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bioRxiv · 10.1101/2020.07.15.204610

Antigenic variation of SARS-CoV-2 in response to immune pressure

Forni, D.·Cagliani, R.·Pontremoli, C.·Mozzi, A.·Pozzoli, U.·Clerici, M.·Sironi, M.
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Abstract

The ongoing evolution of SARS-CoV-2 is expected to be at least partially driven by the selective pressure imposed by the human immune system. We exploited the availability of a large number of high-quality SARS-CoV-2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than non-epitope positions. Similar results were obtained for other human coronaviruses. Conversely, in the SARS-CoV-2 population, epitopes for CD4+ and CD8+ T cells were not more variable than non-epitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8, and ORF3a). Analysis over longer evolutionary time-frames indicated that this effect is not due to differential constraints. These data indicate that SARS-CoV-2 is evolving to elude the host humoral immune response, whereas recognition by T cells might benefit the virus.

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Forni, D., Cagliani, R., Pontremoli, C., Mozzi, A., Pozzoli, U., Clerici, M., Sironi, M.. 2020-07-15. Antigenic variation of SARS-CoV-2 in response to immune pressure. https://doi.org/10.1101/2020.07.15.204610

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