Schema for IEDB Predictions - IEDB-Predicted Epitopes from Grifoni et al 2020
  Database: wuhCor1    Primary Table: cd8Epitopes Data last updated: 2020-04-03
Big Bed File Download: /gbdb/wuhCor1/epitopes/cd8Epitopes.bb
Item Count: 628
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
chromStart19894Start position in chromosome
chromEnd19918End position in chromosome
nameAPAHISTIShort Name of item
score966Score from 0-1000
strand++ or -
thickStart19894Start of where display should be thick (start codon)
thickEnd19918End of where display should be thick (stop codon)
reserved241,142,112Used as itemRgb as of 2004-11-22
scoreValue0.15Epitope score
id440Link to source
descriptionorf1ab_APAHISTIDescription

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedscoreValueiddescription
NC_045512v21989419918APAHISTI966+1989419918241,142,1120.15440orf1ab_APAHISTI
NC_045512v21998120023VFFDGRVDGQVDLF907+1998120023188,209,2460.08441orf1ab_VFFDGRVDGQVDLF
NC_045512v22006820095GLQPSVGPK941+2006820095242,200,1790.12442orf1ab_GLQPSVGPK
NC_045512v22008020107SVGPKQASL899+2008020107170,198,2530.07443orf1ab_SVGPKQASL
NC_045512v22008620122GPKQASLNGVTL941+2008620122242,200,1790.12444orf1ab_GPKQASLNGVTL
NC_045512v22012520155GEAVKTQFNY0+20125201550,0,0-1.0445orf1ab_GEAVKTQFNY
NC_045512v22012820155EAVKTQFNY890+2012820155149,183,2540.06446orf1ab_EAVKTQFNY
NC_045512v22013720164KTQFNYYKK899+2013720164170,198,2530.07447orf1ab_KTQFNYYKK
NC_045512v22022120248QEFKPRSQM0+20221202480,0,0-1.0448orf1ab_QEFKPRSQM
NC_045512v22023020254KPRSQMEI983+2023020254218,90,720.17449orf1ab_KPRSQMEI

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)