Evaluation of pre-existing cross reactive cellular immune responses to SARS-CoV-2 in Uganda

Abstract

Background: A low severity of COVID-19 disease has been reported in the Africa population more so in Uganda as compared to other regions like Europe, America and West Pacific. Over 169,996 people have been infected with COVID-19 disease in Uganda though most of these do not develop severe disease. It is hypothesized that previous exposure to seasonal human common cold coronaviruses (HCoVs) may influence the disease outcome by eliciting a stronger and faster immune response upon exposure to a virus of sufficient similarity. IFN-γ is one of the dominant cytokines produced by T cells and it plays a key role in controlling viral infections by obstructing the various stages of the viral life cycle in the cells stimulated with this cytokine. In this study, cross-reactive cellular immune responses to SARS-CoV-2 that can be conferred by the four human common cold coronaviruses; HCoV-229E, HCoV-OC43, HCoV-HKUI and HCoV-NL63 were evaluated.

Methodology: Fifty PBMC samples collected between October 2013 and February 2015 were stimulated with SARS-CoV-2 structural protein peptides and two HCoVs; HCoV-OC43 and HCoV-229E spike peptides. IFN-γ ELISpot assay was used to assess peptide pools that elicited a positive immune response. Spots formed were read using an AID ELISpot reader. Peptide to peptide blast was used to determine structural sequence similarity between SARS-CoV-2 structural proteins S, N, M and E and HCoV-229E and HCoV-OC43 spike protein peptides.

Results: Using a cut-off of 55 IFN-γ SFU/10^6 PBMCs after subtracting three times the background response, no participant was positive for the SARS-CoV-2 structural proteins S, M, N and E. 14 percent (7) of the fifty participants showed positive response to the HCoV-229E spike. 34 out of 181, 20 out of 59 and 13 out of 31 SARS-CoV-2 S, N and M peptide sequences showed similarity to the S, N and M proteins of HCoV-OC43 in percentages of 18.7, 33.89 and 41.9 respectively. 26 out of 181, 6 out of 59 and 6 out of 31 SARS-CoV-2 S, N and M protein peptide sequences showed similarity to the S, N and M proteins of HCoV-229E in percentages of 14.36, 10.2 and 19.4 respectively.

Conclusion: No pre-existing cross reactive cellular immune responses to SARS-CoV-2 were observed in the Ugandan population (background immunity). Cellular immune responses were observed in HCoV-229E. SARS-CoV-2 shares some structural similarity with HCoVs with the N protein much more conserved across the coronaviruses though not relevant for protection.