Naturally enhanced neutralizing breadth to SARS-CoV-2 after one year
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Zijun Wang
1,*
, Frauke Muecksch
2,*
, Dennis Schaefer-Babajew
1,*
, Shlomo Finkin
1,*
, Charlotte
4
Viant
1,*
, Christian Gaebler
1,*
, Hans- Heinrich Hoffmann
3
, Christopher O. Barnes
4
, Melissa
5
Cipolla
1
, Victor Ramos
1
, Thiago Y. Oliveira
1
, Alice Cho
1
, Fabian Schmidt
2
, Justin da Silva
2
, Eva
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Bednarski
2
, Lauren Aguado
3
, Jim Yee
5
, Mridushi Daga
1
, Martina Turroja
1
, Katrina G. Millard
1
,
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Mila Jankovic
1
, Anna Gazumyan
1, 6
, Zhen Zhao
5
, Charles M. Rice
3
, Paul D. Bieniasz
2, 6
, Marina
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Caskey
1
, Theodora Hatziioannou
2
, Michel C. Nussenzweig
1, 6
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1
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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2
Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
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3
Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY,
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10065, USA.
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4
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena,
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CA, USA.
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5
Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY,
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10065, USA
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6
Howard Hughes Medical Institute
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*equal contribution
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was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.05.07.443175doi: bioRxiv preprint
Address correspondence to: Paul D. Bieniasz, pbieniasz@rockefeller.edu; Marina Caskey,
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mcaskey@rockefeller.edu; Theodora Hatziioannou, thatziio@rockefeller.edu; or Michel C.
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Nussenzweig, nussen@rockefeller.edu.
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Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic
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caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains
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difficult to control despite the availability of several excellent vaccines. Progress in
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controlling the pandemic is slowed by the emergence of variants that appear to be more
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transmissible and more resistant to antibodies
1,2
. Here we report on a cohort of 63 COVID-
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19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of
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whom also received mRNA vaccines
3,4
. In the absence of vaccination antibody reactivity to
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the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number
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of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination
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increases all components of the humoral response, and as expected, results in serum
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neutralizing activities against variants of concern that are comparable to or greater than
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neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naïve
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individuals
2,5-8
. The mechanism underlying these broad-based responses involves ongoing
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antibody somatic mutation, memory B cell clonal turnover, and development of
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monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations,
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including those found in variants of concern
4,9
. In addition, B cell clones expressing broad
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and potent antibodies are selectively retained in the repertoire over time and expand
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dramatically after vaccination. The data suggest that immunity in convalescent individuals
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was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.05.07.443175doi: bioRxiv preprint
will be very long lasting and that convalescent individuals who receive available mRNA
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vaccines will produce antibodies and memory B cells that should be protective against
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circulating SARS-CoV-2 variants.
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We initially characterized immune responses to SARS-CoV-2 in a cohort of convalescent
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individuals 1.3 and 6.2 months after infection
3,4
. Between February 8 and March 26, 2021, 63
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participants between the ages of 26 and 73 years old (median 47 years) returned for a 12-month
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follow-up visit. Among those, 26 (41%) had received at least one dose of either the Moderna
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(mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines, on average 40 days (range 2-82 days)
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before their study visit and 311 days (range 272-373 days) after onset of acute illness
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(Supplementary Table 1). Participants were was almost evenly split between sexes (43% female)
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and of the individuals that returned for a 12-month follow-up, only 10% had been hospitalized
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and the remainder had experienced relatively mild initial infections. Only 14% of the individuals
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reported persistent long-term symptoms after 12 months, reduced from 44% at the 6-month time
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point
4
. Symptom persistence was not associated with the duration and severity of acute disease
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or with vaccination status (Extended Data Fig. 1 a-c). All participants tested negative for active
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infection at the 12-month time point as measured by a saliva-based PCR assay
4
. The
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demographics and clinical characteristics of the participants are shown in Supplementary Tables
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1 and 2.
