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

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About: Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Creator	Dicuccio, Michael Wang, Tony Alexaki, Aikaterini Hamasaki-Katagiri, Nobuko Holcomb, David Kames, Jacob Kimchi, Ofer Kimchi-Sarfaty, Chava Komar, Anton
topic	covid:21d89a4db5e0514c93ebf5aa94813b013d23c818#this
source	BioRxiv; Medline; PMC
abstract	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.
has issue date	2020-03-31(xsd:dateTime)
bibo:doi	10.1101/2020.03.30.016832
bibo:pmid	32511300
has license	cc-by
sha1sum (hex)	21d89a4db5e0514c93ebf5aa94813b013d23c818
schema:url	https://doi.org/10.1101/2020.03.30.016832
resource representing a document's title	Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
has PubMed Central identifier	PMC7217226
has PubMed identifier	32511300
schema:publication	bioRxiv
resource representing a document's body	covid:21d89a4db5e0514c93ebf5aa94813b013d23c818#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/21d89a4db5e0514c93ebf5aa94813b013d23c818
is schema:about of	named entity 'sequence' named entity 'usage' named entity 'specific' named entity 'limited' named entity 'COMPREHENSIVE' named entity 'PANDEMIC' named entity 'TRANSCRIPTOME' named entity 'MEMBERS' named entity 'CODON USAGE' named entity '28S' named entity 'HUMAN GENOME' named entity 'USAGE' named entity 'ANALYSIS' named entity 'DINUCLEOTIDE' named entity 'SARS-CoV-2' named entity 'performed' named entity 'carries' named entity 'lung' named entity 'features' named entity 'pair' named entity 'human genome' named entity 'Sequence analysis' named entity 'vaccine' named entity 'viruses' named entity 'transcriptome' named entity 'genome sequence' named entity 'Sequence analysis' named entity 'viruses' named entity 'mRNA' named entity 'transcriptome' named entity 'codon' named entity 'RNA viruses' named entity 'frameshift' named entity 'attenuated virus' named entity 'codon' named entity 'cotranslational' named entity 'Coronaviruses' named entity 'codon usage' named entity 'cell-surface receptor' named entity 'type II pneumocytes' named entity 'codons' named entity 'codon' named entity 'host cell' named entity 'deoptimize' named entity 'codon' named entity 'MFE' named entity 'deoptimization' named entity 'viruses' named entity 'kidney' named entity 'codon usage' named entity 'coronavirus' named entity 'mRNA' named entity 'codons' named entity 'genome' named entity 'protein' named entity 'codon usage' named entity 'terminal ileum' named entity 'bacteria' named entity 'enumeration algorithm' named entity 'percent difference' named entity 'CpG' named entity 'codon' named entity 'frameshifting' named entity 'codon usage' named entity 'deoptimization' named entity 'nucleocapsid' named entity 'ribosomal' named entity 'coronaviruses' named entity 'Chiroptera' named entity 'small intestine' named entity 'codon'

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