About: Identification of a common deletion in the spike protein of SARS-CoV-2

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About: Identification of a common deletion in the spike protein of SARS-CoV-2 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	Identification of a common deletion in the spike protein of SARS-CoV-2
Creator	Ke, Changwen Rambaut, Andrew Wu, Jie Lu, Jing Sun, Jiufeng Yuan, Runyu Liu, Zhe Zheng, Huanying Pybus, Oliver Bowden, Thomas Hulswit, Ruben Li, Baisheng Li, Mingyue Lin, Huifang Loman, Nick Peng, Jingju Xiong, Qianlin
Source	BioRxiv
abstract	Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 and S2 boundary. For the first feature, the similar RBD identified in SARs-like virus from pangolin suggests the RBD in SARS-CoV-2 may already exist in animal host(s) before it transmitted into human. The left puzzle is the history and function of the insertion at S1/S2 boundary, which is uniquely identified in SARS-CoV-2. In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. More extensive screening indicates the deletion at the flank sites of PRRAR could be detected in 3 of 68 clinical samples and half of 22 in vitro isolated viral strains. These data indicate (1) the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; (2) there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage. The mechanistic explanation for this in vitro adaptation and in vivo purification processes (or reverse) that led to such genomic changes in SARS-CoV-2 requires further work. Nonetheless, this study has provided valuable clues to aid further investigation of spike protein function and virus evolution. The deletion mutation identified in vitro isolation should be also noted for current vaccine development.
has issue date	2020-04-02(xsd:dateTime)
bibo:doi	10.1101/2020.03.31.015941
has license	biorxiv
sha1sum (hex)	197486e60a3a258cd100603d9679c3238803fede
schema:url	https://doi.org/10.1101/2020.03.31.015941
resource representing a document's title	Identification of a common deletion in the spike protein of SARS-CoV-2
schema:publication	bioRxiv
resource representing a document's body	covid:197486e60a3a258cd100603d9679c3238803fede#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'deletion mutations' named entity 'site' named entity 'animal' named entity 'infection' named entity 'transmitted' named entity 'deletion' named entity 'RBD' named entity 'selection' named entity 'samples' named entity 'deletion' named entity 'samples' named entity 'amino acids' named entity 'nucleotide' named entity 'RBD' named entity 'amino acids' named entity 'SARS-CoV-2' named entity 'infection' named entity 'deletion mutations' named entity 'virus' named entity 'genome' named entity 'cleavage site' named entity 'receptor binding domain' named entity 'Guangdong' named entity 'coronavirus' named entity 'global pandemic of COVID-19' named entity 'deletions' named entity 'genome sequences' named entity 'RBD' named entity 'SARS-CoV-2' named entity 'nanopore sequencing' named entity 'China' named entity 'viruses' named entity 'consensus sequences' named entity 'virus' named entity 'virus' named entity 'cleavage site' named entity 'O-linked glycans' named entity 'O-linked glycans' named entity 'deletion mutation' named entity 'cleavage site' named entity 'Guangdong' named entity 'random mutations' named entity 'deletion mutations' named entity 'SARS-CoV-2' named entity 'Multiplex-PCR' named entity 'SARS-CoV-2' named entity 'cleavage site' named entity 'furin' named entity 'receptor binding domain' named entity 'phylogenetic tree' named entity 'genome sequencing' named entity 'SARS-CoV-2' named entity 'primers' named entity 'cleavage site' named entity 'zoonotic' named entity 'high affinity' named entity 'cleavage site' named entity 'genetic information' named entity 'ACE2 receptor' named entity 'multiplex PCR' named entity 'coronaviruses' named entity 'O-linked glycans' named entity 'Vero cells' named entity 'cleavage site' named entity 'SARS-CoV-2' named entity 'genetic evolution' named entity 'SARS-CoV-2'

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