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Plasma SARS-CoV-2 Antibody Reactivity
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Antibody reactivity in plasma to the RBD and nucleoprotein (N) were measured by enzyme-
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linked immunosorbent assay (ELISA)
3
. We limited our analysis to RBD because plasma anti-
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was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.05.07.443175doi: bioRxiv preprint
RBD antibodies are strongly correlated with neutralizing activity
3,10-12
. Convalescent
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participants who had not been vaccinated maintained most of their anti-RBD IgM (103%), IgG
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(82%), and IgA (72%) titers between 6 and 12 months (Fig. 1a and Extended Data Fig. 2a-k).
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Consistent with previous reports
5-8
, vaccination increased the anti-RBD plasma antibody levels,
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with IgG titers increasing by nearly 30-fold compared to unvaccinated individuals (Fig. 1a right).
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The 2 individuals who did not show an increase had been vaccinated only 2 days before sample
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collection. In contrast to anti-RBD antibody titers that were relatively stable, anti-N antibody
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titers decreased significantly between 6 and 12 months in this assay irrespective of vaccination
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(Fig. 1b and Extended Data Fig. 2l-n).
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Plasma neutralizing activity in 63 participants was measured using an HIV-1 pseudotyped with
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the SARS-CoV-2 spike protein
3,4,13
(Fig. 1c-d and Extended Data Fig. 2o). Twelve-months after
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infection, the geometric mean half-maximal neutralizing titer (NT
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) for the 37 individuals that
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had not been vaccinated was 75, which was not significantly different from the same individuals
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at 6.2 months (Fig. 1c). In contrast, the vaccinated individuals showed a geometric mean NT
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of
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3,684, which was nearly 50-fold greater than unvaccinated individuals and slightly better
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compared to the 30-fold increase in anti-RBD IgG antibodies (Fig. 1a, c, and d). Neutralizing
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activity was directly correlated with IgG anti-RBD (Extended Data Fig.2p) but not with anti-N
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titers (Extended Data Fig.2r). We conclude that neutralizing titers remain relatively unchanged
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between 6 to 12 months after SARS-CoV-2 infection, and that vaccination further boosts this
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activity by nearly 50-fold.
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was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.05.07.443175doi: bioRxiv preprint
To determine the neutralizing activity against circulating variants of concern/interest, we
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performed neutralization assays on HIV-1 virus pseudotyped with the S protein of the following
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SARS-CoV-2 variants of concern/interest: B.1.1.7, B.1.351, B.1.526 and P.1
1,14,15
. Twelve-
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months after infection neutralizing activity against the variants was generally lower than against
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wild-type SARS-CoV-2 virus in the same assay with the greatest loss of activity against B.1.351
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(Fig. 1e). After vaccination the geometric mean NT
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rose to 11,493, 48,341, 22,109 and 26,553
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against B.1.351, B.1.1.7, B.1.526 and P.1, respectively. These titers are an order of magnitude
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higher than the neutralizing titers we and others have reported against the wild-type SARS-CoV-
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2 at the peak of the initial response in infected individuals and in naïve individuals receiving both
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doses of mRNA vaccines (Fig. 1d and
2-8
). Similar results were also obtained using authentic
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SARS-CoV-2 WA1/2020 and B.1.351 (Extended Data Fig.2s).
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Memory B cells
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The memory B cell compartment serves as an immune reservoir that contains a diverse collection
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of antibodies
16,17
. Although antibodies to the N-terminal domain and other parts of S can also be
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neutralizing, we limited our analysis to memory B cells that produce anti-RBD antibodies
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because they are the most numerous and potent
18,19
. To enumerate RBD-specific memory B
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cells, we performed flow cytometry using a biotin-labeled RBD
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(Fig. 2a and Extended Data Fig.
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3a and b). In the absence of vaccination, the number of RBD specific memory B cells present at
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12 months was only 1.35-fold lower than the earlier timepoint (p= 0.027, Fig. 2a). In contrast
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and consistent with previous reports
5,8,20
, convalescent individuals that received mRNA vaccines
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showed an average 8.6-fold increase in the number of circulating RBD specific memory B cells
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(Fig. 2a). B cells expressing antibodies that bound to both wild-type and K417N/E484K/N501Y
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was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (whichthis version posted June 2, 2021. ; https://doi.org/10.1101/2021.05.07.443175doi: bioRxiv preprint
