Deletion of V483 in the spike confers evolutionary advantage on SARS-CoV-2 for human adaptation and host-range expansion after a prolonged pandemic

Dear Editor,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone continuous evolution since its initial outbreak in 2019.The emergence of Omicron as the dominant variant occurred abruptly after 2022. 1 A highly mutated Omicron variant, BA.2.86, has recently been identified and reported in multiple countries.The global prevalence of this variant is gradually increasing, as confirmed by the World Health Organization (WHO), which has categorized it as a variant under monitored (VUM). 2 The Spike (S) protein of BA.2.86 has achieved more than 30 amino acid changes since its divergence from the parental BA.2 strain.Among these changes, the deletion of residue 483 (Δ483) in the receptor binding domain (RBD) region stands out (Fig. 1a; Supplementary information, Fig. S1), as deletions in the S protein typically occur in the N-terminal domain (NTD) region of SARS-CoV-2 variants.Interestingly, the absence of residue 483 has been observed in SARS. 3 Phylogenic and receptor usage analysis revealed that Δ483 is widespread among sarbecoviruses and is not linked to ACE2 binding 4 (Fig. 1b).Moreover, the deletion is genetically stable and can be sustained.These findings imply that Δ483 does not hinder the interaction of the virus with ACE2.In fact, it sometimes confers advantage since strains harboring the mutation become new prevalent strains.To assess the impact of the sudden deletion of 483 in SARS-CoV-2 and its potential link to the viral adaptation across different hosts, as well as its role in human pandemic, we conducted a multidimensional analysis covering receptor usage and infection capabilities in different hosts, along with the effects of the deletion on cell-cell fusion, S protein cleavage, and immunogenicity.The findings reported here aid in the understanding of the evolutionary dynamics of the virus.6][7][8] The structural conservation of ACE2 in different species not only makes it possible for many sarbecoviruses to use human ACE2 (hACE2) for infection but also increases the chances of crossspecies transmission. 9To investigate whether BA.2.86 also exhibits high affinity for ACE2 from animals, we tested wild-type (WT), BA.1, BA.2.75, BA.2.86, and BA.2.86-V483ins for their ability to bind ACE2 from animals under identical conditions (Fig. 1c; Supplementary information, Fig. S2).As anticipated, ACE2 from bovine, goat, and cat, which shows high conservation with hACE2, exhibited a greater compatibility for binding with SARS-CoV-2 and its variants.The affinity gradually increased from WT to BA.2.86, aligning with the trends observed for hACE2.Conversely, ACE2s sharing lower conservation with hACE2 showed limited compatibility in binding with SARS-CoV-2 despite weak binding affinities for BA.1 (Fig. 1c).Interestingly, the addition of V483 was more beneficial to the binding of RBD with hACE2, while