Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19

Abstract

Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering the importance of study design, in terms of cohort selection, laboratory methods and analysis. The advances in understanding SARS-CoV-2 immunity that have resulted from bulk TCR repertoire sequencing are also be discussed. The complexity of sequencing data obtained by bulk repertoire sequencing makes analysis challenging, but simple descriptive analyses, clonal analysis, searches for specific sequences associated with immune responses to SARS-CoV-2, motif-based analyses, and machine learning approaches have all been applied. TCR repertoire sequencing has demonstrated early expansion followed by contraction of SARS-CoV-2-specific clonotypes, during active infection. Maintenance of TCR repertoire diversity, including the maintenance of diversity of anti-SARS-CoV-2 response, predicts a favourable outcome. TCR repertoire narrowing in severe COVID-19 is most likely a consequence of COVID-19-associated lymphopenia. It has been possible to follow clonotypic sequences longitudinally, which has been particularly valuable for clonotypes known to be associated with SARS-CoV-2 peptide/MHC tetramer binding or with SARS-CoV-2 peptide-induced cytokine responses. Closely related clonotypes to these previously identified sequences have been shown to respond with similar kinetics during infection. A possible superantigen-like effect of the SARS-CoV-2 spike protein has been identified, by means of observing V-segment skewing in patients with severe COVID-19, together with structural modelling. Such a superantigen-like activity, which is apparently absent from other coronaviruses, may be the basis of multisystem inflammatory syndrome and cytokine storms in COVID-19. Bulk TCR repertoire sequencing has proven to be a useful and cost-effective approach to understanding interactions between SARS-CoV-2 and the human host, with the potential to inform the design of therapeutics and vaccines, as well as to provide invaluable pathogenetic and epidemiological insights.

Comprehensive analysis of T‐cell receptor repertoires reveals antigen‐driven T‐cell clusters in patients with Behçet's syndrome

“…GLIPH2 algorithm offers an optimal solution. By combining global and motif‐based CDR3 sequence, physiochemical properties, V‐gene bias, CDR3 length bias, and clonal expansion bias, GLIPH2 assesses the antigen‐specific nature of the repertoire and aggregates clonally related TCR sequences or very similar CDR3s, or sequences likely binding the same antigen [34]. Our findings revealed that specificity groups of TCRs in BS provide information about the complexity of an immune response or the presence of a meaningful shared specificity across individuals.…”

T cell repertoire profiling in allografts and native tissues in recipients with COVID–19 after solid organ transplantation: Insight into T cell–mediated allograft protection from viral infection

“…Additionally, viral RNA was sometimes found without the concurrent finding of SARS-CoV-2 virions, and viral mutations were identified throughout various extrapulmonary tissues in patients in whom disease course was prolonged ( 35 ). Regarding TCR clones specific for the SARS-CoV-2 virus, previous studies have utilized TCR repertoire profiling in blood to obtain biological insights into COVID-19 infection ( 36 ), including enrichment of SARS-CoV-2-specific TCRs in the blood of patients with more severe disease ( 37 ). However, local tissue coordination of cellular and humoral immune response against SARS-CoV-2 is critical for developing immunological memory necessary for viral protection, including memory responses, in the periphery ( 38 ).…”

T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer

“…The amount of gDNA is proportional to the number of analyzed cells with a 1:1 number of clonotypes and number of cells ratio (1 gDNA template per cell), allowing us to determine the relative abundance of sequences in a sample at the cost of unavoidably detecting potentially irrelevant and non-expressed sequences that must be removed through post-processing bioinformatic analysis [ 45 , 46 ].…”