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

Abstract

The massive assessment of immune evasion due to viral mutations that increase COVID-19 susceptibility can be computationally facilitated. The adaptive cytotoxic T response is critical during primary infection and the generation of long-term protection. Here, potential HLA class I epitopes in the SARS-CoV-2 proteome were predicted for 2,915 human alleles of 71 families using the netMHCIpan EL algorithm. Allele families showed extreme epitopic differences, underscoring genetic variability of protective capacity between humans. Up to 1,222 epitopes were associated with any of the twelve supertypes, that is, allele clusters covering 90% population. Next, from all mutations identified in ~118,000 viral NCBI isolates, those causing significant epitope score reduction were considered epitope escape mutations. These mutations mainly involved non-conservative substitutions at the second and C-terminal position of the ligand core, or total ligand removal by large recurrent deletions. Escape mutations affected 47% of supertype epitopes, which in 21% of cases concerned isolates from two or more sub-continental areas. Some of these changes were coupled, but never surpassed 15% of evaded epitopes for the same supertype in the same isolate, except for B27. In contrast to most supertypes, eight allele families mostly contained alleles with few SARS-CoV-2 ligands. Isolates harboring cytotoxic escape mutations for these families co-existed geographically within sub-Saharan and Asian populations enriched in these alleles according to the Allele Frequency Net Database. Collectively, our findings indicate that escape mutation events have already occurred for half of HLA class I supertype epitopes. However, it is presently unlikely that, overall, it poses a threat to the global population. In contrast, single and double mutations for susceptible alleles may be associated with viral selective pressure and alarming local outbreaks. The integration of genomic, geographical and immunoinformatic information eases the surveillance of variants potentially affecting the global population, as well as minority subpopulations.

Fig 1. Overview of the analysis strategy.

Fig 2. Number and degree of overlap between SARS-CoV-2 epitopes for different HLA-class I allelic families.

(A) Average number of predicted HLA class I epitopes by allele family and protein. The standard deviation resulting from all proteins is indicated as a single error bar. (B) Hierarchical clustering and associated heatmap indicating the degree of inter-family epitope correlation. Color intensity expresses the Jaccard index for the epitope intersection between all family pairs. Perfect location match between epitopes calculated by netMHCIpan 4.1 EL with score ≥ 0.5 and rank ≤ 0.5 were utilized to calculate intersection and union. Intra-family conserved epitopes (≥ 50% alleles in the family by exact match) are in S1 Table.

Fig 3. Comparison between predicted and validated epitopes.

(A) Number of predicted epitopes (score ≥ 0.5 and rank ≤ 0.5) versus validated epitopes per allele. (B) Heatmap showing the family average score (any score, rank ≤ 2) for validated HLA class I epitopes. Predicted epitopes with perfect matches with validated epitopes stored in the IEDB are indicated in S1 Table.

Fig 4. SARS-CoV-2 supermotifs.

(A) Distribution of supermotifs according to the number of supertypes covered. (B) Number of supermotifs per supertype detailed by protein antigen.

Fig 5. Global mutation analysis in NCBI SARS-CoV-2 genomes.

(A) Proportion of cumulative and unique residue mutation events in SARS-CoV-2. (B) Length distribution of insertions (left) and deletions (right). (C) Number of isolates and number of epitopes which location overlap to substitutions (left), insertions (center) and deletions (right).

Fig 6. Supermotif escape mutations.

(A) Influence of supermotif core position and residue conservation in the epitope escape capacity of substitutions. (B) Average percentage of escape supermotifs by any mutation type after incremental filter application. (C) Absolute number of mutated supermotifs for each supertype after incremental filter application. (D) Nightingale rose charts indicating the percentage of escape supermotifs in prevalent M49 zones. Only mutations involving ≥2 isolates in the M49 were considered. Only M49 zones with ≥ 5% escape supermotifs for at least one supertype are shown.

Fig 7. Networks of coupled supermotif escape mutations.

Undirected unweighted graphs showing coupled supermotif escape mutations. Sub-networks are named with roman numbers. Nodes correspond to mutations that were substitutions (position and residue change) or deletions (residue range). No coupled insertions were detected. The node color indicates the antigen protein. The sphere diameter reflects the amount of isolates harboring the mutation. Nodes represent mutations carried by ≥ 25 isolates. Edges represent co-existence of a mutation pair in ≥ 20% isolates of all those carrying at least one of the mutations.

Fig 8. Isolates carrying different combinations of escape mutations.

(A) Each point represents an isolate plotted according to the total number of mutations, the number of escape supermotifs and number of affected supertypes. Only isolates harboring three or more escape supermotifs are represented. (B) Chart panel indicating mutated isolates according to the number of escape supermotifs for each supertype. Isolates are colored by M49 zone of collection.

Fig 9. Escape mutations in allele families with fewest epitopes.

(A) Number of alleles with ≤ 20 epitopes versus the total number of alleles for HLA families of the three loci. Families without any allele with ≤ 20 epitopes are not represented. (B) Average number of escape epitopes, either by substitutions or deletions, respect to the average total number of epitopes for the eight allele families with the fewest epitopes. (C) World map panel indicating the presence of population samples carrying alleles of the eight families with fewest epitopes and isolates with escape mutations for these families. Family allele frequencies are color ranked for both the majority population (red scale) and sub-population (blue scale) samples. Only the highest frequency sample per country was considered. A B*83 map is not shown due to the extremely low prevalence of this allele family. Spheres in green indicate the presence of isolates with escape mutations for the allele family collected in that country. The sphere diameter is proportional to the total number of these isolates. Epitope escape substitutions and deletions for the eight allele family with fewest epitopes are listed on S6 and S7 Tables, respectively. The base layer for the world map was downloaded from https://naturalearthdata.com/downloads/50-m-cultural-vectors/50m-admin-0-details/.