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

Abstract

BACKGROUND. The role of humoral immunity in the coronavirus disease 2019 (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) protein 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. CONCLUSIONS. Epitope-resolved antibody testing not only affords a high-resolution alternativeto conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, it may potentially be used to predict clinical outcome. The epitope peptides can be readily modified to detect antibodies against variants of concern (VOC) in both the peptide array and latex agglutination formats.

Potential autoimmunity resulting from molecular mimicry between SARS-CoV-2 Spike and human proteins

“…Further, cross-reactivity with other TQLPP-containing proteins such as NEK10 cannot be dismissed based on our in-silico results, but in-vivo validation is required. The presence of neutralizing antibodies against peptides with TQLPP in COVID-19 patients' convalescent plasma (Li et al, 2020), particularly in severe and fatal cases (Voss et al, 2021) adds credence to our result. It is also interesting to note that antibodies against a TQLPPcontaining peptide were found in the serum of pre-pandemic, unexposed individuals (Stoddard et al, 2021).…”

“…This motif is well-conserved across beta- coronaviruses and has been shown to bind to a broadly neutralizing antibody effective against all human-infecting beta-coronaviruses (Pinto et al, 2021). Additionally, stronger antibody responses to the epitope containing the ELDKY motif have been recorded for severe (requiring hospitalization) vs moderate cases, while fatal cases had a weaker response than surviving cases (Voss et al, 2021). Together with the 3D-mimics identified here, these results suggest interesting possibilities for the ELDKY motif from the perspective of both protective immunity and an autoimmune response.…”

“…The SARS-CoV-2 Spike protein is responsible for enabling SARS-CoV-2 entry into host cells (Shang et al, 2020). Spike protrudes from the virus surface and is one of the main antigenic proteins for this virus (Voss et al, 2021). Additionally, Spike is the primary component in the vaccines against SARS-CoV-2.…”

Determination of IgG1 and IgG3 SARS-CoV-2 spike protein and nucleocapsid binding – Who is binding who and why?

“…IgG is the most abundant class of antibody found in the convalescent plasma of those recovering from COVID-19 ARDS [6]; and the onset of ARDS appears to correspond with the time of antibody class switch to IgG [7] (see Figure 1 panel A). Antibody responses directed at the spike protein and the receptor binding domain (RBD) in particular, have been identified as the main neutralizing component of the SARS-CoV-2 antibody response [8,9,10]. A distinct antibody signature has been linked to different COVID-19 disease outcomes: early spike-specific responses were associated with a positive outcome, while early nucleocapsid specific responses were associated with a negative outcome and death.…”

Broadly-recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles

“…Immune reponses to the 163/164 region of the SARS-CoV-2 spike protein have been observed in other studies (Deng et al, 2021;Dykema et al, 2021;Low et al, 2021;Loyal et al, 2021;Mateus et al, 2020;Saini et al, 2021;Tarke et al, 2021;Woldemeskel et al, 2021). An overlapping epitope accessible in the pre-fusion conformation was recognized by antibodies from COVID-19 donors as one of the most highly recognized linear epitopes, and antibodies recognizing this sequence were detected in both COVID-19 and unexposed donors (Poh et al, 2020;Shrock et al, 2020;Voss et al, 2021). Several studies of CD4+ and CD8+ T cell responses in SARS-CoV-2 donors, including unbiased epitope screens as well as those based on MHC-binding predictions, identified peptides overlapping the S811-831 sequence among many others (Deng et al, 2021;Dykema et al, 2021;Low et al, 2021;Saini et al, 2021;Tarke et al, 2021;Woldemeskel et al, 2021).…”