The importance of prevalence and pre-test probability on the microbiological diagnosis of SARS-CoV-2: the case of Spain in 2020

OBJECTIVES: The aim of this work was to estimate the conditioned probability for the diagnosis of SARS-CoV-2 infection with reverse transcription polymerase chain reaction (RT-PCR), viral antigen rapid diagnostic tests (Ag-RDT), and antibody detection tests depending on the prevalence in the specific healthcare settings in Spain in 2020, and on the pre-test probability (PTP) according to the clinical situation, age and unknown or close contacts of the patient. MATERIAL AND METHODS: Performance parameters of tests were obtained from literature. Prevalence data and PTP were obtained from Spanish sources and a survey, respectively. The post-test probability is the positive predictive value (PPV) when test is positive. For negative result, we also calculated the probability of having the infection (false negatives). RESULTS: For both RT-PCR and viral Ag-RDT, the lowest PPV values were for the population screenings. This strategy proved to be useful in ruling out infection but generates a high number of false positives. At individual level, both tools provided high PPV (≥ 97%) when the PTP values are over 35%. In seroprevalence studies, though the specificity of IgG alone tests is high, under low seroprevalence, false positives cannot be avoided. Total antibodies tests are useful for diagnosis of COVID-19 in those doubtful cases with RT-PCR or Ag-RDT tests being repeatedly negative. CONCLUSIONS: The interpretating of results depends not only on the accuracy of the test, but also on the prevalence of the infection in different settings, and the PTP associated to the patient before performing the test.