key: cord-0295960-43om0nji
authors: Carreno, J. M.; Alshammary, H.; Tcheou, J.; Singh, G.; Raskin, A.; Kawabata, H.; Sominsky, L.; Clark, J.; Adelsberg, D. C.; Bielak, D.; Gonzalez-Reiche, A. S.; Study Group, P.; Srivastava, K.; Sordillo, E. M.; Bajic, G.; van Bakel, H.; Simon, V.; Krammer, F.
title: Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate
date: 2021-12-21
journal: nan
DOI: 10.1101/2021.12.20.21268134
sha: 373a7f5b36224d1a47255e5cd0e8abb6169ad8e0
doc_id: 295960
cord_uid: 43om0nji

The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in November of 2021 in South Africa and Botswana as well as in a sample of a traveler from South Africa in Hong Kong.1,2 Since then, B.1.1.529 has been detected in many countries globally. This variant seems to be more infectious than B.1.617.2 (Delta), has already caused super spreader events3 and has outcompeted Delta within weeks in several countries and metropolitan areas. B.1.1.529 hosts an unprecedented number of mutations in its spike gene and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness.2,4-6 Here, we investigated the neutralizing and binding activity of sera from convalescent, mRNA double vaccinated, mRNA boosted as well as convalescent double vaccinated and convalescent boosted individuals against wild type, B.1.351 and B.1.1.529 SARS-CoV-2 isolates. Neutralizing activity of sera from convalescent and double vaccinated participants was undetectable to very low against B.1.1.529 while neutralizing activity of sera from individuals who had been exposed to spike three or four times was maintained, albeit at strongly reduced levels. Binding to the B.1.1.529 receptor binding domain (RBD) and N-terminal domain (NTD) was reduced in convalescent not vaccinated but was mostly retained in vaccinated individuals.

has shown the most antigenic drift in terms of reduction of in vitro neutralization rivaled only by 42 B.1.621 (Mu). 7 B.1.617.2 (Delta), which emerged in early 2020 has been the most consequential 43 variant given the fact that it is more infectious than the viruses circulating in the beginning of the 44 pandemic and also partially escapes neutralization in vitro. 8 variant hosts a large number of mutations in its spike protein including at least 15 amino acid 47 changes in the receptor binding domain (RBD). These mutations are predicted to affect most 48 neutralizing antibody epitopes. In addition, B.1.1.529 seems to be fit and highly transmissible 3 49

and it rapidly spread across the globe. In fact, within four weeks this variant has outcompeted 50 B.1.617.2 and is now the dominant circulating variant in several countries and urban areas. 51

Immunity to SARS-CoV-2 in human populations is highly variable and likely differs in individuals 52

with infection induced immunity, double vaccinated individuals, boosted individuals and 53

individuals with hybrid immunity due to the combination of infection followed by vaccination. 54

Understanding residual neutralizing and binding activity against highly antigenically distinct viral 55 variants such as B.1.1.529 in these distinct groups is essential to gauge the level of protection 56 that a specific community has against infection, mild or severe COVID-19. 57

To address these questions, we determined the loss of in vitro neutralizing and binding activity 58 for B.1.1529 in sera from individuals with different levels of immunity (infection, vaccine, hybrid). 59 We Tables 1 and 2 ). First, we tested the in vitro neutralizing 66 activity of the sera against wild type SARS-CoV-2 (as a reference for ancestral strains), B.1.351 (as 67 a reference for the most pronounced in vitro escape phenotype) and B.1.1.529 (isolated from 68 one of the first cases identified in New York City in late November 2021, Supplementary Table  69 3). The neutralization assay used mimics physiological conditions, since it is performed with 70 authentic SARS-CoV-2 in a multicycle replication setting in which serum/antibody is present at all 71 times akin to the situation in a seropositive individual. Across all 85 samples, the reduction in 72 neutralization for B.1.1.529 was greater than 14.5-fold (the actual fold reduction could not be 73 calculated since many samples were below the limit of detection) ( Figure 1B) Figure 1C ).

