Scientist Sophie Prosolek preparing the sample plate using the ARTIC protocol – the world’s most common approach to COVID-19 sequencing

Professor Justin O’Grady and Dr Andrew Page

Our work on the genomic sequencing of SARS-CoV-2 has just reached a major landmark as we successfully sequenced our 10,000^th positive sample at the Quadram Institute in Norwich.

It is hardly a cause for celebration given the context we find ourselves in. Our work on the epidemiological sequencing of COVID-19 samples only started in March 2020 and recent months have seen a very significant rise in the incidence of COVID-19 in our region. Out of 144 countries with public genome data available only four have sequenced more SARS-CoV-2 than the Quadram Institute.

More than 7,000 of those samples were undertaken between October and December 2020 as the combination of the new variant virus and the period between the second and third national lockdowns led to a very significant rise in the spread of the disease.

It’s now 10 months since we joined the then embryonic COVID-19 Genomics UK (COG-UK) consortium. COG-UK was set up in double-quick time to help provide the Scientific Advisory Group for Emergencies (SAGE) with vital public health tracking of genomic changes to the virus in near real-time. This type of genomic epidemiology had never been done at this scale before.

Genomic sequencing helps us understand what is happening to the virus over time. You can think of it as viral detective work. As the virus makes copies of itself, occasionally a random change happens that propagates, and it is through tracking these changes that we can build up a picture of how the virus spreads, and what those changes may mean. With the South African variant, for example, we detected three cases in Norfolk, and were able to trace all back to travel or contacts of travellers to South Africa. This variant can only be identified currently by genome sequencing.

At the Quadram we sequence positive samples from people with COVID-19 that are tested through what are termed Pillar 1 and Pillar 2 testing systems. Most our work is focused on Pillar 1 is made up of hospital laboratories, largely focused on testing samples from patients in our region’s hospitals. Pillar 2 includes the Lighthouse Lab ‘super-laboratories’ that receive swabs from people who are not in hospital, as well as samples from people in long-term care facilities.

Our COG-UK work is also reliant on getting metadata needed to make the sequencing results meaningful. Metadata is the basic demographic information about the people who samples have been taken from. Their age, sex, and geography are vital in terms of understanding how the virus is moving and how it can be tackled.

The 10,000th COVID-19 sample being sequenced at the Quadram

The Norwich Research Park Biorepository team, part of the Norfolk and Norwich University Hospital, are expert at securely providing the metadata we need to make sense of our sequencing work. The combination of Quadram’s bioscience expertise and the skills of the Biorepository team has made Norwich one of the best performing sequencing centres in the country.

Dr Justin O’Grady said: “If setting up our epidemiological sequencing work through COG-UK in March 2020 felt like a world record-breaking sprint, the rest of the year evolved into a scientific ultra-marathon. After the first wave the spring of 2020 we knew we’d need to create more capacity so that we could handle increases in cases and still meet the demands we would face.”

PhD student Ebenezer Foster-Nyarko works on the samples

Gearing up for more sequencing has involved a huge collective effort. Out of 144 countries who have public genome data available, only four countries have sequenced more than 10,000 samples (UK, USA, Denmark, Australia). We are lucky to have access to CLIMB (Cloud Infrastructure for Microbial Bioinformatics), an established and readily accessible cloud bioinformatic infrastructure capable of handling the volume of data and tools necessary. CLIMB’s contribution was recently recognised through an HPCwire award

Dr Andrew Page said: “Once the sequencers finish a vast quantity of data is rapidly processed using a state-of-the-art cloud computing system at Quadram. Our scientists then go through the resulting data to answer questions posed by the clinicians and public health teams, whilst also looking out for unusual patterns which for example may indicate hidden outbreaks. Sequencing has given us the ability to see the evolution of a disease in real-time and to take rapid action.”

Additional funding from central Government also enabled us to recruit more lab scientists and cover the costs of laboratory supplies and kit but we have also focused on honing our processes to maximise the throughput of PCR samples.

The challenge has been how best to increase our PCR capacity, optimise our processes and develop a unified lab pipeline for both the Nanopore and Illumina pipelines. All of this has been needed to enable one or two scientists to process more than 1,000 samples in just a couple of days.

This has meant removing labour-intensive cleanups, quantifications and normalisations. We also developed a method which is essentially the same for Nanopore (fast track/quick results in several hours) and Illumina (high throughput run in a day or so for large numbers) depending on the urgency and response needs.

The UK is now a world leader in genomic sequencing of COVID-19 and the past 10 months have been exhausting for all concerned. We have sequenced far more COVID-19 than we ever expected, and our hope now is to start seeing less samples as we move through 2021.

• You can listen to the Micro Binfie podcast to hear more about how the Quadram team tackled the COVID-19 sequencing challenge. https://soundcloud.com/microbinfie/31-large-scale-sequencing-of-sars-cov-2-genomes-from-one-region