French version
Atelier 5 - Coronavirus and proteins...
Since December 2019, a new coronavirus of animal origin started to infect humans: this is the beginning of a pandemic
This virus is called Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2).
He is responsible for the disease called Coronavirus disease-19 (COVID-19).
These activities highlight how bioinformatics can be harnessed to study a new virus, its genomes, its proteins, its origin...and its evolution !
"We are learning so much, so fast!" E. Hodcroft
Objectives
- Discover SARS-CoV-2 genome(s) and protein(s)
- Compare SARS-CoV-2 genomes sequenced in various countries: look for the differences (mutations) and identify the virus variants
- Discover how to monitor the impact of a mutation such as the N501Y mutation on infectivity and immune response
- Discover bioinformatic databases - GenBank (DNA), UniProtKB (protein), PDB (3D structure), Viralzone
- Discover bioinformatic tools (Blast, BLAT, align, translate)
- Better understand current research... and the challenges faced!
Prerequisite
- DNA (genome) and proteins
- Video: from DNA to protein
- A story and some related activities on the site
'LightOfEvolution.org: "Hunt for variants"
The links below give access to the different chapters of a pdf document.
1.
Introduction
- What is a virus
- Viruses that infect human
- Coronavirus and SARS-CoV-2
2.
The first sequence of SARS-CoV-2 genome
- Discover the genome of SARS-CoV-2 (10 January 2020, Wuhan)
3.
Setting up the RT-PCR test
- Test the specificity of the RT-PCR
4.
SARS-CoV-2 and its genome(s)
- Access and compare the genomes of SARS-CoV-2 sequenced in different countries
- Look for the mutations
- Identify the virus variants
5.
SARS-CoV-2 and its proteins
- Discover the different proteins of the virus
6.
SARS-CoV-2 and its spike protein
- Discover the function of the spike protein, its gene, its amino acid sequence and its 3D structure
- From gene to the protein sequence: translate
- About the RNA vaccines
7.
The spike protein: impact of the mutations
- Translate nucleotide sequences from different virus variants
- Discover the N501Y mutation and its impact
8.
The spike mutations and the SARS-CoV-2 variants
- Combination of mutations: discover the different variants (Alpha, Beta, Gamma, Delta, Omicron, ...)
9.
Inferring the origin of SARS-CoV-2
- Compare the spike sequence of coronavirus infecting different animals (bat, pangolin, ...)
10.
Looking for a treatment …
- Drug, vaccine...
11.
An example of research carried out at the SIB Swiss Institute of
Bioinformatics
- Compare the spike protein sequences from different coronavirus....
12.
SARS-CoV-2 and HIV
- Misinterpretation of similarity searches (BLAST) and fake news...
How to contact us...
This workshop is the result of a collaboration between L'éprouvette, University of Lausanne's public laboratory (Service Culture et Médiation Scientifique) and the Swiss-Prot group - SIB Swiss Institute of Bioinformatics.We can run this workshop in your classrooms or online : do not hesitate to contact us!
- outreach@sib.swiss
About us...
License & disclaimer
This portal is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.