---
title: How to Identify SARS-CoV-2 Virus Derived Peptides
description: The search for a working SARS-CoV-2 vaccine could be long and laborious.
image: https://blog.mblintl.com/hubfs/SARS-2_Derived_Peptides1-1.png
---

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- How to Identify SARS-CoV-2 Virus Derived Peptides

# How to Identify SARS-CoV-2 Virus Derived Peptides

### Topics

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Published by [Yuri Poluektov](https://blog.mblintl.com/author/yuri-poluektov) on Nov 19, 2020 12:00:00 PM

![](https://blog.mblintl.com/hubfs/SARS-2_Derived_Peptides1-1.png)

In our previous blog post ([How to screen SARS-CoV-2 peptides to facilitate T cell research](https://blog.mblintl.com/screen_sars-cov-2_peptides)) we have described how the immune system samples all of the pathogenic proteins by looking at the small fragments of each protein and making a determination on whether that fragment (also referred to as peptide) belongs in the body. We have also described in our previous blog post ([Find Human MHC Class I Dominant Peptides](https://blog.mblintl.com/quickswitch_platform_human_mhc_classi_dominant_peptides)) the multiple MHC alleles that we tested for their ability to present SARS-CoV-2 peptides.

In our experiments of determining the ability of A2, A3, A11 and A24 MHC alleles to bind SARS-CoV-2 derived peptides we found little overlap between the peptides presented by human alleles and the H-2Kb mouse allele.

While a purely theoretical exercise at this point, the discovery of peptide sequences that could bind a human allele as well as a mouse allele could become very useful should a SARS-CoV-2 mouse model become available. We have performed an additional study to find SARS-CoV-2 peptides that can be presented by the H-2Kb mouse MHC molecule and 2 of those peptides (VVFLHVTYV and SIIAYTMSL) also proved to be strong binders of the HLA-A\*02:01 human allele.

We encourage further trials with our QuickSwitch™ system to help the development of a functional SARS-CoV-2 mouse model that could lead to the creation of a robust COVID-19 vaccine.

|   |   | **H-2 Kb** | **HLA-A\*02:01** |
| --- | --- | --- | --- |
| VNFNFNGL | SARS-CoV-2 Chain A, spike glycoprotein (539-546) | + |   |
| MAYRFNGI | SARS-CoV-2 Chain A, spike glycoprotein (902-909) | + |   |
| INITRFQTL | SARS-CoV-2 Chain A, spike glycoprotein (233-241) | + |   |
| VVLSFELL | SARS-CoV-2 Chain A, spike glycoprotein (511-518) | + |   |
| SIVRFPNI | SARS-CoV-2 Chain A, spike glycoprotein (325-332) | + |   |
| GNYNYLYRL | SARS-CoV-2 Chain A, spike glycoprotein (447-455) | + |   |
| VVFLHVTYV | SARS-CoV-2 Chain A, spike glycoprotein (1060-1068) | + | + |
| SIIAYTMSL | SARS-CoV-2 Chain A, spike glycoprotein (691-699) | + | + |
| VTQLYLGGM | SARS-CoV-2 ORF1ab polyprotein (5385-5393) | + |   |
| ITGLYPTL | SARS-CoV-2 ORF1ab polyprotein (5573-5580) | + |   |
| AAYYVGYL | SARS-CoV-2 Chain A, spike glycoprotein (263-270) | + |   |
| YNYLYRLF | SARS-CoV-2 Chain A, spike glycoprotein (449-456) | + |   |

**Summary of SARS-CoV-2 peptide binding to mouse H-2 Kb MHC molecules.**

Click the link below to view a full description of experiment from the Poluektov, Daftarian and Delcommenne manuscript.

[![Free Manuscript Download Here](https://no-cache.hubspot.com/cta/default/424171/597ef7da-c42c-487e-ad2a-11b48db8eaf0.png)](https://cta-redirect.hubspot.com/cta/redirect/424171/597ef7da-c42c-487e-ad2a-11b48db8eaf0)

References:

1.Yiwen Zhang et al.The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I bioRxiv 2020.05.24.111823; doi: [https://doi.org/10.1101/2020.05.24.111823](https://doi.org/10.1101/2020.05.24.111823)

2.Chao Hu et al. Identification of Cross-Reactive CD8+ T Cell Receptors with High Functional Avidity to a SARS-CoV-2 Immunodominant Epitope and Its Natural Mutant Variants bioRxiv 2020.11.02.364729; doi: [https://doi.org/10.1101/2020.11.02.364729](https://doi.org/10.1101/2020.11.02.364729)

 

Tags: [Tetramer](https://blog.mblintl.com/topic/tetramer), [QuickSwitch](https://blog.mblintl.com/topic/quickswitch), [SARS-CoV-2](https://blog.mblintl.com/topic/sars-cov-2)

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