S1 recognizes and binds to the receptor expressed on the host cell surface, and S2 fuses the membranes of the virus and host cells ( Li 2016). The S protein is subdivided into S1 and S2, corresponding to residues 1–685 and 686–1,273, respectively, in the S protein of SARS-CoV-2 ( fig. The Spike (S) protein of coronaviruses forms a trimer and initiates viral entry by interacting with a receptor on the host cell surface to enact virus attachment and induce membrane fusion ( Du et al. SARS-CoV-2, the etiological agent of coronavirus disease 2019 (COVID-19) ( Ren et al. Although HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43 cause the common cold, infection by SARS-CoV and MERS-CoV, both of which are β-CoVs, can result in pneumonia and even death. 2003), and Middle East respiratory syndrome coronavirus (MERS-CoV) ( Zaki et al. 1967), severe acute respiratory syndrome coronavirus (SARS-CoV) ( Drosten et al. Prior to 2019, six human-infecting coronaviruses were known: human coronaviruses (HCoVs) 229E ( Hamre and Procknow 1966), NL63 ( van der Hoek et al. Typically, α-CoVs and β-CoVs infect mammals, γ-CoVs infect birds, and δ-CoVs infect both mammals and birds ( Li 2016). Coronaviruses are divided into four genera, namely, Alphacoronavirus (α-CoV), Betacoronavirus (β-CoV), Gammacoronavirus (γ-CoV), and Deltacoronavirus (δ-CoV). SARS-CoV-2, coronavirus, Spike protein, molecular evolution, positive selection, adaptive evolution IntroductionĬoronaviruses are single-stranded, positive-sense RNA viruses that infect various mammal and avian species ( Li 2016 Cui et al. Although the S1 N-terminal domain exhibits signals of positive selection in the pairwise comparisons in all four coronavirus genera, positive selection is primarily detected in the S1 C-terminal domain (the receptor-binding domain) in the ongoing evolution of SARS-CoV-2, possibly owing to the change in host settings and the widespread natural infection and SARS-CoV-2 vaccination in humans. Here, we show that the S gene, particularly the S1 region, has experienced positive selection in both SARS-CoV-2 and other coronaviruses. It is intriguing to determine whether the selection pressure on the S gene differs between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses due to the host shift from nonhuman animals to humans. As the coronavirus disease 2019 pandemic has developed, many changes in the S protein have been under positive selection by altering the receptor-binding affinity, reducing antibody neutralization activities, or affecting T-cell responses. The interactions between the S proteins of coronaviruses and receptors of host cells are extraordinarily complex, with coronaviruses from different genera being able to recognize the same receptor and coronaviruses from the same genus able to bind distinct receptors. The Spike (S) protein of coronaviruses binds to a receptor on the host cell surface to promote viral entry. Coronaviruses are single-stranded, positive-sense RNA viruses that can infect many mammal and avian species.
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