Evidence for Deleterious Antigenic Imprinting in SARS-CoV-2 Immune Response

  1. Sanjana R. Sen
  2. Emily C. Sanders
  3. Alicia M. Santos
  4. Keertna Bhuvan
  5. Derek Y. Tang
  6. Aidan A. Gelston
  7. Brian M. Miller
  8. Joni L. Ricks-Oddie
  9. Gregory A. Weiss

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Abstract

A previous report demonstrated the strong association between the presence of antibodies binding to an epitope region from SARS-CoV-2 nucleocapsid, termed Ep9, and COVID-19 disease severity. Patients with anti-Ep9 antibodies (Abs) had hallmarks of antigenic imprinting (AIM), including early IgG upregulation and cytokine-associated injury. Thus, the immunological memory of a previous infection was hypothesized to drive formation of suboptimal anti-Ep9 Abs in severe COVID-19 infections. This study identifies a putative primary antigen capable of stimulating production of cross-reactive, anti-Ep9 Abs. Binding assays with patient blood samples directly show cross-reactivity between Abs binding to Ep9 and only one bioinformatics-derived, homologous potential antigen, a sequence derived from the neuraminidase protein of H3N2 Influenza A virus. This cross-reactive binding is highly influenza strain specific and sensitive to even single amino acid changes in epitope sequence. The neuraminidase protein is not present in the influenza vaccine, and the anti-Ep9 Abs likely resulted from the widespread influenza infection in 2014. Therefore, AIM from a previous infection could underlie some cases of COVID-19 disease severity.

Importance

Infections with SARS-COV-2 result in diverse disease outcomes, ranging from asymptomatic to fatal. The mechanisms underlying different disease outcomes remain largely unexplained. Previously, our laboratory identified a strong association between the presence of an antibody and increased disease severity in a subset of COVID-19 patients. Here, we report that this severity-associated antibody cross-reacts with viral proteins from an influenza A viral strain from 2014. Therefore, we speculate that antibodies generated against previous infections, like the 2014 influenza A, play a significant role in directing some peoples’ immune responses against SARS-COV-2. Such understanding of the sources and drivers of COVID-19 disease severity can help early identification and pre-emptive treatment.

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  1. Version published to 10.1101/2021.05.21.445201v2 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.05.21.445201: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    αEp9 Abs binding to the potential epitopes was detected using horse radish peroxidase (HRP) conjugated αHuman Fc IgG (Thermo Fisher Scientific, Waltham MA) or αIgM µ-chain specific (Millipore Sigma, Temecula, CA) Abs diluted 1:5000 in ChonBlock Sample Antibody Dilution buffer.
    HRP) conjugated αHuman Fc IgG
    suggested: None
    Recombinant DNA
    SentencesResources
    Cloning: Predicted OAS epitopes were subcloned for phage display using the pM1165a phagemid vector (Levin, 2006) with an N-terminal FLAG-tag and a C-terminal P8 M13-bacteriophage coat protein.
    pM1165a
    suggested: None
    Expression and Purification of eGFP fusion peptides: pET28c plasmids encoding eGFP fusions to C-terminal Ep9-FLAG, EpNeu-FLAG, EpPred-FLAG and FLAG (negative control) and N-terminal His6 peptide epitopes, were transformed into BL21DE3 Star E. coli chemically competent cells.
    pET28c
    suggested: RRID:Addgene_161936)
    Software and Algorithms
    SentencesResources
    Alignment of Ep9 sequence with the orthologs from other human coronaviruses (hCoVs) such as SARS-CoV, MERS, HKU-1, NL63, 229E and OC43 was conducted using the Benchling sequence alignment tool (Benchling, 2017) (https://benchling.com).
    https://benchling.com
    suggested: (Benchling, RRID:SCR_013955)
    To explore a wider range of human host pathogens pBLAST (Altschul et al., 1997) (https://blast.ncbi.nlm.nih.gov/Blast.cgi) was used to search for Ep9 homology in a database of non-redundant protein sequences; common human-host viruses were specified in the organism category.
    https://blast.ncbi.nlm.nih.gov/Blast.cgi
    suggested: (TBLASTX, RRID:SCR_011823)
    The queries were conducted with the blastp (protein-protein BLAST) program (Altschul et al., 1997) with search parameters automatically adjusted for short input sequences.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Using the ProMod3 3.2.0 tool (Studer et al., 2021), a structural model was generated based on the crystal structure (2.35Å, PDB 4GZS 1.
    ProMod3
    suggested: None
    Statistical Analysis: The ELISA data were analyzed in GraphPad Prism 9 (https://www.graphpad.com).
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.05.21.445201v1 on bioRxiv