Analytic Sensitivity of 3 Nucleic Acid Detection Assays in Diagnosis of SARS-CoV-2 Infection.

Abstract

BackgroundDetection of SARS-CoV-2 by reverse transcriptase polymerase chain reaction is the primary method to diagnose Coronavirus Infectious Disease 2019 (COVID-19). Yet, the analytical sensitivity required is not well defined and it is unclear how available assays compare.MethodsFor the Abbott RealTime SARS-CoV-2 assay (Abbott Molecular Inc.; abbreviated as m2000), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from N = 8,538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of two other assays with more rapid turnaround times (Cepheid Xpert Xpress (Cepheid Inc.; GeneXpert, N = 27 specimens) and a laboratory developed test on the Luminex ARIES system (Luminex Corporation; ARIES LDT, N = 50)) as a function of virus concentrations, from which we projected their false negative rates in our patient population.ResultsSARS-CoV-2 was detected in 27% (95% confidence interval of 26-28%) of all specimens. Estimated viral concentrations were widely distributed and 17% (16-19%) of positive individuals had viral concentrations below 845 copies/mL. Positive percent agreement was strongly related to viral concentration and reliable detection (i.e. ≥95%), was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false negative rates of 4% (0-21%) and 27% (11-46%), respectively.ConclusionsSubstantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with lesser analytical sensitivity.