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

We next examined how the SARS-CoV-2 codon pair usage compares with other coronaviruses and to its current host. Codon pair data inherently contain the codon usage data and therefore are better suited than codon usage data for this type of comparison. As expected, SARS-CoV-2 codon pair usage closely resembles the codon usage of the coronoviridae family, while it is quite distinct from the codon pair usage of the human genome (Table 1) . Bat (Chiroptera) and pangolin (Pholidota) from which the virus may have been transmitted to humans, as well as dog (Canis lupus familiaris) to which the virus is feared may be transmitted next, were included in the analysis. We find that these species have a similar codon usage when compared with human; therefore, viral tropism cannot be inferred based on codon usage data alone (Table 1) . Since SARS-CoV-2 infects bronchial epithelial cells and type II pneumocytes and our recent findings show that transcriptomic tissue-specific codon pair usage can vary greatly from genomic codon pair usage [24] , we also examined the transcriptomic codon pair usage of the lung and how it compares with the SARS-CoV-2 codon pair usage. Rather surprisingly, the codon usage in the lung was more distinct from SARS-CoV-2 codon usage than the Homo sapiens genomic codon usage. The transcriptome codon pair usage of kidney and small intestine, tissues that are also susceptible to the infection, are similarly distant from SARS-CoV-2 (Table 1) .