About: SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics

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About: SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics 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	SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics
Creator	Li, Xiaopeng Uhal, Bruce Bupp, Caleb Gupta, Ruchir Prokop, Jeremy Rajasekaran, Surender Sirpilla, Olivia Bauss, Jacob Carcillo, Joseph Charron, Jacob Cook, Taylor Faber, William Frisch, Austin Hinds, David Lamb, Neil Lind, Eric Morris, Michele Painter, Jared Soehnlen, Xavier Stenger, Cynthia Steward, Hunter Underwood, Adam
Source	BioRxiv; Medline
abstract	The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.
has issue date	2020-05-15(xsd:dateTime)
bibo:doi	10.1101/2020.05.15.098616
bibo:pmid	32511397
has license	biorxiv
sha1sum (hex)	26fa83573c179ee4499f58ff6b3a8719546d9fbb
schema:url	https://doi.org/10.1101/2020.05.15.098616
resource representing a document's title	SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics
has PubMed identifier	32511397
schema:publication	bioRxiv
resource representing a document's body	covid:26fa83573c179ee4499f58ff6b3a8719546d9fbb#body_text
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