Why did we not choose commonly used genes such as the S gene, E gene, or RdRP?
The S gene is subjected to high selection pressure and has a very high mutation rate. Therefore, an assay in the S gene is prone to fail sooner or later. Our goal was to develop a long-term solution.
The E gene is very conserved among different Sarbecoviruses. As specificity is very challenging with the E gene, we did not choose it. As an example, the Charité E gene assay was designed to be inclusive for many Coronaviruses and is not specific for SARS-CoV-2.
Original RdRP assay shows suboptimal sensitivity with all assays we have tested – e.g. the Charité RdRP assay can be up to 10 Cts later than N1+N2, and the redesigned RdRP assay still showed a Ct shift of 4-6 Cts.
The E gene is very conserved among different Sarbecoviruses. As specificity is very challenging with the E gene, we did not choose it. As an example, the Charité E gene assay was designed to be inclusive for many Coronaviruses and is not specific for SARS-CoV-2.
Original RdRP assay shows suboptimal sensitivity with all assays we have tested – e.g. the Charité RdRP assay can be up to 10 Cts later than N1+N2, and the redesigned RdRP assay still showed a Ct shift of 4-6 Cts.