The pneumonia virus originating from the Wuhan fish market, also known as 2019 Novel Coronavirus (2019-nCoV), resembles both the viruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). According to Nature Briefing, by January 28, the number of confirmed cases exceeded 4,500 patients, of which more than 100 people died as a result of the infection. By comparison, SARS spread globally in 2002-03, infecting 8,000 people and killing more than 700.
Traditional vaccines for viral diseases have had limited success in viral epidemics with a high frequency of mutations. The approach we used to identify potential vaccine candidate peptides follows a more personalized strategy, called vaccinomics, which allows the selection of viral target proteins with lower mutation rate and the construction of peptides tailored to the immune genetic characteristics of target populations that may vary by geographic location and ethnicity.
Based on variation in the allele encoding human MHC (human leukocyte antigen), peptide-based vaccines can be developed with specificity for a community or individual. The selection of peptides that can act as a vaccine is determined by the binding capacity of the processed viral peptide with major histocompatibility complex (MHC) class I and II molecules and may vary according to the relevant HLA alleles. Our peptide proposals are applicable to the Romanian population.
Technical details of the peptide design strategy:
We selected potential immunogenic peptides that trigger innate and acquired immune response (CD4+ as well as CD8+ T lymphocytes) against nCov. To this end, we generated 15–30 amino acid long synthetic peptides (SLPs), as proposed by Rabu et al. (2019), using a cathepsin-sensitive linker (LLSVGG) for linking MHC class I-restricted epitopes to MHC class II-specific epitopes, with the MHC class II epitope always located at the N-terminal end of the peptide. These peptides can simultaneously stimulate both CD8+ (cytotoxic) and CD4+ (helper) T lymphocytes (along with the innate immune system).
The Wuhan-Hu-1 coronavirus strain used for analysis is identified as MN908947.3 or Seq Ref NC_045512.
It is a single-stranded, positive-sense polyadenylated RNA virus with a genome size of 29.9 kb (29903 bp), one of the largest of the RNA viruses.
Complete genome sequences to date: S and M proteins important as anti-nCoV vaccine targets; S = spike (for adhesion and fusion); M = membrane (for virion replication and exocytosis).
We used the Immune Epitope Database (IEDB) to identify potent epitopes for T lymphocyte stimulation from S and M protein sequences. For CD8 + T cell-specific epitopes, the prediction method integrated MHC class I binding capacity, proteasomal cleavage of the viral protein and the efficiency of TAP transport. Several epitopes were selected for further analysis based on the overall score obtained and whether they showed high MHC binding affinity (IC50 <50 nM). For the specific epitopes of CD4+ T lymphocytes, the peptide with the highest binding capacity for MHC class II was chosen.
The list of T epitopes selected based on affinity for the most frequent HLA class I and II alleles in the Romanian population (taken as an example to demonstrate the principle of the personalized vaccinomics strategy) can be found in our publication Preprints.
The immunogenic peptides were developed by applying a technology used in personalized cancer vaccination, based on "long neoantigen peptides", currently used in clinical trials to treat cancer.
This model is a compromise between the strategy of large-scale global industrial vaccination and the one tailored at the individual level.
We will continue with the validation of these peptides and the presented model.
Image source: Eye of Science/SPL