Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design

Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty

ORF10 has strikingly low CPB and RSCU given that it is at the very end of the viral genome there may be a structural reason for its nucleotide sequence. The E gene also has a very low CPB; interestingly, although ORF10 has both positive and negative CPS across its sequence, E has mostly negative CPSs, which make it unsuited for codon pair deoptimization. ORF7a is unusual, as it has the highest RSCU of the viral genes, but a rather low CPB (it uses preferred codons in unusual combinations). Although ORF7a is not the most compelling target for codon pair deoptimization, if a codon deoptimization . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.016832 doi: bioRxiv preprint strategy is attempted, this gene should be considered. It should, however, be noted that since it overlaps for a few nucleotides with ORF7b, any sequence changes should be considered in coordination for both genes.