Landscape and selection of vaccine epitopes in SARS-CoV-2

Abstract

Background Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). Methods We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. Results From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. Conclusions Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.

Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2

“…Pioneering bioinformatic studies focused on predicting cytotoxic epitopes of a limited subset of common HLA alleles against the reference viral strain [ 12 , 19 , 22 , 25 ]. Former high-range reports have explored the epitope space of the virus with different purposes such as the assessment of the geographical prevalence of allele-peptide combinations [ 26 ] and the design of epitope-based vaccines [ 27 ]. However, SARS-CoV-2 has substantially evolved after more than a year of pandemic, resulting in a human-viral combination landscape of immense scale only approachable using automated techniques.…”

Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins—A Possible Signature of Adaptive Selection

“…Most indels are significantly (q-value < 0.01 and odds ratio >1) concentrated in NSP1, NSP3, NSP6, ORF3a, ORF6, ORF7a, ORF7b, ORF8, nucleocapsid, and spike glycoprotein ( Figure 1E and Table 1 ), all of which are involved in interactions with the host immune system ( Lei et al, 2020 ; Liang et al, 2021 ; Smith et al, 2021 ). At the same time, proteins involved in the replication–transcription complex show very few or no indels ( Figure 1E and Table 1 ).…”

“…Aggregation and recurrence of indels in hypervariable regions of SARS-CoV-2 proteins are determined by an interplay of the protein structural constraints and functional role of specific regions. Most of the HVRs of SARS-CoV-2 proteins (except ORF7a-HVR) are found on or adjacent to loops forming either experimentally identified ( Liang et al, 2021 ; Smith et al, 2021 ) or predicted antibody epitopes ( Figures 2 , 3 ), suggesting SARS-CoV-2 is optimizing its interactions with the host immune system, possibly in response to the increased immunity of the population. For instance, NSP6-HVR falls on a predicted T-cells ( Smith et al, 2021 ) and B-cells epitope (per IEDB server), forming a short loop between two transmembrane helices ( Figure 2C ).…”

Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology

“…One such example was highlighted by a recent study where PhIP-Seq revealed that vaccination (as compared to SARS-CoV-2 infections) generated more diverse antibody epitopes [ 41 ]. Another study utilized PhIP-Seq epitope mapping data from COVID-19 patients to identify dominant linear B cell epitope regions and then rationally design peptide vaccine candidates against SARS-CoV-2 [ 42 ].…”