THE POWER OF GENOMICS TO UNDERSTAND THE COVID-19 PANDEMIC

About the course

The world was devastated by the COVID-19 pandemic. Genomics is key to understanding and responding to the disease. This course, the first of a series of five, introduces key concepts in viral genomics and how they can be applied to the current pandemic. It explores lessons that can be applied to future pandemic preparedness.

Learning outcomes

• Describe how viruses cause diseases and pandemics
  
• Discuss the use of sequence data for detecting and tracking the SARS-CoV-2 virus and its variants
  
• Describe the development and action of vaccines and therapeutics against SARS-CoV-2
  
• Evaluate the role of genomic epidemiology in pandemic decision-making
  
• Explain how data sharing contributes to developing effective strategies against the pandemic

Target audience

This course is designed for anyone interested in learning more about the genomics response to the current pandemic. While no prior knowledge about COVID-19 is required, it is likely to be most useful to researchers, healthcare professionals, science journalists, policymakers, and those working in public health.

Content

Week 1 - Pandemic and their origins

• Glossary
  
• Hypotheses of where COVID-19 came from
  
• What is a Virus?
  
• The SARS-CoV-2 virus
  
• What is the difference between pandemic, epidemic, and outbreak?
  
• Transmission of respiratory viruses
  
• Genomic technologies for tracking COVID-19
  
• The Great Influenza Pandemic of 1918
  
• DNA, RNA and PCR
  
• What is Genome Sequencing?
  
• Tracking and reacting to outbreaks with genomic knowledge
  
• How is SARS-CoV-2 sequencing done?

Week 2 - Viruses, Variants and Vaccines

• What came before? Comparison with other coronaviruses (MERS/SARS)
  
• The disappearance of SARS
  
• The mechanism of viral replication
  
• The Coronavirus Spike Protein
  
• What is a vaccine?
  
• Some vaccine approaches used for COVID-19
  
• Up next - sequencing for vaccine development
  
• The importance of sequencing in vaccine trials
  
• How has genomics guided therapeutic design?
  
• Variants Explained: Mutation, Variant, VOC
  
• Tracking across a nation
  
• SARS-CoV-2 Variants
  
• Variants arising all over the world

Week 3 - Epidemiology and tracking in a pandemic

• How to tackle a respiratory virus?.
  
• Introduction to Phylogenetics
  
• Surveillance around the world
  
• Identifying transmission clusters: Hospital outbreak investigation in the United Kingdom
  
• Surveillance of viruses in a population
  
• Genomic surveillance and its impacts
  
• Sequencing surveillance options
  
• What can we do better for the pandemics that may come?
  
• Resources

Collaborators

Educators

Leigh Jackson, University of Exeter, United Kingdom
Sophie Prosolek, United Kingdom
Stephanie Hutchings, Bristol Health Security Agency (UKHSA), United Kingdom
Teresa Cutiño-Moguel, Royal College of Pathology, Barts Health, United Kingdom

Contributors

Carlo Lapid, Philippine Genomics Center, Philippines
Carolina Torres, Argentine SARS-CoV-2 Genomics Consortium (PAIS Project), University of Buenos Aires, Argentina
Charlotte Williams, UCL Genomics, University College London, United Kingdom
Gerald Mboowa, Africa Centres for Disease Control and Prevention, Ethiopia
Mariana Viegas, Argentine SARS-CoV-2 Genomics Consortium (PAIS Project), Argentinean Scientific and Technical Research Council (CONICET), Argentina Paola Niola, University College London, United Kingdom
Rachel Williams, UCL Genomics, University College London, United Kingdom
Sandra Cantinela, University College London, United Kingdom
Sunando Roy, University College London, United Kingdom
Stephen Bridgett, Queen’s University Belfast, United Kingdom
Tapfumanei Mashe, Ministry of Health and Child Care, Zimbabwe
Thanat Chookajorn, COVID-19 Network Investigations Alliance, Genomics and Evolutionary Medicine Unit, Mahidol University, Thailand

Reviewers

Camila Romano, Hospital das Clínicas, School of Medicine, University of São Paulo, Brazil
Charles Masembe, Makerere University, Uganda
Varun Shamanna, Central Research Laboratory, Kempegowda Institute of Medical Sciences, India

Education developers

Jorge Batista da Rocha, Wellcome Connecting Science, United Kingdom
Liã Bárbara Arruda, Wellcome Connecting Science, United Kingdom

COG-UK contributors

Sharon Peacock, University of Cambridge, United Kingdom
Alistair Darby, University of Liverpool, United Kingdom
Catherine Ludden, University of Cambridge, United Kingdom
Darren Smith, Northumbria University, United Kingdom
Anna Markov, University of Cambridge, United Kingdom
Peter McEwan, University of Cambridge, United Kingdom

Wellcome Connecting Science contributors

Treasa Creavin, Wellcome Connecting Science, United Kingdom
Alice Matimba, Wellcome Connecting Science, United Kingdom
Rachel Berkson, Wellcome Connecting Science, United Kingdom
Mel Sharpe, Wellcome Connecting Science, United Kingdom
Dusanka Nikolic, Wellcome Connecting Science, United Kingdom

Original version

Original platform: FutureLearn
Original course page: The power of genomics to understand the COVID-19 pandemic
Launch of the original version: 7 February 2022
Launch of the reviewed version: 4 July 2022

Data collected on 31 May 2023
Number of joiners: 4,466
Number of countries reached: 132
Review score: 4.6/5 (37 reviews)

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Any reuse of the course materials is encouraged with due acknowledgement.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

How to cite

COG-Train. (2022). The Power of Genomics to Understand the COVID-19 Pandemic. Zenodo. https://doi.org/10.5281/zenodo.8164924

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