Hand wearing gloves holding a pipette, in a laboratory

Blog / COG Train

18 May 2022

Answering public health questions with testing and sequencing strategies. Learn more with our second COG-Train course ‘From Swab to Server’

How do sequencing experts decide upon their testing and analysis strategy? Our second COG-Train online course “From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic” will take you on the journey of a sample obtained from a COVID-19 patient and support you in comparing the different sample types and how sampling strategy affects test performance.

It’s no secret at this point that sampling and testing are key for understanding how infectious diseases spread through populations. In the COVID-19 pandemic, the testing volume around the world has exceeded that of any previous pandemic. From this experience, we have been able to generate enormous amounts of information and expertise into what makes an effective sequencing programme and what can be improved moving forward.


Prioritisation pyramid of different sampling strategies. Categories include: Untargeted variant tracking: unbiased geographically representative samples. Surveillance of transmission: hospitals, care homes, schools, prisons. Targeted variant tracking: borders, community surveys, wastewater sampling, vaccine trials, therapeutic trials.

Figure 1: Prioritisation pyramid of different sampling strategies.

Selecting the optimal samples to sequence is key in the ongoing global effort to suppress the spread of the virus and it depends both on the stage of the pandemic in a certain country and on the public health issue that you are trying to address (see Figure 1). It is universally accepted that a key activity within genomic surveillance is the tracking of different lineages and variants.

An important approach to sampling is to use random, unbiased, and geographically representative sampling of people with COVID-19, or untargeted variant tracking. This is combined with a targeted approach that aims to enrich the likelihood of detecting a new variant, in which samples are sequenced from people who have travelled recently, or who are part of a rapidly expanding cluster or regional increase in cases. Sampling in hospitals, intensive care units and care homes can answer specific public health questions such as confirming transmission chains or detecting new variant reservoirs. Sequencing in vaccine and therapeutic trials can also provide data on possible immune escape and help to predict efficacy. Additionally, sequencing the virus from people who have become seriously ill with COVID-19 can also form part of studies that examine whether the virus circulating at the time is causing more severe illness. These targeted approaches can complement the unbiased surveillance data and give a more holistic view of the circulating variants in different parts of the community.

The priorities of a country, or local region, will determine which samples should be sequenced, at any given time. Because of this, it is important that all the key stakeholders involved in sequencing know how to decide which type of samples to select.


For these reasons, we are excited to launch our second COG-Train online course: “From Swab to Server: Testing, Sequencing and Sharing During a Pandemic”.

This course takes you on the journey of a sample obtained from a patient with COVID-19, from its collection through to the generation of sequencing and clinical data. We will touch on how experts have overcome the challenges of large-scale testing, sequence and data sharing, in the context of a global pandemic.

The course aims to:

  • Outline the journey from sample collection, through PCR to sequencing and data linkage
  • Compare the different sample types, and how sampling strategy affects test performance
  • Explain the importance of linking genomic data to clinical and epidemiological data sets in order to address public health and scientific questions
  • Identify and explore ethical, legal and social implications of data usage and sharing


It will be led by global experts in the field, including:

  • Rogers Kamulegeya, Director of the Uganda Biobank, Kampala, Uganda
  • Moses Luutu Nsubuga, Biomedical Scientist at Makerere University, Kampala, Uganda
  • Dr Ana da Silva Filipe, Director of the Centre for Virus Research, Glasgow, Scotland
  • Dr Leigh Jackson, COG-Train Scientific Lead, Cambridge, England


If you are involved in the testing and analysis of disease samples, a diagnostic or healthcare professional, or a researcher specialising in diagnostics, diseases or pandemic, register for this course now!

The course will be facilitated by the educators throughout May. If you are interested in participating, more information and registration details can be found here.


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.