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COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes

View ORCID ProfileMarek Prachar, View ORCID ProfileSune Justesen, View ORCID ProfileDaniel Bisgaard Steen-Jensen, Stephan Thorgrimsen, Erik Jurgons, View ORCID ProfileOle Winther, View ORCID ProfileFrederik Otzen Bagger
doi: https://doi.org/10.1101/2020.03.20.000794
Marek Prachar
1Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
2Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
3Immunitrack ApS, Copenhagen, Denmark
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Sune Justesen
3Immunitrack ApS, Copenhagen, Denmark
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Daniel Bisgaard Steen-Jensen
3Immunitrack ApS, Copenhagen, Denmark
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Stephan Thorgrimsen
3Immunitrack ApS, Copenhagen, Denmark
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Erik Jurgons
4INTAVIS Peptide Services GmbH & Co.KG, Waldhäuser Str. 64 Germany-72076 Tübingen
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Ole Winther
1Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
2Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
5Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Frederik Otzen Bagger
1Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
6UKBB Universitats-Kinderspital, Department of Biomedicine, Basel, 4031 Basel, Switzerland
7Swiss Institute of Bioinformatics, Basel, 4053 Basel, Switzerland
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  • For correspondence: frederik.otzen.bagger@regionh.dk
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Abstract

The recent outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cells via the HLA complex. SARS-CoV-2 is a large RNA virus and testing of all overlapping peptides in vitro to deconvolute an immune response is not feasible. Therefore HLA-binding prediction tools are often used to narrow down the number of peptides to test. We tested 15 epitope-HLA-binding prediction tools, and using an in vitro peptide MHC stability assay, we assessed 777 peptides that were predicted to be good binders across 11 MHC allotypes. In this investigation of potential SARS-CoV-2 epitopes we found that current prediction tools vary in performance when assessing binding stability, and they are highly dependent on the MHC allotype in question. Designing a COVID-19 vaccine where only a few epitope targets are included is therefore a very challenging task. Here, we present 174 SARS-CoV-2 epitopes with high prediction binding scores, validated to bind stably to 11 HLA allotypes. Our findings may contribute to the design of an efficacious vaccine against COVID-19.

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  • Figure 1 revised

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 25, 2020.
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COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes
Marek Prachar, Sune Justesen, Daniel Bisgaard Steen-Jensen, Stephan Thorgrimsen, Erik Jurgons, Ole Winther, Frederik Otzen Bagger
bioRxiv 2020.03.20.000794; doi: https://doi.org/10.1101/2020.03.20.000794
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COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes
Marek Prachar, Sune Justesen, Daniel Bisgaard Steen-Jensen, Stephan Thorgrimsen, Erik Jurgons, Ole Winther, Frederik Otzen Bagger
bioRxiv 2020.03.20.000794; doi: https://doi.org/10.1101/2020.03.20.000794

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