No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patients (preprint)

Here, by using mass spectrometry-based methods IgG1 and IgA1 clonal repertoires were monitored quantitatively and longitudinally in more than 50 individual serum samples obtained from 17 COVID-19 patients admitted to intensive care units because of acute respiratory distress syndrome. These serological clonal profiles were used to examine how each patient reacted to a severe SARS-CoV-2 infection. All 17 donors revealed unique polyclonal repertoires and changes after infection. Substantial changes over time in the IgG1 and/or IgA1 clonal repertoires were observed in individual patients, with several new clones appearing following the infection, in a few cases leading to a few very high abundant IgG1 and/or IgA1 clones dominating the repertoire. Several of these clones were de novo sequenced through combinations of top-down, middle-down and bottom-up proteomics approaches. This revealed several sequence features in line with sequences deposited in the SARS-CoV-specific database of antibodies. In other patients, the serological Ig profiles revealed the treatment with tocilizumab, as after treatment, this IgG1-mAb dominated the serological IgG1 repertoire. Tocilizumab clearance could be monitored and a half-life of approximately 6 days was established in these patients. Overall, our longitudinal monitoring of IgG1 and IgA1 repertoires of individual donors reveals that antibody responses are highly personalized traits of each patient, affected by the disease and the chosen clinical treatment. The impact of these observations argues for a more personalized and longitudinal approach in patients diagnostics, both in serum proteomics as well as in monitoring immune responses.

IgG1 responses following SARS-CoV-2 infection are polyclonal and highly personalized, whereby each donor and each clone displays a distinct pattern of cross-reactivity against SARS-CoV-2 variants (preprint)

Using a recently introduced efficient mass spectrometry-based approach we monitored in molecular detail the IgG1 clonal responses in individual donors' IgG1 clonal responses in molecular detail, examining SARS-CoV-2 spike-protein-specific IgG1 repertoires. We monitored the plasma clonal IgG1 profiles of 8 donors (4 male and 4 female) who had recently experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we charted the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer as antigen. We observed that shortly after infection in between <0.1% to almost 10% of all IgG1 antibody molecules present in plasma did bind to the spike protein. Each donor displayed a unique plasma IgG1 repertoire, but also each donor displayed a unique and polyclonal antibody response against the SARS-CoV-2 spike-protein variants. Our analyses revealed that certain clones exhibit (alike) binding affinity towards all four tested spike-protein variants, whereas other clones displayed strong unique mutant-specific affinity. We conclude that each infected person generates a unique polyclonal response following infection, whereby some of these clones can bind multiple viral variants, whereas other clones do not display such cross-reactivity. In general, by assessing IgG1 repertoires following infection it becomes possible to identify and select fully matured human plasma antibodies that target specific antigens, and display either high specificity or cross-reactivity versus mutated versions of the antigen, which will aid in selecting antibodies that may be developed into biotherapeutics.

Human Plasma IgG1 Repertoires are Simple, Unique, and Dynamic (preprint)

The human body produces a vast variety of circulating immunoglobulins (Igs) to recognize and combat pathogens and other non-self molecular components. In human plasma the most abundant class of Igs is the immunoglobulin G subclass I (IgG1) 1. Through somatic recombination and hypermutation, our bodies can theoretically produce several billions of distinct IgG1 variants 2,3. The theoretically available IgG1 repertoire thereby far exceeds the physical number of memory B cells available 4. The theoretical possibilities are highly suggestive of a vastly complex IgG1 plasma repertoire, but here we show that in all studied individuals, this repertoire is dominated by only a few dozens of clones. Our data indicate that each person’s IgG1 repertoire is distinctly unique, representing a personalized barcode. We sequentially measured IgG1 repertoires of critically ill individuals with hospital-acquired sepsis, revealing the occurrence and disappearance of specific IgG1 clones during the evolution of the disease. We demonstrate here that 1) personalized IgG1 profiling by LC-MS is feasible, 2) each person exhibits a unique serological IgG1 repertoire, 3) this repertoire adapts to changes in physiology, and 4) that individual plasma IgG clones can be de novo sequenced by integrative protein-centric and peptide-centric proteomic approaches. We foresee that the presented mass spectrometric approach will accommodate more rapid development of monoclonal antibody treatments, immediately assessing fully human, matured, and optimized molecules. The potential of repertoires from disease survivors can then be used to prevent disease excesses, as was demonstrated for Ebola 5-7, and is the hope for the current COVID-19 pandemic.

Breastmilk; a source of SARS-CoV-2 specific IgA antibodies (preprint)

Background: Since the outbreak of COVID-19, many put their hopes in the rapid development of effective immunizations. For now patient isolation, physical distancing and good hygiene are the sole measures for prevention. Processed breast milk with antibodies against SaRS-CoV-2 may serve as additional protection. We aimed to determine the presence and neutralization capacity of antibodies against SaRS-CoV-2 in breastmilk of mothers who have recovered from COVID-19. Methods: This prospective case control study included lactating mothers, recovered from (suspected) COVID-19 and healthy controls. Serum and breastmilk was collected. To assess the presence of antibodies in breastmilk and serum, we used multiple complementary assays, namely ELISA with the SARS-CoV-2 spike protein, SARS-CoV-2 receptor binding domain (RBD) and with the SARS-CoV-2 nucleocapsid (N) protein for IgG and bridging ELISA with the SARS-CoV-2 RBD and N protein for total Ig. To assess the effect of pasteurization breastmilk was exposed to Holder Pasteurization and High Pressure Pasteurization. Results: Breastmilk contained antibodies against SARS-CoV-2 using any of the assays in 24 out of 29 (83%) proven cases, in six out of nine (67%) suspected cases and in none of the 13 controls. In vitro neutralization of SARS-CoV-2 clinical isolate virus strain was successful in a subset of serum (13%) and milk samples (26%). Although after pasteurization of the milk SARS-CoV-2 antibodies were detected with both methods of pasteurization, virus neutralizing capacity of those antibodies was only retained with the HPP approach. Conclusion: Breastmilk of mothers who recovered from COVID-19 contains significant amounts of IgA against SARS-CoV-2, both before and after pasteurization.