RT Journal Article
SR Electronic
T1 Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.03.30.016832
DO 10.1101/2020.03.30.016832
A1 Jacob Kames
A1 David D. Holcomb
A1 Ofer Kimchi
A1 Michael DiCuccio
A1 Nobuko Hamasaki-Katagiri
A1 Tony Wang
A1 Anton A. Komar
A1 Aikaterini Alexaki
A1 Chava Kimchi-Sarfaty
YR 2020
UL http://biorxiv.org/content/early/2020/03/31/2020.03.30.016832.abstract
AB As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses.