Question

1. The original TaqMan assay that was deployed by the CDC for SARS-CoV-2 had primer/probe sets to amplify regions specific to SARS-CoV-2 (N1 and N2), a primer/probe set to amplify a region from SARS-CoV-2 and other closely related viruses like the virus that causes SARS (N3), and a primer probe set to amplify a human specific gene (RP). Why was a human gene included?

Answer 1

The N1 and N2 primer set amplifies cDNA specific to SARS-CoV-2 region, while the primer set N1 and N3 where N3 is a primer specific to a region of SARS is used to amplify such a cDNA which ideally should not amplify if the region is very specific to CoV2 but might show some cross reactivity as CoV-2 is realted to SARS.

the last primer set is N1 and RP, where N1 is viral primer and RP is human primer , there should be no amplification in this case if the cDNA is highly specific for COV2. this will not allow amplification of the viral cDNA.this is included to check for any false positive results as the sequences that this primer will identify will not be purely of the viral origin.

So to eliminate the possibility this human gene is included.