The emergence of SARS-CoV-2 by an unusual genome reconstitution

Abstract SARS-CoV-2 has been spreading remarkedly fast around the world since its emergence while the origin of the virus remains ambiguous. Here, we constructed all of the original prototype genome sequences of SARS-CoV-2 by selecting the common nucleotide among the different virus strains with species. Phylogenetic analysis on the prototype sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pan-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of 7 amino acids within the spike protein of SARS-CoV-2. Database searches showed that the motif originated from a surface protein of Plasmodium malariae, suggesting that the SARS-CoV-2 was emerged after acquiring the motif of the malaria surface protein.