Deconvoluting the T Cell Response to SARS-CoV-2: Specificity Versus Chance and Cognate Cross-Reactivity

Abstract

SARS-CoV-2 infection takes a mild or clinically inapparent course in the majority of humans who contract this virus. After such individuals have cleared the virus, only the detection of SARS-CoV-2-specific immunological memory can reveal the exposure, and hopefully the establishment of immune protection. With most viral infections, the presence of specific serum antibodies has provided a reliable biomarker for the exposure to the virus of interest. SARS-CoV-2 infection, however, does not reliably induce a durable antibody response, especially in sub-clinically infected individuals. Consequently, it is plausible for a recently infected individual to yield a false negative result within only a few months after exposure. Immunodiagnostic attention has therefore shifted to studies of specific T cell memory to SARS-CoV-2. Most reports published so far agree that a T cell response is engaged during SARS-CoV-2 infection, but they also state that in 20-81% of SARS-CoV-2-unexposed individuals, T cells respond to SARS-CoV-2 antigens (mega peptide pools), allegedly due to T cell cross-reactivity with Common Cold coronaviruses (CCC), or other antigens. Here we show that, by introducing irrelevant mega peptide pools as negative controls to account for chance cross-reactivity, and by establishing the antigen dose-response characteristic of the T cells, one can clearly discern between cognate T cell memory induced by SARS-CoV-2 infection vs. cross-reactive T cell responses in individuals who have not been infected with SARS-CoV-2.

Keywords: COVID-19; ELISPOT; ImmunoSpot; T cell affinity; immune monitoring; mega peptide pools.

Figure 1

Classic representation of SARS-CoV-2 antigen-specific T cell frequencies in SARS-CoV-2 PCR verified subjects(+) versus Pre-COVID Era individuals(-). PBMC of each individual within the cohort is represented by a dot. The PBMC were challenged with peptide pools covering the SARS-CoV-2 antigens specified on the right. (These peptide pools are closer defined in Supplementary Table 2 ). The individual peptides in each pool were tested at 1.5 µg/ml. An ELISPOT assay was performed measuring the numbers of antigen-induced IFN-y-secreting T cells (spot forming units, SFU) in 200,000 PBMC; following convention, the numbers have been normalized to per million PBMC, as shown on the Y axis. Statistical significance between the two cohorts was determined using an independent samples t test. Significant differences between SARS-CoV-2-infected vs. non-exposed cohorts are marked with * denoting p < 0.05, ** p < 0.01, and *** p < 0.001, respectively.