Fig. 2

Deletions within the viral mRNAs encoding the S glycoprotein and N protein. a The read depth over the region deleted in the S glycoprotein together with information on the sequence in the region and the translation in all three frames. b A clustal alignment of four proteins over this region, wild type SARS-CoV, wild type SARS-CoV-2, the artificially deleted version of the wild type SARS-CoV-2 S glycoprotein as reported in Walls et al. [38] and finally the predicted sequence of the deleted protein described here. Highlighted in yellow is the sequence of the unique peptide generated by chymotrypsin digest of the protein which was identified by tandem mass spectrometry. The positions of predicted protease cleavage sites [23] at the S1/S2 boundary are shown. c A proposed deletion in the N protein predicted by multiple aligned transcripts and subsequently identified in trypsin digested protein samples as indicated by the unique peptide highlighted in yellow