A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19

Hong Zhou; Xing Chen; Tao Hu; Juan Li; Hao Song; Yanran Liu; Peihan Wang; Di Liu; Jing Yang; Edward C. Holmes; Alice C. Hughes; Yuhai Bi; Weifeng Shi

The S protein of CoVs is functionally cleaved into two subunits, S1 and S2 15 in a similar manner 151 to the haemagglutinin (HA) protein of avian influenza viruses (AIVs). The insertion of polybasic 152 amino acids at the cleavage site in the HAs of some AIV subtypes is associated with enhanced 153 pathogenicity 16, 17 . Notably, HCoV-19 is characterized by a four-amino-acid-insertion at the 154 junction of S1 and S2, not observed in other lineage B beta-CoVs 18, 19 . This insertion, which 155 represents a poly-basic (furin) cleavage site, is unique to HCoV-19 and is present in all HCoV-156 19 sequenced so far. The insertion of three residues, PAA, at the junction of S1 and S2 in 157 RmYN02 ( Fig. 2h and Extended Data Figure 2 ) is therefore of major importance. Although the 158 inserted residues (and hence nucleotides) are not the same as those in RmYN02, and hence 159 are indicative of an independent insertion event, that they are presented in wildlife (bats) 160 strongly suggests that they are of natural origin and have likely acquired by recombination. 161