A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors . We now report the comparative performance of five real-time diagnostic assays . Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria . The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit . All five assays are one-step reverse transcriptase real-time PCR assays . Testing was done according to each assay's manufacturer instructions for use using real-time PCR platforms . 63 samples were tested using the five qPCR assays, comprising of 15 negative samples , 15 positive samples (Ct = 16-30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36-41 . All assays detected all high positive samples correctly . Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample . The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value . The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected . Comparative assays' performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value.