Towards the middle of December, a sombre Matt Hancock, UK Health Secretary, stood up to deliver an address to the House of Commons.
“Over the last few days, thanks to our world class genomic capability in the UK, we have identified a new variant of coronavirus, which may be associated with the faster spread in the south-east of England,” he told MPs.
It was the news that no one wanted to hear, yet which anyone who understood virus evolution might have anticipated. At the time, around 1,000 cases of infection with the new variant – dubbed the ‘Kent variant’ – had been identified. Just two months later, Professor Sharon Peacock, from Cambridge’s Department of Medicine, would tell the BBC that the variant had “swept the country", and was likely to spread worldwide.
If anyone was well placed to observe this sweep, it was Peacock. She leads the COVID-19 Genomics UK (COG-UK) Consortium, set up early on in the pandemic to deliver large-scale genome sequencing of SARS-CoV-2 to Public Health Agencies, the NHS and the UK government. COG-UK scientists together with Public Health England had been the first to realise that a variant first detected in Kent was rapidly establishing itself as the dominant variant in the UK.
This was not the first time that a variant had emerged and then spread rapidly.
“A variant first detected in Spain rapidly spread to many European countries over the summer months, and we were worried that it was may be more transmissible,” explains Peacock, pulling up a slide that showed the SARS-CoV-2 lineages circulating in the UK since the start of the pandemic.
“If you look at the number of cases that we observed, there was a rapid surge in this variant in the UK – to the point where it become our most common circulating variant. But detailed analysis indicated that this pattern was most likely due to holiday travel.”
The Kent variant – known technically as B.1.1.7 – was different, however. Public health officials were seeing a surge of cases in Kent during a period of lockdown, while elsewhere in the UK numbers were stable. “That started to set alarm bells ringing,” she says.
When COG-UK scientists looked at the sequence data of this new variant, they saw that it had 23 differences in its genetic code compared to the original virus. Returning to the slide, Peacock points to a part of the virus ‘family tree’ that is based on comparing genomes with each other, pointing out what looks like an outlier, a distant, exotic relative – B.1.1.7. “It’s striking that it was clearly genetically different from other circulating SARS-CoV-2 in the UK.”
Phylogenetic tree showing SARS-CoV-2 lineages. B.1.1.7 is shown in green at the bottom.
Phylogenetic tree showing SARS-CoV-2 lineages. B.1.1.7 is shown in green at the bottom.
Looking back through their samples, they discovered that the first case of B.1.1.7 had appeared on 20 September 2020. For a while, there had been only a smattering or cases: it was only when this lineage began to expand towards the end of November and beginning of December that it became clear something was wrong.
