TABLE 1.
Spike mutations present in the Omicron variant of concern and their functional characterizationa
| Mutation | Variant | Location | Potential impact |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Increased infectivityb | Increased transmissibilityc | Increased disease severityd | Monoclonal and polyclonal antibody escape | Convalescent sera escape | Vaccine escape | Diagnostic assays escape | |||
| Amino acid mutations characterizing SARS-CoV-2 variants | |||||||||
| A67V | Omicron | NTD | NA | NA | NA | NA | NA | NA | NA |
| T95I | Omicron | NTD | No | No | No | NA | NA | NA | NA |
| G142De | Omicron, Delta | NTD | NA | NA | NA | Yes | NA | NA | NA |
| L212I | Omicron | NTD | NA | NA | NA | NA | NA | NA | NA |
| G339D | Omicron | RBD | Yes | NA | NA | Yes | NA | NA | NA |
| S371L | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| S373P | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| S375F | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| K417Ne | Beta, Omicron | RBD | No | No | No | Yes | Yes | Yes | No |
| N440K | Omicron | RBD | Yes | NA | NA | Yes | Yes | Yes | NA |
| G446S | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| S477Ne | Omicron | RBD | Yes | Yes | No | Yes | Yes | Yes | No |
| T478Ke | Delta, Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| E484A | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| Q493R | Omicron | RBD | Yes | NA | NA | Yes | NA | NA | NA |
| G496S | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| Q498R | Omicron | RBD | Yes | NA | NA | Yes | NA | NA | NA |
| N501Ye | Alpha, Beta, Gamma, Omicron | RBD | Yes | Yes | No | Yes | Yes | Yes | No |
| Y505H | Omicron | RBD | NA | NA | NA | Yes | NA | NA | NA |
| T547K | Omicron | S1/S2 | NA | NA | NA | NA | NA | NA | NA |
| D614Ge | All variants | S1/S2 | Yes | Yes | No | No | No | No | No |
| H655Ye | Gamma, Omicron | S1/S2 | Yes | NA | NA | No | No | No | No |
| N679K | Omicron | S1/S2 | Yes | NA | NA | No | No | No | No |
| P681He | Alpha, Omicron | S1/S2 | Yes | NA | No | No | No | No | No |
| Deletions and insertions characterizing SARS-CoV-2 variants | |||||||||
| Deletion of H69-V70e | Alpha, Omicron | NTD | Yes | No | No | Yes | No | No | Yes |
| Deletion of V143-Y144-Y145e | Alpha, Omicron | NTD | No | No | No | Yes | No | No | No |
| Deletion of N211 | Omicron | NTD | NA | NA | NA | NA | NA | NA | NA |
| Insertion of 214 EPE | Omicron | NTD | NA | NA | NA | NA | NA | NA | NA |
The nomenclature of variants is that reported by the World Health Organization (WHO). The Omicron S2 mutations (N764K, D796Y, N856K, Q954H, N969K, and L981F) have not been reported in the table since no data are yet available on their functional characterization. NA, not available; NTD, N-terminal domain (amino acids [aa] 13 to 305); RBD, receptor-binding domain (aa 319 to 541); SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; S1/S2, the junction between subunit S1 and S2 (aa 542 to 690).
Infectivity was evaluated in pseudotyped viruses and/or by structural analysis from studies published on PubMed or bioRxiv.
Transmissibility was evaluated by molecular epidemiology-based studies and/or in vivo studies published on PubMed or bioRxiv.
Disease severity was evaluated by analyzing clinical outcomes in term of long-lasting infections and/or hospitalization period.
These mutations are also present in other identified VOCs, with the exception of S477N, which was detected in the variants B.1.620 and B.1.160. The role of these mutations has been extensively discussed in our recently published article (14).