symptom onset on positive RT-PCR test result probabilities for SARS-CoV-2 infected individualsa using (A) nasopharyngeal swabs and (B) oropharyngeal swabs, 2020 (n = 95)
Figure 2
Figure 2
Aggregate probability of false-negative tests for gamma-distributed cohorts of individuals tested for SARS-CoV-2 infectiona including a scenario where infected individuals are tested (A) mostly early but with a long-tail of individuals taking a long time to be tested, (B) mainly later, with a similarly long tail, (C) consistently early, (D) consistently tested later, 2020
Figure 3
Figure 3
Comparison of the discretised distributions of estimated time from symptom onset to confirmation among SARS-CoV-2 symptomatic individuals from the data in Bi et al. (2020) [22], China (n = 391), and these data combined with the false negative test probability results from the present studya, 2020 (n = 95)
Figure 4
Figure 4
How the probability of obtaining a false-positive RT-PCR test result for SARS-CoV-2 infections changes (A) the estimated number of cases and (B) the estimated percentage change in number of cases for South Korea (n = 316,644) and United Kingdom (n = 64,621), 20 March 2020
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