Analysis of the SARS-CoV-2 Spike Protein: Identification of Conserved Targets and Mutations for Diagnostic Applications

SARS-CoV-2 is the etiological agent of COVID-19. Its transmission has become a major concern over the last decade due to the recent pandemic. Due to its high transmissibility, the global healthcare system has faced significant strain, in addition to causing countless deaths. The spike protein has been recognized as responsible for facilitating the entry of the pathogen into host cells by interacting with the ACE-2 receptor of human cells. This characteristic makes it a focal point for scientific research, which aims to target it as a potential immunological marker and for pathogen tracking. To control the virus's spread, it is necessary to monitor its genetics by mapping the emergence of new mutations. Such mutations sometimes represent greater viral infectivity, besides abstracting the effectiveness of previously considered therapeutic and diagnostic measures. The objective of this work is to identify the possible conserved regions of the SARS-CoV-2 spike protein, focusing on regions amenable to antigen targeting, aiming at virus specificity, and developing an electronic optical analysis diagnostic method. The methodology involves comparing the wild-type spike protein sequence, obtained from Wuhan and available in the Uniprot database, with sequences of other variants from the EpiCoV™ section of the GISAID database. These sequences were aligned using the U-GENE program, utilizing the Clustal Omega algorithm. The positions of the regions favorable for antigenic targeting, with conservative mutations and without mutations, were represented in a 3D model using Pymol to locate accessible surface regions. As a result, 199 sequences were obtained from the following variants: Omicron (61), Beta (3), Alpha (10), Delta (8), Epsilon (1), Zeta (1), Eta (1), Theta (1), Iota (3), Kappa (1), Lambda (3), Mu (3), and Pango (30). The multiple sequence alignment between these variant sequences and the wild-type sequence enabled the identification of 124 non-conservative mutations, including: S12F, P26del/S, G75V, S255F, K77T, Q613H, D614G, I666S, S112L. It is concluded that the 3D structure of the spike contains antigenic targets on its surface, regions that should be evaluated through the prediction of antigen-antibody interactions, aiming to develop specific antibodies for SARS-CoV-2 using immunoinformatics, bioinformatics, and molecular modeling tools.

This work was supported by Conselho Nacional Desenvolvimento Cientifico e Tecnologico (CNPq),Fundação Carlos Chagas Filho à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).