Assignment:
Bioinformatics
Papers to consider:
Teo, S.P. (2021). Review of COVID-19 mRNA Vaccines: BNT162b2 and mRNA-1273. Journal of Pharmacy Practice. Online ahead of print.
Ward, D., Higgins, M., Phelan, J.E., Hibberd, M.L, Campino, S., and Clark, T.G. (2021). An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Genome Medicine 13:e4.
Assignment: Read the papers of Teo (2021) and Ward et al. (2021) (see first two papers above) and then work through the process below:
• Open the COVID Profiler webpage referenced in Ward et al. (2021) using the following link:
• Read the ‘Step 1' box and click on the button for the ‘SARS-CoV-2 Immunoanalytics tool + HLA-I Data' (warning: it will take quite some time to load the full genome layout with features, but after the loading process has completed, you should see a circular representation of the genome and the associated mapped metadata)
• Explore the SARS-COV-2 genome and associated metadata, paying close attention to the pop-up windows that appear as you roll over the genome features - especially the links contained therein
• Use the tool and information provided in the papers to address the questions below in an essay format (other supplemental information is also provided (see below)
• completed your term paper,
Now consider the questions below for this term paper, and address each of these questions in essay format
Questions:
1) What do current serological diagnostics (i.e., "COVID-19 tests") "target"?
2) Are there other potential diagnostic "targets" available? If so, what are the advantages/disadvantages of this/these over the conventional targets used now (e.g., especially considering the "non-synonymous mutation' metadata in the ‘SARS-CoV-2 Immunoanalytics tool'), and what is/are the functions of this/these target/s?
3) What role do/can modern bioinformatics tools play in vaccine/serological diagnostic development, specifically, and in COVID-19 epidemiology, more generally?
4) How would you characterize the role of bioinformatics in the current pandemic, caused by the SARS-CoV-2 virus and all its mutated variants (e.g., the ‘delta' and "omicron" strains), versus pandemics of the past?