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

To inspect the sequence features of SARS-CoV-2 in more detail, we plotted its codon usage per amino acid and compared it with the human genome and lung transcriptome ( Figure 1 ). SARS-CoV-2 clearly exhibits a preference in codons ending in T and A (71.7%), which is not observed in the human genome (44.9% ending in T or A) and lung transcriptome (37.6% ending in T or A). Similarly, the kidney and small . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 intestine transcriptome show a preference for codons ending in C and G (62.5% in the kidney and 61.8% in the small intestine, Supplemental Figure 1 ). The codon pair usage of SARS-CoV-2 was also examined in juxtaposition with the human codon usage (Figure 2A and 2B ). The differences in codon usage of the two genomes are highlighted in Figure 2C .