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

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...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports 2020-09, Vol.10 (1), p.15643-15643, Article 15643
Main Authors: Kames, Jacob, Holcomb, David D., Kimchi, Ofer, DiCuccio, Michael, Hamasaki-Katagiri, Nobuko, Wang, Tony, Komar, Anton A., Alexaki, Aikaterini, Kimchi-Sarfaty, Chava
Format: Article
Language:English
Subjects:
631/114
631/250/590
631/61
Base Sequence
Betacoronavirus - genetics
Coronavirus Infections - immunology
Coronavirus Infections - prevention & control
Coronavirus Nucleocapsid Proteins
COVID-19
COVID-19 Vaccines
Genome, Viral - genetics
Genomes
Humanities and Social Sciences
Humans
multidisciplinary
Nucleocapsid Proteins - genetics
Nucleocapsid Proteins - immunology
Nucleocapsids
Nucleotide sequence
Pandemics
Pandemics - prevention & control
Phosphoproteins
Pneumonia, Viral - prevention & control
SARS-CoV-2
Science
Science (multidisciplinary)
Sequence analysis
Severe acute respiratory syndrome coronavirus 2
Spike Glycoprotein, Coronavirus - genetics
Spike Glycoprotein, Coronavirus - immunology
Transcriptomes
Vaccine development
Vaccines
Vaccines, Inactivated - immunology
Viral Vaccines - immunology
Viruses
Whole Genome Sequencing
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-020-72533-2