Nick Saffell/University of Cambridge

Professor Sharon Peacock is the Director and Chair of the UK’s world-leading COVID-19 Genomics consortium (COG-UK). To date, COG-UK has sequenced over a million SARS-CoV-2 genomes — providing vital information for vaccine development as well as crucial ongoing disease monitoring.

Sequencing this “extraordinary number” of genomes has been “challenging”, made possible only due to widespread commitment and “willingness to help”, says Peacock.

Back in the early stages of the pandemic, Peacock decided to establish COG-UK in order to “prepare for what SARS-CoV-2 could have in store for us.”

Explained How does Covid-19 genome sequencing actually work?

“It starts with a PCR test. If your test is positive, that's the starting material for sequencing of the virus. We cannot sequence every positive sample, so we combine random sampling from cases across the UK, with targeted sequencing for travellers and in areas where disease is surging and for people who develop COVID after vaccination or after already having a previous infection.

The basic principle is that the sequence provides a read out of the approximately 30,000 bases or points in the genetic code of the virus. We can detect where mutations (typos) have occurred at any given point in this genetic code.

We upload the sequence into CLIMB-COVID (a cloud infrastructure for microbial bioinformatics), where the sequence is checked for quality, and analysed to detect mutations and variants. We also look at the relatedness of once virus versus other viruses, constructing ‘family trees’.”

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“Even as early as February or March in 2020, it was clear that, as living organisms mutate over time and through evolution, it was only a matter of time before SARS-CoV-2 evolved through natural selection to keep pace with the changes in the human population, most notably increases in immunity as more people got infected. So we developed the capabilities to detect these changes and to learn about what that what they meant for virus behaviour.”

A world leader in Covid-19 genome sequencing, the UK benefited from a number of factors in getting a speedy start on sequencing: “We had a very strong and well-networked genomics community in the UK already, and there was a real willingness of academic institutions and the public health agencies, as well as the Wellcome Sanger Institute, to work together.”

Moreover, support from Sir Patrick Vallance and Professor Chris Whitty and funding from the UK COVID-19 fighting fund was “instrumental”. Peacock notes specifically that Sir Patrick Vallance, the government’s chief science adviser and “an incredibly wise scientist”, was “keen on genomics from the outset”.

When it came to forming the consortium, scientists — conscious of the imminent threat posed by Covid-19 — were “incredibly eager”.

“Egos were left at the door”, says Peacock. “People worked together, all of the data was given into public databases and everybody was incredibly keen. It was a coalition of the willing.”

“The bottom line is that you need to be able to sequence to keep drugs and and vaccines effective”

Asked why sequencing is important, she tells me: “The bottom line is that you need to be able to sequence to keep drugs and and vaccines effective.”

The very first genome was released on the 3rd of February, 2020. This genome — the original virus from China — was “instrumental for vaccine design”. Looking ahead to the future, consistent genomic sequencing “will be essential for further vaccine development” and for “public health at large”, especially when it comes to tracking emerging Covid-19 variants.

She is largely positive about our present situation, telling me that “because we have so many vaccines available to us, we’re in a really good place”. Genome sequencing, she emphasises, will be vital in ensuring that we stay on top of emerging disease developments.

As for other essential strategies to tackle the pandemic, Peacock is keen to stress that ensuring the availability of vaccination globally is important from both a “moral” and a “strategic standpoint”.

“In my view, the best way of reducing the risk of new variants of concern emerging is to really squash the number of cases that we see, and the surefire way to do that is through vaccination.”

Considering other long term strategies beyond vaccination will all depend on what happens to case rates, says Peacock. She emphasises that it’s very hard to predict the future of the pandemic, especially going into winter: “We’re always living in a period of unknown because each day creates the history that we will then use to understand the virus better.”

Nevertheless, she remains optimistic: “I believe that we’ll come out of this pandemic much better prepared for the next one: scientifically, we’re in a stronger place, both in the way we work and also in the way that we’ve expanded our disciplines.”

For the scientific community, Peacock tells me, the key lesson of the pandemic has been “the importance of working across boundaries”.

As for genome sequencing specifically, “there’s been a massive explosion in people’s awareness of why it might be important in public health and how the information could be actionable. People are already talking about how that could be useful for antibiotic resistance, for example.”

Peacock herself, having “always been invested in infectious diseases”, began focusing on genome sequencing around ten years ago, attracted to the field by the major advances in sequencing technology. Back in 2001, she tells me, one E. coli bacterium would take 18 months to sequence, and would cost around half a million pounds. By 2014, you could do it in less than a day and it would cost around £100.


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Asked how, on a personal level, her life might change post-pandemic, Peacock tells me: “I’ll continue to lead a life of contribution, but there may be some diversification from genomics”. She notes that recently became a Samaritan, and is “passionate about the importance of mental health care”.

She is also “really interested in providing educational opportunities for people who don’t necessarily have easy access to them.” Having herself left school at 16 without any GCSEs or A Levels, Peacock entered medicine later in life, and is eager to work to provide access opportunities for talented prospective students in similar situations.

Overall, Peacock is positive about the future: “I’m generally an optimist and I’m optimistic that that we will find a way to live with this virus. It’s very unlikely that we will eradicate it, but I think that we will find ways to live with it so that over time we can return to all the things in life that we want to experience.”