About: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

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About: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
Creator	Antón, Andrés Piñana, Maria Rando, Ariadna Campins, Magda Esperalba, Juliana Andres, Cristina Gregori, Josep Quer, Josep Pumarola, Tomás Anton, Andres Almirante, Benito Ferrer, Ricard Codina, Maria Martín, Maria Rodriguez-Frias, Francisco Esteban, Juan Garcia-Cehic, Damir Goterris, Lidia Guerrero-Murillo, Mercedes Quer, Susanna
Source	BioRxiv
abstract	The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We propose that natural selection has favored a “Don’t burn down the house” strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.
has issue date	2020-06-08(xsd:dateTime)
bibo:doi	10.1101/2020.06.03.129585
has license	biorxiv
sha1sum (hex)	fa7923aa0ccabd1c530e835b272fdc88571fc47f
schema:url	https://doi.org/10.1101/2020.06.03.129585
resource representing a document's title	Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients
schema:publication	bioRxiv
resource representing a document's body	covid:fa7923aa0ccabd1c530e835b272fdc88571fc47f#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'generating' named entity 'VACCINE DEVELOPMENT' named entity 'INITIAL' named entity 'GENERATE' named entity 'SUGGEST' named entity 'QUASISPECIES' named entity 'GENE' named entity 'FRAMESHIFT' named entity 'ITS' named entity 'VIRAL PARTICLES' named entity 'PATIENTS' named entity 'THESE' named entity '282' named entity 'ENTRY' named entity 'large' named entity 'viral quasispecies' named entity 'Here' named entity 'target' named entity 'tissue' named entity 'site' named entity 'gene' named entity 'damage' named entity 'generate' named entity 'Our' named entity 'mutation' named entity 'development' named entity 'mild' named entity 'Initial' named entity 'severe' named entity 'virus' named entity 'protein' named entity 'viral quasispecies' named entity 'cleavage site' named entity 'spike (S) protein' named entity 'virus' named entity 'neutralizing antibodies' named entity 'protein' named entity 'sequenced' named entity 'COVID19' named entity 'strategy' named entity 'deletions' named entity 'cleavage site' named entity 'virus' named entity 'angiotensin converting enzyme 2' named entity 'nucleotides' named entity 'deletions' named entity 'deletions' named entity 'subgenomic' named entity 'premature stop codon' named entity 'RT-PCR' named entity 'SARS-CoV-2' named entity 'protein' named entity 'ACE2' named entity 'antiviral agents' named entity 'infection' named entity 'DPP4' named entity 'RNA genome' named entity 'amino acid' named entity 'haplotypes' named entity 'primers' named entity 'RT-PCR' named entity 'dipeptidyl peptidase 4' named entity 'nucleotides' named entity 'viral quasispecies'

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