PATHOGEN GENOMICS: A NEW ERA IN GLOBAL HEALTH SURVEILLANCE AND STRATEGY

_@Canva

About the course

In recent years pathogen genomics has proven to be a valuable tool to understand infectious disease dynamics and improve the epidemiology, surveillance and vaccine and treatment development for pathogens of public health relevance. One of the SARS-CoV-2 pandemics’ legacy is the expansion of pathogen genomics applications to tackle infectious diseases of public health relevance. This course will provide tools, discussion and resources to strengthen genomics surveillance approaches around the world.

Learning outcomes

• Describe basic concepts of epidemiology and pathogen genomics
  
• Identify key elements and tools to support a successful pathogen surveillance
  
• Interpret and discuss scientific evidence to inform the public health system
  
• Critique approaches used in global health surveillance
  
• Describe principles and procedures for responsible public communication of pathogen genomics information

Target audience

This course is designed for professionals from various disciplines who are interested in the implementation of genomic surveillance for pathogens of public health relevance and its impact on decision-making

Content

Week 1 - Introduction to genomics surveillance

• Glossary
  
• Pathogen monitoring
  
• Working together to build capacity
  
• What genomic data could tell us
  
• Transferring knowledge
  
• Laboratory quality management
  
• Why biobanks are important
  
• Metadata
  
• The ethics of data sharing
  
• How to share pathogen genomic data
  
• Data sharing in a public health emergency

Week 2 - Pathogen genomics for global health

• What is One Health?
  
• Genomics surveillance in One Health
  
• Genomics for antimicrobial resistance surveillance
  
• National genome surveillance for antimicrobial resistance
  
• Regional health organisations and antimicrobial resistance
  
• How is the influenza vaccine developed each year?
  
• Genomics in tuberculosis drug-resistance
  
• Genomics for tuberculosis: impact and challenges
  
• Primer to malaria genomic surveillance
  
• Disease X and future pandemics in the age of climate crisis
  
• Legionellosis in Argentina: evolution of the laboratory diagnosis strategy
  
• Using wastewater to monitor COVID-19
  
• Wastewater monitoring for SARS-CoV-2 in India
  
• Establishing genomics surveillance
  
• Genomic surveillance of cholera in South America
  
• Cholera in Yemen

Week 3 - Communicating genomics surveillance with impact

• Effective communication
  
• Ethics of communication
  
• Communicating with the public
  
• How to prevent misinformation
  
• Media and the public
  
• Informing public health professionals: Viet Nam case study part 1
  
• Engaging with policymakers: Viet Nam case study part 2
  
• Scientific evidence and policy
  
• Informing policymakers
  
• Research and public health
  
• Health policy lessons from COVID-19
  
• Impacting public health policy
  
• How we can be prepared
  
• COVID-19 in the European Union
  
• The biggest lessons learnt
  
• Resources

Collaborators

Educators

Josefina Campos, Argentine Medical Research Institute (ANLIS Malbrán), Argentina
Nchangwi Syntia Munung, University of Cape Town, South Africa
Thanat Chookajorn, Mahidol University, Thailand and Molecular Infection Medicine, Sweden
Tobias Hoffmann

Contributors

Abena Animwaa Yeboah-Banin, University of Ghana, Ghana
Amsha Viraragavan, South African Medical Research Council, South Africa
Ana Filipe, MRC-University of Glasgow Centre for Virus Research, United Kingdom
Anastasia Koch, Eh!woza and the University of Cape Town, South Africa
Andrea Cabibbe, IRCCS San Raffaele Scientific Institute, Italy
Audrey Gadzekpo, University of Ghana, Ghana
Brigitte Glanzmann, South African Medical Research Council, South Africa
Christine Carrington, The University of the West Indies, Trinidad and Tobago
Collins Otieno, African Society for Laboratory Medicine, Ethiopia
Craig Kinnear, South African Medical Research Council, South Africa
Emma Hodcroft, University of Bern and University of Geneva, Switzerland
Farah Ishtiaq, Tata Institute for Genetics and Society, India
Farirai Mutenherwa, Kwazulu-Natal Research Innovation and Sequencing Platform, South Africa and Biomedical Research and Training Institute, Zimbabwe
Gideon Nsubuga, IRH3AU, Makerere University, Uganda
Gilbert Tietaah, University of Ghana, Ghana Harper VanSteenhouse, BioClavis Ltd, United States of America Iruka Okeke, University of Ibadan, Nigeria
Ismail Mahat Bashir, WHO Yemen Country Office, Yemen
Jeffrey Barrett, Wellcome Sanger Institute, United Kingdom Johan Fabian Bernal Morales, The Colombian Agriculture Research Corporation (AGROSAVIA), Colombia
Kate Baker, University of Liverpool, United Kingdom
Katrina Lawson, Oxford University Clinical Research Unit (OUCRU), Viet Nam
Linzy Elton, University College London, United Kingdom
Marcelo Galas, Pan American Health Organization (PAHO), United States of America
Marjorie Santamaria, The Colombian Agriculture Research Corporation (AGROSAVIA), Colombia
Matthew Dorman, Wellcome Sanger Institute, United Kingdom
Mónica Prieto, Argentine Medical Research Institute (ANLIS Malbrán), Argentina
Paúl Cardenas, Universidad San Francisco de Quito, Ecuador
Philippe Lemey, KU Leuven/University of Leuven, Belgium
Pilar Donado-Godoy, The Colombian Agriculture Research Corporation (AGROSAVIA), Colombia
Renée Street, South African Medical Research Council, South Africa
Richard Orton, MRC-University of Glasgow Centre for Virus Research, United Kingdom
Roberto Melano, Pan American Health Organization (PAHO), United States of America
Rogers Kamulegeya, IRH3AU, Makerere University, Uganda
Tomas Poklepovich Caride, Argentine Medical Research Institute (ANLIS Malbrán), Argentina
Tracey Calvert-Joshua, South African National Bioinformatics Institute, South Africa
Zeb Jamrozik, University of Oxford, United Kingdom

Reviewers

Camila Romano, University of São Paulo, Brazil
Charles Masembe, Makerere University, Uganda

Education developer

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
Darren Smith, Northumbria University, United Kingdom
Ewan Harrison, Wellcome Sanger Institute, United Kingdom Leigh Jackson, University of Exeter, United Kingdom
Anna Markov, University of Cambridge, United Kingdom
Ellena Brooks, University of Cambridge, United Kingdom
Kim Smith, University of Cambridge, United Kingdom
Laia Delgado Callico, University of Cambridge, United Kingdom
Peter McEwan, University of Cambridge, United Kingdom

Wellcome Connecting Science contributors

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

Original version

Original platform: FutureLearn
Original course page: https://www.futurelearn.com/courses/pathogen-genomics-a-new-era-in-global-health-surveillance-and-strategy/1
Launch of the original version: 6 March 2023

Data collected on 31 May 2023
Number of joiners: 1,614
Number of countries reached: 121
Review score: 4.9/5 (20 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. (2023). Pathogen Genomics: A New Era In Global Health Surveillance And Strategy. Zenodo. https://doi.org/10.5281/zenodo.8234152

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