We briefly review the situations arising out of epidemics that erupt rather suddenly, threatening life and livelihoods of humans. Ebola, Zika and the Nipah virus outbreaks are recent examples where the viral epidemics have led to considerably high degree of fatalities or debilitating consequences. The problems are accentuated by a lack of drugs or vaccines effective against the new and emergent viruses, and the inordinate amount of temporal and financial resources that are required to combat the novel pathogens. Progress in computational, biological and informational sciences have made it possible to consider design of synthetic vaccines that can be rapidly developed and deployed to help stem the damages. In this review, we consider the pros and cons of this new paradigm and suggest a new system where the manufacturing process can be decentralized to provide more targeted vaccines to meet the urgent needs of protection in case of a rampaging epidemic.

The Nipah virus disease is a lethal infection that has led to 40% to 75% fatalities in Malaysia, Bangladesh and India. The reports of human-to-human transmission documented in Bangladesh has raised the specter of pandemic potential and has caused the World Health Organization to list the Nipah virus as one of the pathogens to be considered for development of drugs and vaccines on urgent basis, neither of which exist against the Nipah virus as of now, although many proposals have been made and trials initiated. Given that there are established country-specific differences in the virus’ effects and fatalities, meeting the sudden need for a vaccine in case of an epidemic will require design, development and preparation for a peptide vaccine. Thus, we propose a protocol for creating peptide vaccines that can be tailor-made for these specific countries, an approach which is being advocated for the first time. Here, we analyze the surface proteins, Fusion protein and Glycoprotein, of the strains currently affecting the three countries on a large scale and determine the specific country-based epitope differences.

Among the nucleotide sequences of flaviviruses that include Zika virus, Dengue virus, yellow fever virus, Japanese encephalitis virus and West Nile virus, those of the Zika virus and Dengue type 2 virus are believed to share a high degree of similarity as can be commonly shown by BLAST pairwise analysis. Our study of the nucleotide sequences of the envelope and NS5 genes shows that the sequences of the Dengue type 2 virus are sharply different compared to other aforementioned human infecting flaviviruses. This is emphatically seen in a 2D graphical representation where each axis represents a nucleotide base and distinctly discriminated in terms of relevant RNA descriptors. The descriptors indicate the quantitative spread of nucleotide sequence graphs. In this report, we demonstrate this difference in terms of base distribution in the gene sequences through various parameters and consider possible reasons for such variations that seem to have been largely neglected in the literature.

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