About: Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

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About: Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome 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
has title	Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome
Creator	Morgan, Brittany Massi, Francesca Ryder, Sean
Source	BioRxiv; Medline; WHO
abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of SARS-CoV-2 genomic sequences to identify rapidly emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, twenty variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5’UTR, including a set of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-stable molecular switch in the 3’UTR. Finally, five variants destabilize structured elements within the 3’UTR hypervariable region, including the S2M stem loop, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. This analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences, as rapidly emerging variations in these regions could lead to drug resistance.
has issue date	2020-06-30(xsd:dateTime)
bibo:doi	10.1101/2020.05.27.120105
bibo:pmid	32577650
has license	biorxiv
sha1sum (hex)	5f12371d20f594c2159ccf08ec7e818ae9d18978
schema:url	https://doi.org/10.1101/2020.05.27.120105
resource representing a document's title	Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome
has PubMed identifier	32577650
schema:publication	bioRxiv
resource representing a document's body	covid:5f12371d20f594c2159ccf08ec7e818ae9d18978#body_text
is schema:about of	named entity 'SARS-COV-2' named entity 'SPREAD' named entity 'MECHANISMS' named entity 'RAPIDLY' named entity 'SEQUENCING TECHNOLOGY' named entity 'PRESENT' named entity 'USEFUL' named entity 'GENOME' named entity 'co-occurring' named entity 'genome sequences' named entity 'genome' named entity 'SARS-CoV-2' named entity 'severe acute respiratory syndrome coronavirus 2' named entity 'Genome' named entity 'pseudoknot' named entity 'Coronaviridae' named entity 'regulatory RNA' named entity 'nucleotides' named entity 'molecular switch' named entity 'protein synthesis' named entity 'evolution' named entity 'GISAID Initiative' named entity 'GISAID' named entity 'MHV' named entity 'coronaviridae' named entity 'MSA' named entity 'base pair' named entity 'GISAID' named entity 'RNA editing' named entity 'betacoronaviruses' named entity '11.9' named entity 'pseudoknot' named entity 'Langevin dynamics' named entity 'coronaviridae' named entity 'antiviral' named entity 'secondary structure' named entity 'infection' named entity 'viruses' named entity 'nucleotide' named entity 'replicase' named entity 'Madhugiri' named entity 'positive strand' named entity 'National Center for Biotechnology Information' named entity 'RNA synthesis' named entity 'MAFFT' named entity 'stem loop structures' named entity 'nucleotide' named entity 'protein coding sequence' named entity 'betacoronaviruses' named entity 'virus' named entity 'cell culture' named entity 'GISAID' named entity 'initiation codon' named entity 'sequence divergence' named entity 'MERS' named entity 'Maxwell distribution' named entity 'base pairing' named entity 'kcal' named entity 'allele frequency' named entity 'RNA' named entity 'uORF' named entity 'viral RNA' named entity 'single-stranded' named entity 'vaccines' named entity 'global pandemic' named entity 'viral replication' named entity 'MAF' named entity 'algorithm' named entity 'pathogenesis' named entity 'pseudoknot' named entity 'molecular switch' named entity 'ribosomes' named entity 'conjugate gradient method' named entity 'MHV' named entity 'molecular dynamics' named entity 'viral replication' named entity 'Coronaviridae' named entity 'minor allele frequency' named entity 'amine' named entity 'selective pressure'

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