Title : Reverse vaccinology approach in strategically constructing mRNA vaccine derived from conserved and experimentally validated epitopes of avian influenza A virus
Avian influenza (AI), commonly known as bird flu, is caused by influenza A viruses (IAV) that circulate in humans, horses, dogs, swine, and birds . AI has captured the attention of international and local communities over the years due to its devastating consequences to the health of wild birds, poultry, and livelihood of farmers. A major concern is the emergence of highly infectious strains that may result in pandemics.Since early 2022, the new H5N1 strain has been responsible for the current outbreaks leading to the death of over 37 million poultry in the USA alone . Available AI vaccines are not commonly used due to reduced vaccination efficacy over time . Unequivocally, antigenic drift and antigenic shift of avian influenza A virus (AIAV) in the field requires constant vaccine reformulation . The development of vaccines that can confer protection against multiple AI antigens across currently circulating AIAV strains can be a more practical strategy to prevent the emergence of highly infectious strains. Thus, this study conducted reverse vaccinology in strategically constructing mRNA vaccine (mVAIA) to induce cross-protection while targeting diverse avian influenza A (AIA) virulence factors.
Methods: Experimentally validated avian influenza A (AIA) T-cell and B-cell epitopes with positive assay results were retrieved from the Immune Epitope Database and Analysis Resource. Manually curated protein sequences were aligned in Clustal Omega server and used as input in the Protein Variability Server tool. Conserved epitopes were identified using Epitope Conservancy Analysis tool. . Potential toxicity and cross-reactivity of each epitope were evaluated using ToxinPred server and sequence similarity search through Protein BLAST, respectively. CD8+ epitopes were docked with dominant chicken MHC II BF2*2101 while two universal Th cell epitopes were docked with BL2*02 to evaluate the favorability of complex formation. Favorability was further investigated by estimating the binding free energy (?Gbind) and the dissociation constant (Kd) of complex formation. Conserved epitopes were adjoined in a protein construct and a signal sequence for targeted secretory expression was included. The protein sequence was back-translated and its mRNA sequence was optimized for efficient expression in G. gallus. Tertiary structure of its protein sequence was modeled and validated in silico to investigate accessibility of adjoined B-cell epitope. Potential immune responses were also simulated in C-ImmSim.
Results and Conclusion: Eighteen experimentally validated epitopes with Shannon index < 2.0 were identified as conserved . These include one B-cell (SLLTEVETPIRNEWGCR) and seventeen CD8+ epitopes which were all adjoined in a single mRNA construct. CD8+ epitopes docked favorably with MHC peptide-binding groove as supported by acceptable ?Gbind (-28.45 to -40.59 kj/mol) and Kd (< 1.00). The incorporated Sec/SPI cleavage site sequence in the vaccine was also recognized with high probability (0.964814). The optimized sequence has 56.4% GC content and a codon adaptation index (CAI) of 0.93 in G. gallus. The secondary structure of the optimized mRNA sequence has a minimum free energy (MFE) of -1635.94 kj/mol which suggests great thermal stability . Adjoined B-cell epitope was found within the disordered and accessible region of the vaccine. Immune simulation results project cytokine production, lymphocyte activation, and memory cell generation after the 1st dose of mVAIA. Overall results suggest that mVAIA possesses stability, safety and immunogenicity. In vitro and in vivo confirmation in subsequent studies are anticipated.