Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients

Abstract

Some individuals do not return to baseline health following SARS-CoV-2 infection, leading to a condition known as Long COVID. The underlying pathophysiology of Long COVID remains unknown. Given that autoantibodies have been found to play a role in severity of COVID infection and certain other post-COVID sequelae, their potential role in Long COVID is important to investigate. Here we apply a well-established, unbiased, proteome-wide autoantibody detection technology (PhIP-Seq) to a robustly phenotyped cohort of 121 individuals with Long COVID, 64 individuals with prior COVID-19 who reported full recovery, and 57 pre-COVID controls. While a distinct autoreactive signature was detected which separates individuals with prior COVID infection from those never exposed to COVID, we did not detect patterns of autoreactivity that separate individuals with Long COVID relative to individuals fully recovered from SARS-CoV-2 infection. These data suggest that there are robust alterations in autoreactive antibody profiles due to infection; however, no association of autoreactive antibodies and Long COVID was apparent by this assay.

Figure 1:. PhIP-Seq autoreactivities distinguish post-COVID sera from pre-COVID controls.

Logistic regression comparing PhIP-Seq autoreactivities in all individuals with prior COVID infection compared to pre-COVID controls. Barplot showing autoreactivities with the top 20 logistic regression coefficients.

Figure 2:. Post-COVID anti-ARHGAP31 autoreactivities target specific region with similarity to SARS-CoV-2

(A) Stripplots showing distribution of ARHGAP31 autoreactivities in Long COVID, individuals with prior COVID infection but without Long COVID, and pre-COVID controls. Dotted line at 6 standard deviations above mean of pre-COVID controls. (B) Distribution of anti-ARHGAP31 autoreactivity signal within ARHGAP31 full length protein. One specific fragment is targeted. (C) Amino-acid sequence of the autoreactive region of ARHGAP31 and amino-acid sequence of a region of SARS-CoV-2 Orf1a with similarity. Shown below is the multiple sequence alignment(ClustalOmega; asterisk=identical amino acid; colon=strongly similar properties with Gonnet PAM 250 matrix score >0.5; period=weakly similar with Gonnet PAM 250 matrix score between 0 and 0,5) and strong physical-chemical conservation (JalView; amino acid physical-chemical conservation scored on a scale of 1-11, Asterisk=score of 11 and identical amino acid, Plus=10, all properties conserved).

Figure 3:. Post-COVID autoreactivities are similarly distributed among Long COVID and controls.

Hierarchically clustered (Pearson) heatmaps showing the PhIP-Seq enrichment for the top 20 autoreactivities ranked by logistic regression coefficient in each Long COVID patient, each COVID convalescent patient, and each pre-COVID control.

Figure 4:. Few significantly increased autoreactivities in Long COVID symptom phenotypes.

(A) Heatmap with p-values (Kolmogorov-Smirnov testing) of differences in autoantigen enrichment for all individuals with prior COVID infection with and without additional clinical factors. Top-row compares those with and without Long COVID. Lower rows show subcategories of Long COVID. (B) Stripplots showing the three autoantibodies with statistically significant enrichment in a post-COVID clinical phenotype. Dotted-lines show 6 standard-deviations above the mean of pre-COVID signal.