Discrepancies in the detection of SARS-CoV-2 by qRT-PCR are dependent on the target gene used for its amplification: Implications in the diagnosis of clinical infection

Discrepancies exist in Cycle threshold (Ct) values during detection of SARS-CoV-2 by qRT-PCR. We demonstrate that Ct values depend on the position of the target gene in the viral genome. Simultaneous detection of five genes in positive samples revealed lower Ct values as we move further to the 3’ end (orf1AB/RdRp>E>M>orf7a>N). These findings were confirmed in a retrospective analysis with 363 positive clinical samples. Our findings have key implications in clinical diagnostics of SARS-CoV-2, patient management and public health interventions.