COVID-19 pandemics has led us to consider vaccine development options that were previously not in the spotlight. Genomics information of SARS-CoV-2, the causal agent of COVID-19, has been deciphered early in the pandemic, and it bolsters the vaccine development efforts. The deployment of various COVID-19 vaccines, mainly with Inactivated, mRNA, vector, recombinant approaches, have shown us that immunoinformatics methods have eventually assisted in resolving the threat of pandemics. Some modern COVID-19 vaccines, such as mRNA, vector, and protein recombinant vaccines, are developed with the assistance of immunoinformatics methods. Only inactivated vaccines that did not develop directly with the immunoinformatics pipeline. So, what is immunoinformatics anyway?

Immunoinformatics is a computational method that is heavily influenced by two different majors, namely Bioinformatics and Biomedicine. The computational methods are mainly derived from established bioinformatics pipelines such as sequence analysis and molecular simulation. Meanwhile, the object of study was heavily influenced by biomedicine, mainly in depicting the immunological pathway. In short, immunoinformatics is a study of immunology with computational methods. Hence, the studies were mainly in two parts. First, the sequence analysis of the B and T-cell epitopes. Second, the molecular simulation of the vaccine leads. 

Pertaining to the first part, regardless of the vaccine types, the immunoinformatics methods always aim to recognise the epitopes. The portion of an antigen known as an epitope, also known as an antigenic determinant, is recognized by the immune system, more specifically by antibodies, B cells, or T cells. Typically, non-self proteins in the form of short peptides, make up the epitopes. The second part, was composed of both Peptide Modeling and Molecular Simulation (Docking and Dynamics) with B cell receptor (BCR) or with MHCs molecule. The logical steps afterward would be validation in the wet laboratory setting, whether it is within the framework of in vitro, in vivo, and clinical trials settings. As per now, according to the www.clinicaltrials.gov, several peptide vaccine candidates are already enrolled in clinical trials. They are vaccines for HIV/AIDS, Influenza, COVID-19, cancers, and others. 

COVID-19 epitopes vaccine, still under development. However, other types of vaccine such as mRNA and vector based, are all influenced by immunoinformatics methods. mRNA vaccine for instance. It is a transcribed version of a gene that encodes for spike proteins. Sequence analysis method was necessary to determine the open reading frame (ORF) of the spike gene, promotor, start and stop codon. Vector-based vaccines also elicited similar methods, with sequence analysis for gene prediction and recognition, as well as finer-grained host prediction program. 

COVID-19 pandemic is definitely not the first coronavirus outbreak. Previously, the world has been ravaged by both SARS and MERS epidemics. In this regard, caution should be devised accordingly. Beside improving the coverage and scalability of our public health system, it is essential to consider the development of the universal coronavirus vaccines. The threat is there, as there are an unknown number of animal coronaviruses that could spill to the human population in the future, and they could have potentials to elicit other pandemics. Moreover, the existing COVID-19 vaccine should be updated with the antigens from the currently circulating variants. Beside deploying current improvement in artificial intelligence and/or machine learning to improve the fidelity of immunoinformatics methods, to materialize the universal coronavirus vaccine, acceptable viral models for wet lab experiments are necessary. The four types of coronaviruses, the beta coronaviruses OC43 and HKU1 and the alpha coronaviruses 229E and NL63, could be studied within the laboratory animals setting. Virologists could do that, as those viruses are considered not as pathogenic as SARS,MERS, and SARS-CoV-2. However, challenges remain for the eradication of this pathogen. Only one human pathogen that could be eradicated, namely the variola virus as the causative agent of smallpox. So far, although there are some outbreaks in both Pakistan and Afghanistan, the eradication program for polio has not been successful. In the end, a more realistic target pertaining to coronavirus outbreak in the future, and the current one with COVID-19, will be to put them under control with better health promotion, and improved public health quality. 

References:

Morens, D. M., Taubenberger, J. K., & Fauci, A. S. (2022). Universal Coronavirus Vaccines — An Urgent Need. New England Journal of Medicine, 386(4), 297–299. https://doi.org/10.1056/nejmp2118468

Fauci, A. S. (2021). The story behind COVID-19 vaccines. Science, 372(6538), 109–109. https://doi.org/10.1126/science.abi8397 

Hamley, I. W. (2022). Peptides for Vaccine Development. In ACS Applied Bio Materials (Vol. 5, Issue 3, pp. 905–944). American Chemical Society. https://doi.org/10.1021/acsabm.1c01238 

Kharisma, V. D., Ansori, A. N. M., Posa, G. A. V., Rizky, W. C., Permana, S., & Parikesit, A. A. (2021). Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach. Jurnal Teknologi Laboratorium, 10(1), 06–13. https://doi.org/10.29238/TEKNOLABJOURNAL.V10I1.274 

Aldino, M., Maulani, R., Probojati, R., Karisma, V. D., Ansori, A. N. M., & Parikesit, A. A. (2021). Potential Vaccine Targets for COVID-19 and Phylogenetic Analysis Based on the Nucleocapsid Phosphoprotein of Indonesian SARS-CoV-2 Isolates. Indonesian Journal of Pharmacy, 32(3), 328–337. https://doi.org/10.22146/IJP.1497