We found that a single nucleotide polymorphism (SNP) in the nucleoprotein gene of SARS-CoV-2 from a patient interfered with detection in a widely used assay. Although was still detected by another probe, this underlines the necessity of targeting two independent essential regions of a pathogen for reliable detection. In a particular case of COVID 19 infection showed a discrepant qRT-PCR test result. A nasopharyngeal swab tested with the Xpert Xpress SARS-CoV-2 (GXP) assay was reported as SARS-CoV-2 presumptive-positive for the E gene, but a negative result for the N2 gene. For confirmation, the sample was reanalysed with the Allplex SARS-CoV-2 assay which revealed positive results for three targets: E gene, RdRp gene and N gene. We also performed a qRT-PCR with the CDC and assays N1, N2 and N3 were positive. To estimate the frequency of strains with this SNP, we downloaded the complete SARS-CoV-2 sequences from the GISAID EpiCoV Database and retrieved 209 isolates containing this SNP. Only five strains had the two SNPs C28858T/C29200T and other isolates from Romania had C28858T/C29451T like our case. It is therefore likely that the SNPs were the product of spontaneous and independent mutation. Therefore presumptive GXP result should be confirmed by another test. This underlines the necessity of targeting two independent essential regions of a pathogen for reliable detection.