UK among nations now sharing less data on Covid variants with rest of world, analysis shows

A number of countries – including the UK – that have led the way in tracking the evolution of Covid are now sharing less data on new variants with the rest of the world.

In the case of Britain, the US, France, Canada and Norway, up to 53 per cent fewer genome sequences have been uploaded to Gisaid – the global variant database – since the beginning of the year, analysis shows.

The online depository has allowed scientists to identify and track emerging clusters of new strains, as seen with the recent Omicron sub-variants. Since the beginning of the pandemic, millions of sequences have been shared with the platform from countries across the globe.

But as nations move to end mass testing programmes and wind down surveillance infrastructures, meaning there are fewer Covid cases to sequence and upload to Gisad, scientists are concerned by the prospect of “blind spots” in which new and dangerous variants could emerge.

“It is a gamble to wind down infrastructure, because the detection of new variants is going to be compromised,” said Ravi Gupta, a professor of clinical microbiology at the University of Cambridge and member of the government’s Scientific Advisory Group for Emergencies (Sage).

“The thing that worries me is that we’ve scaled down capability in such ways that it might be difficult to rescale up if needed.”

In the UK, daily testing has plummeted. Up to 24 May, an average of 352,450 tests were being conducted across the four nations every day — down from a peak of 3,790,000 at the beginning of January.

As a result, the number of genomes that have been sequenced from these test samples — to ascertain the genetic profile of the virus behind the infection — has dropped, meaning less data is available to submit to Gisaid.

According to figures shared with The Independent, the UK submitted 277,005 genomes to Gisaid in January. This rose to 330,490 and 393,439 respectively for February and March, but dropped to 140,346 for April — a decrease of 49 per cent.

The US, in comparison, has recorded a month-by-month fall over the same period, having shared 345,407 genomes with Gisaid in January, 330,490 in February, 313,439 in March and 140,346 in April — an overall drop of 54 per cent.

Norway, France and Canada shared 17 per cent, 13 per cent and 10 per cent less data, respectively, in this time frame, the figures show.

Denmark, renowned for its genomic surveillance network, has consistently sequenced and shared between 40,000 and 50,000 genomes since November 2021.

Aris Katzourakis, a professor of evolution and genomics at the University of Oxford, said it “will take longer to spot new variants” as testing and sequencing infrastructure is dismantled.

“We run the risk of failing to identify variants before they have the opportunity to spread, giving up the opportunity to intervene to limit the spread of concerning variants,” he said.

“Sequence surveillance has been a real success of the during the pandemic, as demonstrated both by our ability to detect and respond to the Alpha variant early on in the UK.”

Throughout the pandemic, the UK has sequenced and shared 12 per cent of all its cases — one of the highest rates in the world. This figure stands at 16.3 per cent for Denmark, 8.3 per cent for Canada, 4 per cent for the US, 4.4 per cent for Norway, 2.4 per cent for Germany, and 1 per cent for France.

South Africa has sequenced and shared an average of 1 per cent of cases since January 2020, but its well-developed surveillance network has played a crucial role in monitoring and detecting the emergence of new variants, including both Beta and Omicron.

Professor Christina Pagel, the director of the Clinical Operational Research Unit at University College London, said “blind spots” could emerge as testing and sequencing is scaled back.

She said there was no need for “all-encompassing” surveillance, but insisted “it must be a decent representative sample across as many places as possible”.

“The UK should keep encouraging hospital PCR tests and sequencing a substantial proportion of them, and we should be sequencing all ONS infection survey positive tests,” Prof Pagel added.

Prof Gupta acknowledged that there were “cost constraints” in maintaining a fully-functioning surveillance network, adding that testing and sequencing teams were likely being reduced in size as governments cut their Covid funding and look beyond the pandemic.

“I think smart surveillance is the way to go,” he said. “It’d be good if it was done in a joined up way across Europe. I think the key thing is that we need a quick way of getting back to doing more if needed to.”