key: cord-0843367-pk9nuu74
authors: Vogt, Anne-Cathrine; Augusto, Gilles; Martina, Byron; Chang, Xinyue; Nasrallah, Gheyath; Speiser, Daniel E.; Vogel, Monique; Bachmann, Martin F.; Mohsen, Mona O.
title: Increased receptor affinity and reduced recognition by specific antibodies contribute to immune escape of SARS-CoV-2 variant Omicron
date: 2022-03-11
journal: bioRxiv
DOI: 10.1101/2022.03.11.483934
sha: b68218054e4256ed78211ba3a3e1445e4dce8745
doc_id: 843367
cord_uid: pk9nuu74

In this report, we mechanistically reveal how the Variant of Concern (VOC) SARS-CoV-2 Omicron (B.1.1.529) escapes neutralizing antibody responses, by characterization of this variant, and wildtype Wuhan and Delta variant (B.1.617.2). Convalescent sera as well as sera obtained from participants who received two or three doses of mRNA vaccines (Moderna-mRNA-1273® or Pfizer-BNT162b2®) were used for comparison in this study. Our data demonstrate that both the Delta as well as Omicron variants exhibit higher affinity for the receptor ACE2, facilitating infection and causing antibody escape by receptor affinity (affinity escape), due to reduced ability of antibodies to compete with RBD-receptor interaction and virus neutralization. In contrast, only Omicron but not Delta variant escaped antibody recognition, most likely because only Omicron exhibit the mutation at position E484 associated with reduced recognition, resulting in further reduced neutralization (specificity escape). Nevertheless, the immunizations with RNA based vaccines resulted in marked viral neutralization in vitro for all strains, compatible with the fact that Omicron is still largely susceptible to vaccination-induced antibodies, despite affinity- and specificity escape.

The appearance of the SARS-CoV-2 Omicron variant B.1.1.529 was reported in South Africa 38 (SA) on 24 th November 2021 by the World Health Organization (WHO) (1) . Two days later,

Omicron was designated as a new variant of concern (VOC) due to its potential to spread 40 rapidly worldwide. The first known sample was collected in SA on the 8 th November 2021 41 and the first sample detected outside SA was found in a traveler arriving in Hong Kong from 42 SA via Qatar on 11 th November 2021. On 7 th January 2022, Omicron was confirmed in 135 43 different countries world-wide (2).

The WHO has estimated the danger from Omicron as potentially high due to the 45 following reasons: the global risk of perpetuating SARS-CoV-2 pandemic remains high; 46 recent data have indicated that Omicron shows a significantly higher R-value than the Delta 47 VOC with already enhanced transmission (3, 4). Increased numbers of cases have 48 previously led to increased hospitalization and mortality, threatening to overwhelm health-49 care systems. Preliminary evidence suggested an increased risk of reinfection with Omicron 50 as compared to other VOCs (2). The concern was also growing because Omicron has also 51 spread amongst doubly vaccinated people (5). In turn, COVID-19 caused by Omicron 

Until recently, the Delta (B.1.617.2) VOC was the predominant SARS-CoV-2 variant 57 before the emergence of Omicron. Delta VOC was discovered in late 2020 in India and had 58 spread to more than 163 nations by 24 th August 2021. In June 2021, WHO has stated, that 59 SARS-CoV-2 Delta strain would become the most prevalent strain in the world (6). Based on 60 recent evidence, the Delta strain is 40-60% more transmissible than the previous forms such 61 as wild type (WT) Wuhan or other recent VOCs such as the Alpha (B.1.1.7) VOC. Delta has 62 also been associated with increased risk of hospitalization mostly for unvaccinated or 63 partially vaccinated people (7) 

Interestingly, T478K mutation has also been detected in the Omicron VOC. Similar to 155 L452R, T478K is in the RBD of the spike protein, also located within RBM of ACE2, making 156 direct contact with the receptor (23). Figure 1 and Table 1 show the mutations in the RBD 178 receptor ( Fig. 2A) which is consistent with our previous findings (9, 11). Interestingly,

RBD Delta and RBD Omicron exhibit an approximately similar two-fold increase in the binding 180 affinity to ACE2 (RBD Delta K D = 10.5 nM, Figure 2B ) and (RBD Omicron K D =11.6 nM, Figure 2C ).

The affinity increase of both RBD Delta and RBD Omicron is caused by an enhanced association 182 rate and decreased dissociation rate ( 

When measuring the OD 50 of the induced antibody titer, results indicate, as expected 207 the superiority of the additional booster dose (Group III) (Fig. 3D ). No statistical difference has been detected in recognizing RBD WT, RBD Delta or RBD Omicron after 2 doses of mRNA 209 vaccine (Fig. 3E ). However, a significant reduction in recognizing RBD Delta and RBD Omicron 210 following 3 doses of vaccine (p. <0.0001) was stated (Fig. 3E) . Analysis of AUC for 211 convalescent demonstrates strongly impaired recognition of RBD Omicron but not RBD 212 RBD Delta (Fig. 3F ). convalescent sera (Fig. 4A and B) . 

Omicron variant (B.1.1.529) of SARS-CoV-2: 351 Threat assessment and plan of action

Probable 356 Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel

Omicron leads to fresh wave of meeting cancellations

CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 362 complex

Delta variant: What is happening with transmission, hospital admissions, 364 and restrictions?

The Delta Variant Mutations in the Receptor Binding 368 Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2

In vitro data 371 suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both 372 receptor affinity and immune evasion

A scalable and 374 highly immunogenic virus-like particle-based vaccine against SARS-CoV-2

Molecular 377 definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain 378 mutations: Receptor affinity versus neutralization of receptor interaction

SARS-CoV-2 Omicron 381 RBD shows weaker binding affinity than the currently dominant Delta variant to human 382 ACE2

The puzzling 384 mutational landscape of the SARS-2-variant Omicron

SARS-CoV-2 structural 386 features may explain limited neutralizing-antibody responses

AP205 VLPs 390 Based on Dimerized Capsid Proteins Accommodate RBM Domain of SARS-CoV-2 and 391 Serve as an Attractive Vaccine Candidate. Vaccines (Basel)

Development of a 393 Vaccine against SARS-CoV-2 Based on the Receptor-Binding Domain Displayed on Virus-394 Like Particles. Vaccines (Basel)

BNT162b2 396 mRNA COVID-19 vaccine induces antibodies of broader cross-reactivity than natural 397 infection, but recognition of mutant viruses is up to 10-fold reduced

To the editor: The Future of SARS-CoV-2 400 Vaccination

The Future of SARS-CoV-2 Vaccination New 402

Omicron variant (B.1.1.529) of SARS-CoV-404 2: Mutation, infectivity, transmission, and vaccine resistance

407 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers 408 recent massive expansion of SARS-Cov-2 variants

Preliminary report on severe 410 acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K

Mutations on RBD of SARS-CoV

Omicron variant result in stronger binding to human ACE2 receptor

Updates on immunologic correlates of vaccine-induced protection. 416 Vaccine

Insights into RNA synthesis, 418 capping, and proofreading mechanisms of SARS-coronavirus

Structural basis of receptor 420 recognition by SARS-CoV-2

Sensitivity of 422 SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Germinal centers

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.1.1.529 leads to widespread escape from neutralizing antibody responses

Neutralization of 432 SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine-elicited human sera

We thank Saiba GmbH for funding the project 336 337