How did bioinformatics allow for swift development of the SARS-CoV-2 vaccine?

Traditionally, vaccine development takes years. However, the urgent need for a vaccine to mitigate the effects of this pandemic sped up the process. Bioinformaticians played a crucial role in enabling the swift development of effective SARS-CoV-2 vaccines in many ways.

Bioinformatics is the science of performing computational analysis and applying computational tools to capture and interpret biological data. The SARS-CoV-2 virus, with its rapid transmission and mutation rates, quickly became one of the most widespread and economically disruptive pandemics in history. According to Naseer et al. (2022), the global economy has been estimated to lose nearly 9 trillion due to the pandemic by the chief of the International Monetary Fund (IMF).

Scientists sequenced the SARS-CoV-2 virus within the first few months of the viral outbreak, and the first SARS-CoV-2 genome sequence was published on GenBank on 10 January 2020 (Torrington, 2022). However, a sequence on its own means little, that is until the genes and regulatory elements present in the genome are determined. This was made possible by many bioinformatic tools and pipelines such as: 

- BLAST (Basic Local Alignment Search Tool): A sequence alignment tool used to find on regions of similarity and infer function and evolutionary relationships. 

- VADR (Viral Annotation DefineR): An automated annotation tool specifically for viral genomes

- Velvet: A de novo sequence assembler i.e. it constructs a longer, full sequence from short read data obtained from next-generation sequencing. 

The information collected by different labs was shared worldwide, which allowed for a global collaborative effort towards developing a SARS-CoV-2 vaccine. 

Bioinformaticians also played a role in predicting the 3D structures of the proteins on the surface of the SARS-CoV-2 virus including the spike protein, which is protein against which vaccines build immunity. By using computational tools such as AlphaFold, they could model the structure of the spike protein and identify key sites to target in immunisation strategies. 

Another method used to identify key sites to target is Epitope Mapping, which is the identification of specific regions on an antigen that are recognised by parts of the immune system such as T Cell Receptors and antibodies. Tools such as IEDB Analysis Resource and BepiPred allow for the identification of epitopes on the SARS-CoV-2 spike that are highly immunogenic, meaning they are able to stimulate a strong immune response, and are therefore ideal targets for vaccines. 

SARS-CoV-2 is a highly mutagenic virus and one incredibly important bioinformatic platform known as GISAID which has enabled the real-time monitoring of these mutations. This comprehensive and open-access database was key to updating vaccine formulations and maintaining efficacy against emerging variants. 

In conclusion, although sometimes overlooked, bioinformatics played a crucial factor in fighting SARS-CoV-2 as efficiently and quickly as we did. From genome sequencing to mutation mapping, bioinformaticians have taken arms at every stage of battling the SARS-CoV-2 pandemic.

Written by Devanshi Shah

Related articles: Origins of COVID / COVID-19 glossary / Correlation between HDI and mortality rate during the pandemic

REFERENCES

Chatterjee, R., Ghosh, M., Sahoo, S., Padhi, S., Misra, N., Raina, V., Suar, M. & Son, Y.-O. (2021) Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development—A Perspective Review. Vaccines. 9 (8), 812. doi:10.3390/vaccines9080812. 

Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C., et al. (2020) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics. 22 (2), 642–663. doi:10.1093/bib/bbaa232. 

Ma, L., Li, H., Lan, J., Hao, X., Liu, H., Wang, X. & Huang, Y. (2021) Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic. Computational Biology and Chemistry. 95, 107599. doi:10.1016/j.compbiolchem.2021.107599. 

Torrington, E. (2022) Bioinformaticians: the Hidden Heroes of the COVID-19 Pandemic. BioTechniques. 72 (5), 171–174. doi:10.2144/btn-2022-0039. 

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