Furin cleavage sites naturally occur in coronaviruses

Abstract

The spike protein is a focused target of COVID-19, a pandemic caused by SARS-CoV-2. A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.

Graphical abstract

Fig. 1

Structure of SARS-CoV-2 spike protein (PDB ID: 6VYB (Walls et al., 2020). A) Spike homotrimer in open conformation. B) Cleavage sites on spike protein (marked by arrows). Red cartoon, S1; light/dark blue cartoon, S2; dark blue cartoon, S2′). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Phylogenetic tree of coronavirus spike protein sequences. A) Noting genera of coronavirus. B) Subtree of Betacoronavirus, noting subgenera.

Fig. 3

Mapping of furin recognition motif on phylogenetic tree of spike protein sequences, the Sarbecovirus + Hibecovirus + Nobecovirus clade. Sequences in the SARS-CoV-2 clade were clustered with 95% identity threshold; in the SARS-CoV-2 clade were clustered with 99% identity threshold.

Fig. 4

Mapping of furin recognition motif on phylogenetic tree of spike protein sequences, A) Merbecovirus (for uncompressed tree see Fig. S2) and B) Embecovirus (for uncompressed tree see Fig. S3).

Fig. 5

Mapping of furin recognition motif on phylogenetic tree of spike protein sequences, the Alphacoronavirus + Gammacoronavirus + Deltacoronavirus clade. Sequences clustered with 95% identity threshold.

Fig. 6

Positions of furin cleavage sites at the linking region of S1 and S2. A) Multiple sequence alignment of representative Betacoronavirus spike protein S1/S2 region, with furin recognition motifs highlighted (red colorboxes in sequence alignment). Phylogenetic tree of spike protein sequences is colored to indicate subgenera (coloring scheme the same as in Fig. 2B). B) Positions of furin cleavage sites in different coronavirus genera (red cartoon, furin recognition motif; red arrow, cleavage site); structures: SARS-CoV-2, PDB ID 6VYB (Walls et al., 2020), with missing loop added; feline coronavirus (FCoV) UU16, homology model based on PDB ID 5SZS (Walls et al., 2016); infectious bronchitis coronavirus (IBV), PDB ID 6CV0 (Shang et al., 2018). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)