Fig. 2: Using the WashU Virus Genome Browser to discover conserved immune-epitopes.

a, Browser view of the SARS-CoV-2 gene encoding the nucleocapsid (N) protein with SNV tracks of two SARS-CoV strains (DQ071615.1 and AY278488.2) and five SARS-CoV-2 strains (MN938384.1, MN975262.1, MN985325.1, MN988668.1 and MN988669.1) loaded in the view. The track of putative SARS-CoV immune epitopes is also displayed in density mode. b, A zoomed-in view of the orange box in a, displaying the first 9 amino acids of the SARS-CoV-2 N protein. SNVs at positions 28296 (T>C) and 28299 (G>A) are silent mutations; however, the ‘TCA’ insertion at position 28294 in SARS-CoV accession AY278488.2 (BJ01) results in the insertion of a serine residue in the SARS-CoV N protein relative to the SARS-CoV-2 N protein. Of note, this insertion is not present in the other SARS-CoV accession (DQ071615.1). Owing to the variability in the amino acid sequence within this region across SARS-CoV and SARS-CoV-2 strains, this region is unlikely to be a good candidate for epitope design. c, A zoomed-in view of the purple box in a, displaying a region that is likely to be a good candidate for epitope design because it is fully conserved across SARS-CoV and SARS-CoV-2 strains, and it also encodes several putative antigenic epitopes.