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21 Jul 2022

“We kept learners engaged in a virtual setting” – Our COG-Train educators tell us about their experience

COG-Train provides open-access learning in SARS-CoV-2 genomics and is facilitating an increase in global genome sequencing and analysis capacity, reducing sequencing inequality, and helping to enhance pathogen surveillance. With two successful course launches, and an upcoming one, supporting over 4,000 learners to date, we spoke to some of the COG-Train educators and contributors to learn more about their experience, and the challenges they overcame in developing the course content.

The emergence of SARS-CoV-2 variants of concern is still a global threat, and the need for increased SARS-CoV-2 sequencing capacity remains urgent worldwide. Training programmes play an essential role in this, helping to support scientific growth and independence in lower resource settings especially across many countries in Africa, Asia and Latin America.

COG-Train courses’ educators and contributors bring a wealth of sequencing experience to our programme, which ensures that course content is globally relevant and incorporates educator’s specific learnings from the COVID-19 pandemic. We spoke to them to understand their perspectives, and how that informed the development of our courses. See below for a full list of the panellists and their roles.

At the start of the pandemic, the sequencing capacity and knowledge gap between some countries became more apparent than ever. “Resources in India are limited, so my team and I struggled at the beginning of the pandemic to learn the most basic things”, says Varun, “it was important for me to make sure that other people had the necessary skills moving forward”.

One “silver lining” from this time period, was our expansion of online communication and education. “We had a much wider reach of learners by hosting the courses virtually, compared to what we might have done with face-to-face teaching” recalls Carlo, “especially when there were travel bans due to COVID-19”. “Not only that, but face-to-face learning might have been too expensive for many students, particularly in Africa. Online education removes the extra cost of travel expenses, and reduces the logistical barriers to accessing education”, adds Gerald.

Before getting to that point, the course educators overcame quite a few challenges in developing the course content. The courses underwent vigorous rounds of refining and editing, to ensure that the content was as engaging as possible for the virtual setting.

“We knew that it would be more challenging to keep learners engaged in a virtual setting”, Carlo acknowledges. “We wanted to make sure that the information we put in the courses was clear and easy to digest, for thousands of people from across different backgrounds”, says Rogers, “The motto we had throughout the whole process was ‘Prepare, Review, Refine!’”.

Not only this, but there were multiple collaborators working together on the material, with many having different experiences and skills from one another. “No one knows everything, so collaboration when developing these courses was really important, and was an amazing learning opportunity for us too!” says Teresa. “Developing the material and working together helped to gain a lot of skills, and provided a networking opportunity”, agrees Claudine.

Something else that the course educators had to consider was the disparity in access to equipment and software across nations. “To study bioinformatics, students need high speed internet as well as special software, which was a challenge to set up”, recalled Carlo.

“Moving to an online setting made me more aware that access to basic educational tools remains a huge issue”, says Malebo. “It was eye opening to see the challenges students from different parts of the world face”, agrees Paúl.

Just as countries, communities, and organisations came together during the pandemic, the COG-Train organisers were blown away by the support received from the global genomics community in ensuring the success of the programme.

“As soon as I heard that COG-Train was looking for educators, I approached them directly to volunteer, and then became a course educator”, says Ana. “One of my colleagues asked me if I wanted to contribute to sequencing training”, says Malebo, “for genetics councillors, ethics is imperative, especially now when there are very public concerns about data collection and storage. I felt that there was a lot I could share with other scientists to help them with this”.

So far, COG-Train has launched three online courses on FutureLearn, which have seen more than 4,000 learners from across 130 countries. The courses currently available include:

There are two more courses scheduled for the coming months:

  • ‘A practical guide for SARS-CoV-2 whole-genome sequencing – sequencing, quality control, and variant-calling’
  • ‘Genomic surveillance for public health emergencies’

We are excited to see how COG-Train can increase the reach and impact of its learning materials, ensuring that scientists around the world have all the necessary tools to carry out effective sequencing for COVID-19 and future pandemics.

Watch the recordings from the webinars here.

Webinar 1: Wednesday 22 June 2022, 09:00 – 10:00 BST
Chair: Dr Laia Delgado Callico, Communications Coordinator, COG-UK and COG-Train, University of Cambridge, UK

  • Dr Ana Da Silva Filipe, Research Fellow, Centre for Virus Research, University of Glasgow, UK
  • Carlo Lapid, Senior Bioinformatics Specialist, Philippine Genome Center, Philippines
  • Claudine Nkera-Gutabara, PhD candidate, University of the Witwatersrand, South Africa
  • Malebo Malope, PhD student, Division of Human Genetics, University of Cape Town, South Africa


Webinar 2: Tuesday 28 June 2022, 15:00 – 16:00 BST
Chair: Dr Laia Delgado Callico, Communications Coordinator, COG-UK and COG-Train, University of Cambridge, UK

  • Dr Gerald Mboowa, Human Genetics and Genomics Research Fellow, Genomics Laboratory, Makerere University, Uganda
  • Dr Paúl Cárdenas Aldaz, Principal Investigator, Instituto de Microbiología, Universidad San Francisco de Quito, Ecuador
  • Rogers Kamulegeya, Coordinator, Integrated Biorepository of H3Africa Uganda, Uganda
  • Dr Teresa Cutiño-Moguel, Virology Clinical Lead, Barts Health NHS Trust, UK
  • Varun Shamanna, Research Associate, Kempegowda Institute of Medical Sciences, India

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.