Fig. 3.

a Representation of the SARS-CoV-2 genome sequence depicting annotated genes. This scheme uses the nucleotide coordinates of a virus sequenced in China (NC_045512). b Positions of the primer/probe targets used for detection by institutions in six countries. Colors of primers and probes correspond to countries: China, CDC (red); USA, CDC (blue); Germany (yellow); China/Hong Kong (gray); France (pink); Japan (black); and Thailand (orange). The numbers above each primer and probe indicate nucleotide position (coordinate) in the genome. Important details: France developed two assays for the RdRP gene (identified in the figure as ORF1a and ORF1b, according to the reference sequence [NC_045512] used). The assay developed by Germany for gene E was also tested in France. Germany developed two probes for the same RdRP gene region indicated in the image, one being specific for SARS-CoV-2 and another common for SARS-CoV-2, SARS-CoV, and bat SARS-related coronavirus, but only one assay is indicated in the image. Japan also indicated assays for nested RT-PCR, but the image above only represents RT-qPCR assays. An important aspect of RT-qPCR assay development for viral detection is confirming that primers and probes are specific to the virus of interest and do not detect viruses from the same family. This is particularly important for coronaviruses, since members of this group already circulate in the human population