For samples from individuals double vaccinated with BNT162b2 and mRNA-1273, we observed a 79 more than 23-fold and a 42-fold reduction in neutralizing activity respectively (Figure 1D and E) . 80 However, most individuals retained low but detectable neutralizing activity. Boosted individuals 81 experienced lower reduction with a 7.5-fold drop in neutralization for BNT162b2 boosted 82 individuals and a 16.7-fold reduction in mRNA-1273 boosted individuals (Figure 1F and G) . Of 83 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint note, the lower fold change and the higher starting neutralization titers led to considerable  84  residual neutralizing activity in those groups. Convalescent individuals who received two  85  BNT162b2, two mRNA-1272 or three BNT162b2 vaccine doses showed 14-fold, 11-fold and 13-86 fold drops in B.1.1.529 neutralization ( Figure 1H , I and J). However all individuals in these groups 87 maintained relatively robust neutralization activity. These data indicate that convalescent 88 individuals greatly benefit from vaccination, an observation that is of significant public health 89

importance. 90

While in vitro neutralization is an important antibody function, antibody binding -even in the 91 absence of detectible neutralizing activity -can provide protection through Fc-mediated effector 92

functions. This type of protection has been described in detail for influenza virus 9-11 but binding 93 antibody titers also represent a correlate of protection for SARS-CoV-2. 12 (Figure 2A) . Overall, reduction in binding to B.1.1.529 RBD was much less 102 pronounced than reduction in neutralization ( Figure 2B ). However, this reduction was 103

significantly higher than what we observed here and in the past for B.1.351. 8 Reduction in binding 104 was most pronounced for convalescent individuals ( Figure 2C ) with a drop of more than 7.5-fold 105 and undetectable reactivity by enzyme linked immunosorbent assay (ELISA) in two thirds of the 106 convalescent individuals who were infected early in the pandemic prior to the circulation of viral 107 variants of concern. In all other groups binding was relatively well maintained with a reduction 108 in binding ranging from a 2.9-fold drop in individuals who had received two vaccinations with 109 mRNA-1273 to a 1.5-fold drop in individuals boosted with BNT162b2 ( Figures 2D to 2J) . 110

In addition to the RBD, the NTD is a prime target for B-cells after COVID-19 mRNA vaccination. 14 111

The NTD also hosts neutralizing epitopes within and outside of the immunodominant 'super site'. 112

The NTD of B. site' or the presence of a large number of unchanged epitopes within this domain (Figure 3) . 120

Our data aligns well with initial reports on the impact of B.1.1.529 on in vitro neutralizing activity 121 of convalescent and vaccine serum and expands on these initial reports by inclusion of 122 subcohorts with divergent SARS-CoV-2 exposure history including infection induced, primary 123 vaccine regimen as well as booster induced and hybrid immunity. 2,5, 6 We found that neutralizing 124 activity of B.1.1.529 is most impacted in unvaccinated, convalescent individuals and in naive 125 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint This study also provides first insights into B.1.1.529 RBD and NTD specific binding changes. 134

Compared to the changes in neutralizing activities, binding was surprisingly well preserved 135 especially against NTD, in general, and against the RBD in vaccinated, boosted and convalescent 136 vaccinated individuals. It is conceivable, that these binding antibodies which often have non-137 neutralizing phenotypes in cell culture, contribute to protection from disease as has been seen 138

for other viral infections. 9-11 In addition, the presence of strong binding antibodies suggest that, 139

while some antibodies may have lost affinity for the drifted epitopes, B-cells may be recalled 140 when encountering B. USA-WA1/2020 was used as wild-type reference (BEI resources, NR-52281). Supplemental Table  183 3 summarizes the amino acid substitutions, insertions and deletions in the spike region of each 184 of the three viral isolates 185

Viruses were grown by adding 200ul of viral transport media from the nasopharyngeal swabs to 186

Vero-E6-TMPRSS2 cells in culture media supplemented with 0.5 μg/ml amphotericin B (Gibco, # 187 15290-018). Cytopathic effects (CPE) appears within 4-6 days at which point the culture 188 supernatants was clarified by centrifugation at 4,000 g for 5 minutes. Expanded viral stocks used 189

were sequence-verified and titered by the 50% tissue culture infectious dose (TCID 50 ) method on 190

Vero-E6-TMPRSS2 cells prior to use in micro neutralization assays. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint 

The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-293 2 serological assays and NDV-based SARS-CoV-2 vaccines which list Florian Krammer as co-294

inventor. Viviana Simon is also listed on the serological assay patent application as co-inventor. 295

Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2. Florian 296

Krammer has consulted for Merck and Pfizer (before 2020), and is currently consulting for Pfizer, 297

Third Rock Ventures, Seqirus and Avimex. The Krammer laboratory is also collaborating with 298

Pfizer on animal models of SARS-CoV-2. 299 300 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint 410 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint

The copyright holder for this this version posted December 21, 2021. ; https://doi.org/10.1101/2021.12.20.21268134 doi: medRxiv preprint

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