PXD027995

PXD027995 is an original dataset announced via ProteomeXchange.

Title	Functional Assessment of US SARS-CoV-2 L452R Epsilon Variant
Description	The multiple mutations comprising the epsilon variant demonstrates the independent convergent evolution of SARS-CoV-2 with its spike protein mutation L452R also present in the delta variant. Cells infected with live viral samples of the epsilon viral variant compared to non-epsilon variant displayed increased sensitivity to neutralization antibodies (NAb) suggesting an intact humoral response (P< 1.0 e-4). The ability for SARS-CoV2 to become more infectious but less virulent is supported mechanistically in the downregulation of viral processing pathways seen by multiomic analyses. Importantly, this paired transcriptomics and proteomic profiling of cellular response to live virus revealed an altered leukocyte response and metabolic mRNA processing in cells upon live viral infection of the epsilon variant. To ascertain host response to SARS-CoV-2 infection, primary COVID-19 positive nasopharyngeal samples were transcriptomically profiled a differential innate immune response (P<2.0 e-12) but, a relatively unaltered T cell response in the patients carrying the epsilon variant (P< 2.0 e-3). In fact, patients infected with SARS-CoV-2 and those vaccinated with the BNT162b2 vaccine have comparable CD4+/CD8+ T-cell immune responses to the B.1.429 variant (P<5 e-2). The epsilon variant alters viral processing response in infected cells, and the host innate immune response in COVID-19 positive nasopharyngeal swabs, but generates a protective host T cell response molecular signature in both vaccinated and unvaccinated patients.
HostingRepository	PRIDE
AnnounceDate	2022-05-06
AnnouncementXML	Submission_2022-05-06_07:18:14.476.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aleksandr Stotland
SpeciesList	scientific name: Chlorocebus sabaeus; NCBI TaxID: 60711;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-17 23:48:10	ID requested
⏵ 1	2022-05-06 07:18:15	announced

Plummer JT, Contreras D, Zhang W, Binek A, Zhang R, Dezem F, Chen SS, Davis BD, Sincuir Martinez J, Stotland A, Kreimer S, Makhoul E, Heneidi S, Eno C, Shin B, Berg AH, Cheng S, Jordan SC, Vail E, Van Eyk JE, Morgan MA, US Severe Acute Respiratory Syndrome Coronavirus 2 Epsilon Variant: Highly Transmissible but With an Adjusted Muted Host T-Cell Response. Clin Infect Dis, 75(11):1940-1949(2022) [pubmed]

submitter keyword: COVID19, Vero, FAIMS

Jennifer Van Eyk
contact affiliation	Smidt Heart Institute Cedars Sinai Medical Center
contact email	jennifer.vaneyk@cshs.org
lab head
Aleksandr Stotland
contact affiliation	Cedars-Sinai Medical Center
contact email	aleksandr.stotland@cshs.org
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD027995

PRIDE project URI

• PRIDE
  1. PXD027995
     1. Label: PRIDE project
     2. Name: Functional Assessment of US SARS-CoV-2 L452R Epsilon Variant