Blog / COG Train

4 Nov 2022

“There are so many lessons from the pandemic”: Hear from global experts on why strengthening genomic surveillance approaches is critical for the future

A key lesson resulting from the COVID-19 pandemic is the importance of strong and agile genomic surveillance capabilities globally, to be able to react at pace to public health threats. Global experts share their personal learnings from the pandemic, and explain why tools and resources to strengthen genomic surveillance approaches are so important.

At the beginning of the pandemic, genomic researchers had to find innovative ways to urgently scale up their sequencing capacities. Some were able to draw on support from other scientists within their network until they could train and build up their teams, while others utilised students and staff volunteers to expand their output. “Working together with other teams and groups was the best option for us, because we could go further and produce more,” says Dr Paola Cristina Resende, Virologist, Oswaldo Cruz Institute (Brazil), “The power of collaboration was my greatest lesson.”

In Portsmouth, Dr Sam Robson, Lead Bioinformatician at the Centre for Enzyme Innovation (United Kingdom), had to quickly grow his lab team. He recalls that in the first few weeks of the pandemic, “there were only a small number of samples being sequenced, but they had a very big impact to help the local hospital, so we knew being able to upscale our output at pace would be critical.” For this reason, the ability of scientists across the world to be able to call upon researchers and bioinformaticians who were confident in genome sequencing and analysis was a hugely important component of the fight against COVID-19.

Labs also needed to embrace automated processes to streamline and standardise  sequencing so that it could be shared with other facilities. “It’s so important that we share our data with the world so that they can make responsible decisions from it,” says Dr Senjuti Saha, Director and Scientist at the Child Health Research Foundation (Bangladesh).

Professor Christian Happi, Professor of Molecular Biology and Genomics and Director of the African Centre of Excellence for Genomics of Infectious Diseases (Nigeria), says that the biggest lesson he learnt from the pandemic was that “in Africa we are very dependent on others, and need to invest in necessary infrastructure, to ensure our own health security.” This inequality in genomic sequencing infrastructure is one of the key reasons why COG-Train exists today and aims to facilitate an increase in global genome sequencing and analysis capacity, alongside efforts from other organisations such as H3ABioNet, ARTIC Network, PhasAGE and SAGESA. Our training courses compliment other training offerings to help support global genomic surveillance efforts and pandemic preparedness.

We are therefore thrilled with our fourth COG-Train course, titled ‘A Practical Guide for SARS-CoV-2 Whole Genome Sequencing’. To date, over 1000 learners from over 100 countries have already joined the course. This free 3-week online training programme, housed on FutureLearn, provides tools and resources for capacity building aiming to strengthen genomics surveillance approaches.

By the end of this course learners can:

  • Compare sequencing methodologies
  • Critically evaluate different approaches to determine SARS-CoV-2 genomes and variants
  • Apply SARS-CoV-2 sequencing best practices
  • Identify ways in which to scale up SARS-CoV-2 sequencing
  • Describe SARS-CoV-2 analysis pipelines

Sign up for the course by clicking here to register now.


COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.