bioinformatics: please check the attached document.
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. https://doi.org/10.1177/08971900211009650
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. https://doi.org/10.1186/s13073-020- 00822-6
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: http://genomics.lshtm.ac.uk/immuno/
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:
What do the BNT162b and mRNA-1273 mRNA vaccines both encode?
How “safe” are these vaccines given the information in Teo (2021)? How many genomic features (i.e., genes) does the SARS-CoV-2 virus have and what is the length of its genome?
What are the advantages of using mRNA-based vaccines over conventional vaccine types?
What do current serological diagnostics (i.e., “COVID-19 tests”) “target”?
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?
What role do/can modern bioinformatics tools play in vaccine/serological diagnostic development, specifically, and in COVID-19 epidemiology, more generally?
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?
Links for Other Supplemental Information:
CDC: “Past Pandemics” https://www.cdc.gov/flu/pandemic-resources/basics/past-pandemics.html
CDC: “Understanding mRNA COVID-19 Vaccines” https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html
CDC: “What You Need to Know About Variants” https://www.cdc.gov/coronavirus/2019-ncov/variants/about-variants.html
Elixir-bio tools: "Everything COVID-19" https://bio.tools/t?page=1&q=COVID-19&sort=score
GIS-AID: “Tracking Variants” https://www.gisaid.org/hcov19-variants/ (including "3D Structure of Spike with Amino Acid Changes") John Hopkins: “Coronavirus Resource Center” https://coronavirus.jhu.edu/map.html
(an image of the ‘Dashboard’ is provided as a .pdf file in Content/Exams/Final Exam should your browser not be compatible)
PMC: “Figure, Single-stranded RNA genome of SARS-CoV-2” https://www.ncbi.nlm.nih.gov/books/NBK554776/figure/article-52171.image.f5/
Science Focus Magazine: “Would Spanish flu be as deadly if it occurred today?” https://www.sciencefocus.com/science/would-spanish-flu-be-as-deadly-if-it-occurred-today
B
i
oinformatics
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.
https://doi.org/10.1177/08971900211009650
Ward, D., Higgins, M., Phe
lan, 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. https://doi.org/10.1186/s13073
-
020
-
00822
-
6
As
signment: 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:
http://genomics.lshtm.ac.uk/immuno/
·
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 afte
r 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 o
ver 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 p
aper,
Now consider the questions below for this term paper, and address each of these questions in essay
format
Questions:
What do the BNT162b and mRNA
-
1273 mRNA vaccines both encode?
How “safe” are these vaccines given the information in Teo (2021)?
How many genomic features (i.e.,
genes) does the SARS
-
CoV
-
2 virus have and what is the length of its genome?
What are the advantages of using mRNA
-
based vaccines over conventional vaccine types?
What do current serological diagnostics (i.e., “COVID
-
19 tests”) “target”?
Are there other potential diagnostic “targets” availab
le? 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/thes
e target/s?
What role do/can modern bioinformatics tools play in vaccine/serological diagnostic development,
specifically, and in COVID
-
19 epidemiology, more generally?
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. https://doi.org/10.1177/08971900211009650
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. https://doi.org/10.1186/s13073-020- 00822-6
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:
http://genomics.lshtm.ac.uk/immuno/
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:
What do the BNT162b and mRNA-1273 mRNA vaccines both encode?
How “safe” are these vaccines given the information in Teo (2021)? How many genomic features (i.e.,
genes) does the SARS-CoV-2 virus have and what is the length of its genome?
What are the advantages of using mRNA-based vaccines over conventional vaccine types?
What do current serological diagnostics (i.e., “COVID-19 tests”) “target”?
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?
What role do/can modern bioinformatics tools play in vaccine/serological diagnostic development,
specifically, and in COVID-19 epidemiology, more generally?