Figure 1.
Mutations in the nucleoprotein gene of a SARS-CoV-2 patient virus and strategy to reveal the mutation responsible for loss of detection in the Xpert Xpress SARS-CoV-2 assay, Germany, July 2020
CDC: Centers for Disease Control and Prevention; Cterm: C terminus; FP: forward primer; N: nucleoprotein; Nterm: N terminus; ORF: open reading frame; RP: reverse primer; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2.
Three C to T conversions were detected by sequencing of patient virus amplicons 1 and 2 (position 28,858, 29,200 and 29,451 of the SARS-CoV-2 reference genome NC_045512.2, depicted in orange). Three shorter amplicons, N-Nterm, N-mid and N-Cterm, containing one single mutation each were PCR-amplified with indicated oligonucleotides (Table) to detect the responsible mutation. All positions are numbered according to the SARS-CoV-2 reference genome NC_045512.2.
