Assessment of the clinical and analytical performance of three Seegene 1 Allplex SARS-CoV-2 assays within the VALCOR framework

The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%–100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%–99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947–1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%–100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000–1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.

CHUNG Pui Yan Jenny;  DHILLON Sharonjit Kaur;  SIMOENS Cindy;  CUYPERS Lize;  LIES Laenen;  BONDE Jesper;  CORBISIER Philippe;  BUTTINGER Gerhard;  COCUZZA Clementina;  VAN GUCHT Steven;  VAN RANST Marc;  MARC Arbyn; 

2024-07-05

AMER SOC MICROBIOLOGY

JRC135979

2165-0497 (online),   

https://publications.jrc.ec.europa.eu/repository/handle/JRC135979,   

10.1128/spectrum.02397-23 (online),