On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.

No abstract

ARS-CoV-2 was first detected in December 2019, leading to a pandemic with an estimated 5-6% mortality rate 1. Akin to SARS-CoV-1, the causative agent of the 2003 SARS outbreak, this is an enveloped betacoronavirus with protrusions of large trimeric 'spike' proteins. Receptor binding domains (RBDs) located at the tips of these spikes facilitate host cell entry via interaction with angiotensin-converting enzyme 2 (ACE2) 2. Spikes are type I transmembrane glycoproteins, formed from a single polypeptide, which transitions into a post-fusion state via cleavage into S1 (N-terminal) and S2 (C-terminal) chains following receptor binding or trypsin treatment 3. In the pre-fusion state, the apical RBD (~22 kDa) is folded down, enshrouded by the N-terminal domain (NTD) of the spike so that the receptor binding site is inaccessible until, it is assumed, an RBD stochastically swings upwards to present the ACE2 binding site 4-7. ACE2 interaction locks the RBD in the 'up' conformation, which drives conversion to the post-fusion form where the S2 subunit engages the host membrane while dispensing with S1 4,5. Neutralizing human monoclonal antibodies (mAbs) that recognize the ACE2 receptor binding site for SARS-CoV-1 and SARS-CoV-2 are generally not cross-reactive between the two viruses and are susceptible to escape mutation 8-12. Indeed, a natural mutation (Y495N) has already been identified at this site (GISAID 13 : accession ID: EPI_ISL_429783 Wienecke-Baldacchino et al.). By contrast, the CR3022 antibody (derived from a SARS-CoV-1-infected patient) cross-reacts strongly with SARS-CoV-2 (see Methods and Fig. 1) and has been shown to recognize a cryptic, conserved footprint on the RBD distinct from the binding epitope of