Objective: To investigate the possible cause of discrepancy between clinical and RT-PCR based diagnosis of patients with COVID-19.
Results: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested using the Roche SARS-CoV-2 Cobas assay and were found to be negative. Further investigation for other viral causes of pneumonia was conducted using the Filmarray RP2.1 assay, which identified SARS-CoV-2 as the pathogen in all ten cases. To investigate whether this could be due to discrepancies between PCR assay, additional testing was conducted using the TaqPath TM COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, could be due to variation in the primer binding sites. The identification of strains with SGTF identify the possible presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.