In silico identification of vaccine targets for 2019-nCoV

F1000Res. 2020 Feb 25;9:145. doi: 10.12688/f1000research.22507.2. eCollection 2020.


Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.

Keywords: Coronavirus; T cell cross-reactivity; adaptive immunity; immunogenicity; vaccine development.

MeSH terms

  • Betacoronavirus / immunology*
  • COVID-19
  • COVID-19 Vaccines
  • China
  • Computer Simulation
  • Coronavirus Infections / immunology
  • Coronavirus Infections / prevention & control*
  • Coronavirus Nucleocapsid Proteins
  • Databases, Protein
  • Epitopes / immunology*
  • Humans
  • Nucleocapsid Proteins / immunology
  • Pandemics / prevention & control*
  • Peptides / immunology
  • Pneumonia, Viral / prevention & control*
  • SARS-CoV-2
  • Spike Glycoprotein, Coronavirus / immunology
  • T-Lymphocytes / immunology
  • Viral Vaccines / immunology*


  • COVID-19 Vaccines
  • Coronavirus Nucleocapsid Proteins
  • Epitopes
  • Nucleocapsid Proteins
  • Peptides
  • Spike Glycoprotein, Coronavirus
  • Viral Vaccines
  • spike protein, SARS-CoV-2

Supplementary concepts

  • COVID-19
  • severe acute respiratory syndrome coronavirus 2

Grant support

This study was funded by the Medical Research Council Human Immunology Unit.