Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern
Courtney Voss, Sally Esmail, Xuguang Liu, Michael J. Knauer, Suzanne Ackloo, Tomonori Kaneko, Lori Lowes, Peter Stogios, Almagul Seitova, Ashley Hutchinson, Farhad Yusifov, Tatiana Skarina, Elena Evdokimova, Peter Loppnau, Pegah Ghiabi, Taraneh Haijan, Shanshan Zhong, Husam Abdoh, Benjamin D. Hedley, Vipin Bhayana, Claudio M. Martin, Marat Slessarev, Benjamin Chin-Yee, Douglas D. Fraser, Ian Chin-Yee, Shawn S.C. Li
Courtney Voss, Sally Esmail, Xuguang Liu, Michael J. Knauer, Suzanne Ackloo, Tomonori Kaneko, Lori Lowes, Peter Stogios, Almagul Seitova, Ashley Hutchinson, Farhad Yusifov, Tatiana Skarina, Elena Evdokimova, Peter Loppnau, Pegah Ghiabi, Taraneh Haijan, Shanshan Zhong, Husam Abdoh, Benjamin D. Hedley, Vipin Bhayana, Claudio M. Martin, Marat Slessarev, Benjamin Chin-Yee, Douglas D. Fraser, Ian Chin-Yee, Shawn S.C. Li
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Clinical Research and Public Health COVID-19 Infectious disease

Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern

Abstract

BACKGROUND The role of humoral immunity in COVID-19 is not fully understood, owing, in large part, to the complexity of antibodies produced in response to the SARS-CoV-2 infection. There is a pressing need for serology tests to assess patient-specific antibody response and predict clinical outcome.METHODS Using SARS-CoV-2 proteome and peptide microarrays, we screened 146 COVID-19 patients’ plasma samples to identify antigens and epitopes. This enabled us to develop a master epitope array and an epitope-specific agglutination assay to gauge antibody responses systematically and with high resolution.RESULTS We identified linear epitopes from the spike (S) and nucleocapsid (N) proteins and showed that the epitopes enabled higher resolution antibody profiling than the S or N protein antigen. Specifically, we found that antibody responses to the S-811–825, S-881–895, and N-156–170 epitopes negatively or positively correlated with clinical severity or patient survival. Moreover, we found that the P681H and S235F mutations associated with the coronavirus variant of concern B.1.1.7 altered the specificity of the corresponding epitopes.CONCLUSION Epitope-resolved antibody testing not only affords a high-resolution alternative to conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, but it also may potentially be used to predict clinical outcome. The epitope peptides can be readily modified to detect antibodies against variants of concern in both the peptide array and latex agglutination formats.FUNDING Ontario Research Fund (ORF) COVID-19 Rapid Research Fund, Toronto COVID-19 Action Fund, Western University, Lawson Health Research Institute, London Health Sciences Foundation, and Academic Medical Organization of Southwestern Ontario (AMOSO) Innovation Fund.

Authors

Courtney Voss, Sally Esmail, Xuguang Liu, Michael J. Knauer, Suzanne Ackloo, Tomonori Kaneko, Lori Lowes, Peter Stogios, Almagul Seitova, Ashley Hutchinson, Farhad Yusifov, Tatiana Skarina, Elena Evdokimova, Peter Loppnau, Pegah Ghiabi, Taraneh Haijan, Shanshan Zhong, Husam Abdoh, Benjamin D. Hedley, Vipin Bhayana, Claudio M. Martin, Marat Slessarev, Benjamin Chin-Yee, Douglas D. Fraser, Ian Chin-Yee, Shawn S.C. Li

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Figure 3

Epitope-specific antibody responses distinguish COVID-19 patients with disparate disease severity and outcome.

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Epitope-specific antibody responses distinguish COVID-19 patients with d...
(A) Antibodies from patients with severe disease (n = 34) recognized significantly more epitopes than those with moderate conditions (n = 31). (B) Distribution of epitopes in moderate versus severe cases. (C) Number of epitopes/patient in the alive (n = 51) versus fatal (n = 14) groups. (D) Distribution of epitopes in alive versus fatal cases. (E) Heatmap representation of epitope-specific antibodies detected by the master array. Note that the heatmap was based on signals detected at low exposure. (F) Fatal cases showed significantly stronger antibody responses for the S-811 (alive n = 10, fatal n = 6) and S-881 (alive n = 10, fatal n = 8) epitopes. *, P < 0.05; **, P < 0.002; NS, not significant; unpaired Student’s t test with Welch’s correction. (G) Structure models to show location of the critical epitopes on the S protein. The epitopes S-671, S-811, and S-881 are shown on the domain structure diagram of S as well as its prefusion (left) and postfusion (right) conformation. The S protein has 2 cleavage sites, S1/S2 and S2′. The S-671 epitope is located at the C-terminus of S1 and disordered in the prefusion cryo–electron microscopy structure (left panel: Protein Data Bank 6XR8). A homology model from the SWISS-MODEL repository was employed to draw an S-671 epitope model in the left panel (colored blue), without cleavage at S1/S2. The Pro681 site is shown with a red sphere. The S2′ cleavage site is located on the S-811 epitope. The S-881 epitope is buried and inaccessible in the prefusion state but is disordered in the postfusion conformation (right panel: Protein Data Bank 6XRA). The S1 region is colored orange, except for the RBD, which is in cyan. The region between the S1/S2 and S2′ cleavage sites is shown in green. The S-811 and S-881 epitopes are colored magenta in the prefusion conformation.