key: cord-0985872-43c1vind
authors: Redd, Andrew D; Nardin, Alessandra; Kared, Hassen; Bloch, Evan M; Pekosz, Andrew; Laeyendecker, Oliver; Abel, Brian; Fehlings, Michael; Quinn, Thomas C; Tobian, Aaron A R
title: CD8+ T cell responses in COVID-19 convalescent individuals target conserved epitopes from multiple prominent SARS-CoV-2 circulating variants
date: 2021-03-30
journal: Open Forum Infect Dis
DOI: 10.1093/ofid/ofab143
sha: 005556432d607b9a940c9aeec9116d58b6550beb
doc_id: 985872
cord_uid: 43c1vind

This study examined whether CD8+ T-cell responses from COVID-19 convalescent individuals (n=30) potentially maintain recognition of the major SARS-CoV-2 variants (n=45 mutations assessed). Only one mutation found in B.1.351-Spike overlapped with a previously identified epitope (1/52), suggesting that virtually all anti-SARS-CoV-2 CD8+ T-cell responses should recognize these newly described variants.

Due to the proofreading ability of the coronavirus (CoV) RNA-dependent RNA polymerase, the evolution of the global SARS-CoV-2 viral population during the current pandemic has been relatively constrained as compared to other endemic RNA viruses that do not possess this ability [1] . However, during late 2020, three distinct variants that each They also all contain unique additional mutations throughout the genome, and are not phylogenetically linked, indicating that they evolved independently (Table S1 ). Due in part to the mutations found in the RBD and other areas of the spike protein, these primary viral variants, or pseudoviruses expressing the combination of polymorphisms found in each variant, have been examined for their sensitivity to NAb responses detected in plasma from COVID-19 convalescent donors, preclinical or clinical trial post-vaccination plasmas, and monoclonal antibodies [4] [5] [6] [7] . These studies have shown that the variants are variably susceptible to neutralization, with B.1.1.7 exhibiting only minor decreases in susceptibility to convalescent and post-vaccination plasma. In addition, preliminary press reports from ongoing Phase 2b/3 vaccine trials performed in the United Kingdom during the rise of B.1.1.7 suggest that the efficacy of spike-based vaccines has not diminished significantly; however, these studies have not been published or peer-reviewed. Conversely, the B.1.351 variant has demonstrated a significant increase in resistance to neutralization by some individuals' convalescent plasma, as well as a decline in neutralization potential for the mRNA based vaccine induced NAb responses; although it should be noted that this neutralization potential was still estimated to be high enough to confer complete protection [4] [5] [6] [7] . Of greater concern, two ongoing Phase 2/3 vaccine trials of a recombinant A c c e p t e d M a n u s c r i p t independently reviewed. Interestingly, these same reports claimed that there was no difference in the effectiveness of the vaccines to prevent serious illness between the two countries, suggesting that while protection from initial infection may be somewhat hindered, the vaccines ability to prevent further disease progression is preserved.

While the correlates of protection in convalescent individuals and vaccinees are unknown, it is assumed that both a broad humoral and cell-mediated immunological response are most likely necessary to fully protect against COVID-19. NAb almost certainly serves as the first line of defense against infection, but the CD8+ T cell response is also important for prevention of further disease progression.

Previously, our group reported a detailed analysis of the CD8+ T cell epitopes and cytokine responses to the original strain of SARS-CoV-2 in a collection of convalescent individuals from North America with varying levels of disease and NAb responses [8] . This earlier report identified a broad CD8+ T cell response in these individuals with virtually all subjects having detectable responses to several viral epitopes.

Detailed methods of the previous study have been published [8] . Patient consent Statement: All study participants provided informed consent. This study was approved by the Johns Hopkins Institutional Review Board.

As previously described, 60% of individuals included in the analysis were male and samples were collected a median of 42.5 days (interquartile range 37.5-48.0) from initial diagnosis [8] .

The group was selected evenly from tertiles (10 each) according to their overall anti-SARS-CoV-2 IgG titers [8, 9] . Among the convalescent individuals, there were 132 SARS-CoV-2specific CD8+ T cell responses corresponding to 52 unique epitope reactivities directed against several structural and non-structural target epitopes from the entire proteome.

Of all the mapped mutations, insertions, and deletions (n=45; Table S1), only one mutation was found to fall within one of the 52 unique epitopes identified in the previous study (Figure 1 & S1) . This mutation is the D80A mutation in the Spike protein, and occurs in the third residue of the RFDNPVLPF epitope. This is a HLA*A24:02-restricted epitope for which a CD8+ T cell response was detected in one of the five HLA*A24:02+ individuals, and at a low frequency (0.005 of total CD8+ T-cells), indicating this is not a high-prevalence A c c e p t e d M a n u s c r i p t 6 epitope within the studied cross-sectional sample. The individual in which this epitope response was detected, was part of the high IgG tertile.

As the global SARS-CoV-2 pandemic continues, it is inevitable that new viral variants will emerge. Many of these variants will disappear unnoticed due to a combination of incomplete or non-existent genotypic surveillance, changes that have deleterious impact on viral fitness, and conditions that do not promote their further spread in the population. This analysis identified only one mutation from the three most prominent new global SARS-CoV-2 variants that overlapped with 52 CD8+ T cell epitopes previously identified in a group of convalescent individuals. Additionally, this mutation was found on the third residue of the epitope, and given that the predicted anchor residues for HLA binding of this epitope are residues two and nine, one could speculate that this mutation may not significantly affect HLA binding and subsequent TCR recognition [11] .

The data on CD8+ T cell responses from these 30 convalescent individuals are also in line with another recent report showing that the great majority of CD4+ and CD8+ T cell epitopes from the spike protein of the SARS-CoV-2 variants are also conserved in vaccinated individuals [12, 13 ]. Yet it should be noted, that new variants are continuing to be identified all over the world, and it will be important to continually examine these for the possible accumulation of T cell escape mutations. [4] [5] [6] [7] . Yet, it must be highlighted many of these results have not been published in full detail or peer-reviewed. This possible prevention of severe disease may be due in part to the cell-mediated immunity generated due to natural COVID-19 infection or vaccination, which the results presented here would suggest are minimally affected by the mutations found in these variants.

It should be noted that this study had several limitations including the relatively small size of the population examined. In addition, the participants in the study were all from North America and were selected in part on the presence of one or more of the target HLA types examined (73% coverage of the continental US population). It will also be important to examine for T cell escape in more diverse HLA types moving forward.

These data highlight the potential significant role of a multi-epitope T cell response in limiting viral escape, and partly mediate protection from disease caused by the SARS-CoV-2 variants. It is important that vaccines used for widespread campaigns generate strong multivalent T-cell responses in addition to NAb and other humoral responses in order to optimize efficacy against the current SARS-CoV-2 and emerging strains. It will be important to continue to monitor the breadth, magnitude, and durability of the anti-SARS-CoV-2 T cell responses in recovered and vaccinated individuals as part of any assessment to determine if booster vaccinations are needed.

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Role of strong anchor residues in the effective binding of 10-mer and 11-mer peptides to HLA-A(*)2402 molecules

A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t Figure 1