Development of the RealTime SARS-CoV-2 quantitative Laboratory Developed Test and correlation with viral culture as a measure of infectivity

Berg, Dr. Michael G; Zhen, Wei; Lucic, Danijela; Degli-Angeli, Emily J; Anderson, Mark; Forberg, Kenneth; Olivo, Ana; Sheikh, Farah; Toolsie, Dan; Greninger, Alexander L; Cloherty, Gavin A; Coombs, Robert W; Berry, Gregory J

While diagnosis of COVID-19 relies on qualitative molecular testing for the absence or presence of SARS-CoV-2 RNA, quantitative viral load determination for SARS-CoV-2 has many potential applications in antiviral therapy and vaccine trials as well as implications for public health and quarantine guidance. To date, no quantitative SARS-CoV-2 viral load tests have been authorized for clinical use by the FDA. In this study, we modified the FDA emergency use authorized qualitative RealTime SARS-CoV-2 assay into a quantitative SARS-CoV-2 Laboratory Developed Test (LDT) using newly developed Abbott SARS-CoV-2 calibration standards. Both analytical and clinical performance of this SARS-CoV-2 quantitative LDT was evaluated using nasopharyngeal swabs (NPS). We further assessed the correlation between Ct and the ability to culture virus on Vero CCL81 cells. The SARS-CoV-2 quantitative LDT demonstrated high linearity with R(2) value of 0.992, high inter- and intra-assay reproducibility across the dynamic range (SDs ±0.08-0.14 log(10) copies/mL for inter-assay reproducibility and ±0.09 to 0.19 log(10) copies/mL for intra-assay reproducibility). Lower limit of detection was determined as 1.90 log(10) copies/mL. The highest Ct at which CPE was detected ranged between 28.21-28.49, corresponding to approximately 4.2 log(10) copies/mL. Quantitative tests, validated against viral culture capacity, may allow more accurate identification of individuals with and without infectious viral shedding from the respiratory tract.