Pillar 6
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)

Understanding how the immune system responds to SARS-CoV-2, the virus responsible for COVID-19, is crucial for developing better diagnostics, treatments, and vaccines. This study focuses on identifying specific parts of the virus (epitopes) that are recognized by the immune system and how mutations in the virus affect this recognition.

Researchers used a high-density peptide array (HDPA), which includes tiny pieces of all the proteins from SARS-CoV-2 and other common coronaviruses, to identify which parts of these proteins are recognized by antibodies in the blood of people who have had COVID-19 or were asymptomatic. They compared these responses to those from people who had not been infected with COVID-19.

The team also used a computational framework to analyze these immune responses in detail and to study how these viral protein segments (epitopes) have evolved. The researchers examined a large public dataset of over 38,000 viral genomes to see how these epitopes changed over time and across different variants of SARS-CoV-2.

Key Findings

  • Epitope Identification: The study identified several B cell epitopes, which are specific parts of the virus recognized by antibodies. Some of these epitopes were common across different coronaviruses, while others were unique to specific types.
  • Cross-Reactive Epitopes: The researchers found certain epitopes that could trigger an immune response against multiple coronaviruses, potentially enhancing the overall immune response to SARS-CoV-2.
  • Evolutionary Analysis: By examining the viral genomes, the study showed how different epitopes have evolved over time. They found that mutations in the spike and nucleocapsid proteins were under stronger selection pressure between different hosts (when the virus spreads from one person to another) than within the same host (as the virus replicates within a single person). This suggests that most of the pressure for the virus to evade the immune system happens during transmission between individuals.


This study highlights the dynamic nature of the SARS-CoV-2 virus and its ability to evolve in response to immune pressures. The findings emphasize the importance of monitoring viral mutations for developing effective vaccines and treatments. The discovery of cross-reactive epitopes also opens the door for potential broad-spectrum vaccines that could provide immunity against multiple coronaviruses.

Key Takeaways

  • Improved Diagnostics and Vaccines: Identifying specific viral segments that trigger immune responses helps in creating better diagnostic tools and more effective vaccines.
  • Viral Evolution: The virus tends to mutate more during transmission between people, which helps it evade the immune system.
  • Cross-Reactive Immune Responses: Some immune responses can target multiple coronaviruses, which could be useful for developing broad-spectrum vaccines.

This research enhances our understanding of how SARS-CoV-2 interacts with the immune system and provides valuable insights for future public health strategies against COVID-19 and other coronaviruses.

Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis. Arnaud N’Guessan, Senthilkumar Kailasam, Fatima Mostefai, Raphael Poujol, Jean-Christophe Grenier, Paola Contini, Raffaele De Palma, Carsten Haber, Volker Stadler, Guillaume Bourque, Julie G. Hussin, B. Jesse Shapiro, Jörg H. Fritz, Ciriaco A. Piccirillo.bioRxiv.2022.06.01.494373; https://www.biorxiv.org/content/10.1101/2022.06.01.494373v1