Influence of Mutations on Physicochemical Properties of Spike Proteins from Prototypical SARS-CoV-2 Variants of Concern Detected in Amazonian Countries

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the viral spike protein (S) has become a target to describe appropriate epitopes for vaccine development and to carry out epidemiological surveillance, especially regarding the variants of concern (VOCs). This study aimed to evaluate the influence of mutations on physicochemical properties of S proteins from prototypical SARS-CoV-2 VOCs detected in Amazonian countries. Using multiple computational tools, seven VOCs (B.1.1.7/P.1/B.1.617.2/BA.1/BA.2/BA.4/BA.5) were identified and compared to the ancestral lineage of the virus (B). In all variants, most amino acids were nonpolar; among the polar amino acids, B.1.617.2/BA.1/BA.2/BA.4/BA.5 presented a slightly higher proportion of basic residues and a lower proportion of neutral residues. Unlike B.1.1.7/P.1/B.1.617.2, BA.1/BA.2 had a greater content of secondary structures, such as α-helices and β-sheets. Regarding post-translational modifications, BA.2/BA.4/BA.5 presented fewer glycosylations and phosphorylations. Finally, a more prominent antigenic propensity in the N-terminal domain of BA.2/BA.4/BA.5 and in the receptor-binding domain of B.1.617.2/BA.4/BA.5 was observed. In conclusion, the omicron variants of SARS-CoV-2 presented greater sequence variability in S proteins compared to the other VOCs, influencing structural aspects that can potentially modulate its interaction with cellular receptors and recognition by the immune system.