Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies

Syed Faraz Ahmed; Ahmed A. Quadeer; Matthew R. McKay

Acquisition and processing of sequence data. A total of 80 whole genome sequences of SARS- The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.03.933226 doi: bioRxiv preprint http://virological.org/t/novel-2019-coronavirus-genome/319/11) and two sequences (EPI_ISL_406959 and EPI_ISL_406960) that were partial genomes. These nucleotide sequences were aligned to the GenBank reference sequence (accession ID: NC_045512.2) and then translated into amino acid residues according to the coding sequence positions provided along the reference sequence for SARS-CoV-2 proteins (orf1a, orf1b, S, ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, and ORF10). These sequences were aligned separately for each protein using the MAFFT multiple sequence alignment program (Katoh & Standley, 2013) . Reference protein sequences for SARS-CoV and MERS-CoV were obtained following the same procedure from GenBank using the accession IDs NC_004718.3 and NC_019843.3, respectively. (Pickett et al., 2012) by querying for the virus species name: "Severe acute respiratory syndrome-related coronavirus" from human hosts. We limited our search to include only the experimentally-determined epitopes that were associated with at least one positive assay: (i) positive B cell assays (e.g., enzyme-linked immunosorbent assay (ELISA)based qualitative binding) for B cell epitopes; and (ii) either positive T cell assays (such as enzymelinked immune absorbent spot (ELISPOT) or intracellular cytokine staining (ICS) IFN-γ release), or positive major histocompatibility complex (MHC) binding assays for T cell epitopes. Strictly speaking, the latter set of epitopes, determined using positive MHC binding assays, are candidate epitopes, since a T cell response has not been confirmed experimentally. However, for brevity and to be consistent with the terminology used in the ViPR database, we will not make this qualification, and will simply refer to them as epitopes in this study. The number of B cell and T cell epitopes obtained from the database following the above procedure is listed in Table 1 .