Clinical Performance of SARS-CoV-2 Molecular Tests

Abstract

Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the clinical performance of these tests is still poorly understood, particularly with regard to disease course, patient-specific factors, and viral shedding. From 10 March to 1 May 2020, NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed for 3,432 patients, of which 2,413 had initial negative and 802 had initial positive results. Repeat-tested patients were more likely to have severe disease and low viral loads. The negative predictive value of the first-day result among repeat-tested patients was 81.3% The clinical sensitivity of SARS-CoV-2 molecular assays was estimated between 58% and 96%, depending on the unknown number of false-negative results in single-tested patients. Conversion to negative was unlikely to occur before 15 to 20 days after initial testing or 20 to 30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Conversion from first-day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. Sixty patients fluctuated between positive and negative results over several weeks, suggesting that caution is needed when single-test results are acted upon. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely, 15 to 20 days after a positive test and the same day or next 2 days after a negative test for patients with high suspicion for COVID-19.

Keywords: COVID-19; SARS-CoV-2; laboratory utilization; negative predictive value; sensitivity.

FIG 1

Density distribution of cobas SARS-2-CoV-2 target 2 (E gene, pan-Sarbecovirus target) C_T values in repeat-tested versus single-tested patients. (Top) C_T values from results reported as “intermediate”; (bottom) C_T values from results reported as “detected.”

FIG 2

Kaplan-Meier estimate of conversion from an initially positive SARS-CoV-2 status on day 1 to a subsequent negative result. The number of patients at risk is shown at the bottom for each time point after removal of censored patients, represented by vertical ticks in the curve.

FIG 3

Kaplan-Meier estimate of conversion rate from initially negative SARS-CoV-2 status on day 1 to a subsequent positive result.