High concordance in SARS-CoV-2 detection between automated (Abbott m2000) and manual (DaAn gene) RT-PCR systems: The EDCTP PERFECT-Study in Cameroon

Abstract

Molecular diagnosis of COVID-19 is critical to the control of the pandemic, which is a major threat to global health. Several molecular tests have been validated by WHO, but would require operational evaluation in the field to ensure their inter-operability in diagnosis. In order to ensure field interoperability in molecular assays for detection of SARS-CoV-2 RNA, we evaluated the diagnostic concordance of SARS-CoV-2 between an automated (Abbott) and a manual (DaAn gene) real-time PCR (rRT-PCR), two commonly used assays in Africa. A comparative study was conducted on 287 nasopharyngeal specimens at the Chantal BIYA International Reference Centre (CIRCB) in Yaounde-Cameroon. Samples were tested in parallel with Abbott and DaAn gene rRT-PCR, and performance characteristics were evaluated by Cohen’s coefficient and Spearman’s cor-relation. A total of 273 participants [median age (IQR) 36 (26-46) years] and 14 EQA specimens were included in the study. Positivity was on 30.0% (86/287) Abbott and 37.6% (108/287) DaAn gene. Overall agreement was 82.6% (237/287), with k=0.82 (95%CI: 0.777-0.863), indicating an excellent diagnostic agreement. The positive and negative agreement was 66.67% (72/108) and 92.18 % (165/179) respective-ly. Regarding Viral Load (VL), positive agreement was 100% for samples with high VLs (CT<20). Among positive SARS-CoV-2 cases, the mean difference in Cycle Threshold (CT) for the manual and Cycle Number (CN) for the automated was 6.75±0.3. The excellent agreement (>80%) between the Abbott and DaAn gene rRT-PCR platforms supports interoperability between the two assays. Discordance occurs at low-VL, thus underscoring these tools as efficient weapons in limiting SARS-CoV-2 community transmission.