In tracking coronavirus mutations, most of the countries flying blind


To monitor changes to the coronavirus that could supercharge the pandemic or render vaccines less effective, scientists must sequence its genetic code to catalogue potentially dangerous mutations as they emerge.
But so few countries are conducting and sharing surveillance that experts are as worried about the mutations they cannot see as those they can.
Publication of the first genomic sequence of SARS-CoV-2 in January last year, at the very outset of the pandemic, allowed scientists to identify it as a new coronavirus, and begin developing diagnostic testing and vaccines.
Since then, tens of thousands of sequences have been uploaded on public databases, enabling mutations to be tracked with a degree of detail and a speed never achieved before.
But the lion’s share of this information has come from just one country: Britain.
As of mid-January, GISAID — a major data sharing platform originally created to monitor influenza — had received 379,000 sequences.
Of these, 166,000 were from Britain’s COVID-19 Genomics UK (COG-UK), a partnership between health authorities and academic institutions.
“This is the first time we are ever seeing how a pathogen evolves at this scale,” said Ewan Harrison, Director of Strategy and Transformation at COG-UK and a fellow at the Wellcome Sanger Institute where much of the sequencing is being done.
“We are learning that these mutations accrue way faster than we thought.”
Currently the programme is sequencing 10,000 genomes a week — roughly six per cent of known cases in Britain although that fluctuates — and the plan is to double that.
“The UK blows everyone else out of the water,” said Emma Hodcroft, an epidemiologist at the University of Bern and co-developer on the Nextstrain virus tracking project.
“To me, this has been the moonshot of the pandemic, alongside the vaccines.”
Denmark, she noted, also routinely sequences and shares data, but the information coming from most other countries is sporadic at best.
Sequencing has identified distinct variants — strains that have acquired clusters of new mutations — in Britain, South Africa and Brazil in recent weeks.