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. 2020 Apr 8;27(4):671-680.e2.
doi: 10.1016/j.chom.2020.03.002. Epub 2020 Mar 16.

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Alba Grifoni  1 , John Sidney  1 , Yun Zhang  2 , Richard H Scheuermann  3 , Bjoern Peters  4 , Alessandro Sette  5
Affiliations

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Alba Grifoni et al. Cell Host Microbe. .

Abstract

Effective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it. However, little information is available about the targets of immune responses to SARS-CoV-2. We used the Immune Epitope Database and Analysis Resource (IEDB) to catalog available data related to other coronaviruses. This includes SARS-CoV, which has high sequence similarity to SARS-CoV-2 and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in SARS-CoV-2 that have high homology to the SARS-CoV virus. Parallel bioinformatic predictions identified a priori potential B and T cell epitopes for SARS-CoV-2. The independent identification of the same regions using two approaches reflects the high probability that these regions are promising targets for immune recognition of SARS-CoV-2. These predictions can facilitate effective vaccine design against this virus of high priority.

Keywords: B cell epitope; COVID-19; SARS-CoV; SARS-CoV-2; T cell epitope; coronavirus; infectious disease; sequence conservation.

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Conflict of interest statement

Declaration of Interests La Jolla Institute for Immunology (LJI) has filed a patent application regarding this manuscript.

Figures

None
Graphical abstract
Figure 1
Figure 1
Comparison of SARS-CoV-2 (Wuhan-Hu-1) Genome Structure with Its Closest Bat Relative (bat-SL-CoVZXC21), Tor2 SARS-CoV, and HCoV-EMC MERS-CoV Above: Coding sequence (CDS) regions corresponding to homologous proteins between the four viruses are filled with the same color in the genome schematic to indicate homology; regions with no homology to the predicted SARS-CoV-2 proteins are colored white. Below: Table of pairwise protein similarities (expressed as % identity) between SARS-CoV-2 and the other three viruses.
Figure 2
Figure 2
B Cell Immunodominant Regions Based on SARS-Specific Epitope Mapping RF score for each amino acid position was calculated (see STAR Methods) and plotted over the SARS-CoV consensus sequence of spike glycoprotein (A), membrane protein (B), and nucleoprotein (C).
Figure 3
Figure 3
SARS-CoV-2 Spike Glycoprotein (PDB: 6VSB) The calculated surface of the top 13 amino acid residues predicted to be B cell epitopes based on ranking performed with Discotope 2.0 are shown in red. The monomer is shown in the upper left. The upper right and lower center present the trimer in two different orientations. 3D-rendering was performed using YASARA (Krieger and Vriend, 2014).
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