Schema for IEDB Predictions - IEDB-Predicted Epitopes from Grifoni et al 2020
  Database: wuhCor1    Primary Table: bCellEpitopes Data last updated: 2020-03-24
Big Bed File Download: /gbdb/wuhCor1/epitopes/bCellEpitopes.bb
Item Count: 36
The data is stored in the binary BigBed format.

Format description: Browser extensible data, with extended fields for detail page
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart21589Start position in chromosome
chromEnd21628End position in chromosome
nameLVSSQCVNLTTRTShort Name of item
score0Score from 0-1000
strand++ or -
thickStart21589Start of where display should be thick (start codon)
thickEnd21628End of where display should be thick (stop codon)
reserved0,0,0Used as itemRgb as of 2004-11-22
scoreValue0Epitope score
id0Link to source
descriptionSurface glycoprotein_LVSSQCVNLTTRTDescription

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedscoreValueiddescription
NC_045512v22158921628LVSSQCVNLTTRT0+21589216280,0,000Surface glycoprotein_LVSSQCVNLTTRT
NC_045512v22175421787FHAIHVSGTNG0+21754217870,0,001Surface glycoprotein_FHAIHVSGTNG
NC_045512v22188621940TLDSKTQSLLIVNNATNV0+21886219400,0,002Surface glycoprotein_TLDSKTQSLLIVNNATNV
NC_045512v22199722066HKNNKSWMESEFRVYSSANNCTF0+21997220660,0,003Surface glycoprotein_HKNNKSWMESEFRVYSSANNCTF
NC_045512v22231222348PGDSSSGWTAGA0+22312223480,0,004Surface glycoprotein_PGDSSSGWTAGA
NC_045512v22239922426NENGTITDA0+22399224260,0,005Surface glycoprotein_NENGTITDA
NC_045512v22249522522IYQTSNFRV0+22495225220,0,006Surface glycoprotein_IYQTSNFRV
NC_045512v22262722690KRISNCVADYSVLYNSASFST0+22627226900,0,007Surface glycoprotein_KRISNCVADYSVLYNSASFST
NC_045512v22286122894IAWNSNNLDSK0+22861228940,0,008Surface glycoprotein_IAWNSNNLDSK
NC_045512v22296623011STEIYQAGSTPCNGV0+22966230110,0,009Surface glycoprotein_STEIYQAGSTPCNGV

IEDB Predictions (epitopes) Track Description
 

Description

This composite track indicates the immune epitope predictions for B cells, CD4 T-cells and CD8 T-cells, using these software packages: B cells = BebiPred 2.0, CD4 = IEDB Tepitool, CD8 = NetMHCpan4.0EL

The color range for the markers is from dark blue (strong prediction) to dark red (weak prediction). Black is used for markers with no calculated prediction.

From the publication: Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions, full reference below.

The prediction of epitopes for CD8 T-cells was run for the following HLA alleles, as they have a worldwide population frequency > 6%

HLA allelesFrequency in worldwide population
HLA-A*01:0116.2
HLA-A*02:0125.2
HLA-A*03:0115.4
HLA-A*11:0112.9
HLA-A*23:016.4
HLA-A*24:0216.8
HLA-B*07:0213.3
HLA-B*08:0111.5
HLA-B*35:016.5
HLA-B*40:0110.3
HLA-B*44:029.2
HLA-B*44:037.6

Summary

We identified potential targets for immune responses to 2019-nCoV and provide essential information for understanding human immune responses to this virus and evaluation of diagnostic and vaccine candidates.

Abstract

Effective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses. However, little information about the targets of immune responses to 2019-nCoV is available. We used the Immune Epitope Database and Analysis Resource (IEDB) resource to catalog available data related to other coronaviruses, including SARS-CoV, which has high sequence similarity to 2019-nCoV, and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in 2019-nCoV that have high homology to SARS virus. Parallel bionformatic predictions identified a priori potential B and T cell epitopes for 2019-nCoV. The independent identification of the same regions using two approaches reflects the high probability that these regions are targets for immune recognition of 2019-nCoV.

Credits

Data collected by Arkal Arjun Rao for the Sgourakis Research Group, U.C. Santa Cruz

References

Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A. Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions, BioRxiv 2020 (doi: https://doi.org/10.1101/2020.02.12.946087)