Our findings characterize the limitations of commonly used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2. Our comparative results of primer-probe sets used in qRT-PCR assays indicate that overall, all assays are able to detect SARS-COV-2; however, detection limits and ability to differentiate between true negatives and positives at low RNA concentrations are variable between sets. This should be carefully evaluated to determine CT value cut-offs to differentiate between positives and negatives. The US CDC assay, for example, uses a cut-off value of CT 40, but we generated CT values in the range of 37-40 when the 2019-nCoV_N2 set was tested on RNA from nasopharyngeal swabs void of SARS-CoV-2 RNA. Considering that both the US CDC 2019-nCoV_N1 and N2 sets need to be >40 CTs to be considered as negative, background amplification in one of the sets would result in inconclusive results.