British holidaymakers risk bringing new variants back to the UK this summer as data “blind spots” in Europe make it difficult to know which nations are harbouring newly mutated forms of the virus, scientists have warned.
While the UK has established an extensive genomic surveillance network that has allowed officials to detect new variants when they emerge, other European countries have struggled to increase their sequencing capabilities.
The ability to effectively sequence Covid cases and share genomic data is one factor taken into consideration by the government when assessing which nations to add to Britain’s green list, along with wider transmission risks, weekly incidence rates and evidence of “variants of concern” (VoC).
However, these travel arrangements could be in danger due to the spread of the Indian variant in the UK, with experts now calling for overseas summer holidays to be scrapped in order to prevent its exportation.
Information on sequenced cases – which allows scientists to determine which type of Covid variant has caused a patient’s infection – is uploaded in each country to a number of publicly available sources, including the Global Initiative on Sharing All Influenza Data (Gisaid).
However, Gisaid data shows that the likes of Spain, France, Italy and Greece – four of the most popular destinations for UK holidaymakers – have sequenced and shared just 0.805 per cent, 0.649 per cent, 0.67 per cent and 0.437 per cent of their reported cases respectively.
Cog-UK, which leads Britain’s surveillance network, believes countries need to be sequencing at least 5 per cent of all cases to identify virus mutations and deliver a clear picture of the spread of new variants. In the UK, 9.34 per cent of infections are sequenced and uploaded to Gisaid.
The Wellcome Sanger Institute, which helps to run Cog-UK’s work, said there was an “urgent need to increase sequencing capacity in all areas of the world” and share data “quickly and effectively” between countries, therefore allowing health officials to take proactive measures in response to new threats.
Aris Katzourakis, a professor of evolution and genomics at Oxford University, said his team of experts had hoped to carry out an analysis of the spread of variants across Europe but had been unable to do so due to the limited availability of surveillance data.
“We basically realised how little genomic data is available on the public repositories in other European countries,” he said.
He also raised concern that some countries may be sequencing their cases but then not immediately sharing them with public sources like Gisaid.
In Greece, some 13,000 genomes have been sequenced by health officials out of 393,538 cases, Prof Katzourakis said, but only 1,718 of these have been uploaded to Gisaid.
Cog-UK said there is “a lag between genomes being sequenced to genomes being deposited in Gisaid” – a delay that could carry consequences for identifying and controlling a variant-fuelled outbreak.
“But it’s not just Greece. There’s a lot of other poorly resourced countries in Europe,” Prof Katzourakis said.
“As nations come out of their lockdown and the travel restrictions are lifted, and everyone is going to start moving around over the next few weeks and months, it’s going to be a real problem as we’re not going to be able to track the emergence of new variants, where they come from, and how they spread.”
This, he said, could lead to the creation of “blind spots”, where British travellers may be infected with a highly infectious or immune-evading variant before bringing it back to the UK. Tourist destinations with high case loads and growing local epidemics “could lead to importations” as well, Prof Katzourakis warned.
Christina Pagel, a professor of operational research at University College London, echoed these concerns. “There are some countries where they don’t sequence at all, so we have no idea what’s going on,” she said. “And there are some countries where they sequence very little, which is actually a lot of mainland Europe.”
With countries like Spain, Italy, France, Greece and many others sequencing at such low rates, this raises questions of whether the government will continue to dictate that British tourists can only visit countries with reliable scientific data and genomic surveillance.
Currently, the joint biosecurity centre assesses whether any new countries can be added to UK’s green list every three weeks, with the next review to take place on 3 June. If more destinations in Europe are made available to visit from next month, this will likely increase the risk of variant importation and exportation.
“All decisions on red, amber or green listings and our border controls are taken by ministers based on the latest scientific data, the joint biosecurity centre’s risk assessment and wider public health factors,” a government spokesperson said.
British tourists can now travel to Spain without taking a Covid test on arrival, though France has said travellers must quarantine upon arrival due to the spread of the Indian variant in the UK. Both Greece and Italy remain on the amber list for now, which means travel is discouraged but not prohibited.
Ravi Gupta, a professor of clinical microbiology at Cambridge University and scientific adviser to the government, said increased sharing of genomic data would allow authorities to “pick up much earlier” circulating variants with worrying characteristics, such as immune evasion or increased transmissibility.
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As for why other nations hadn’t followed the UK’s example in ramping up surveillance capabilities, Prof Gupta said “each country has to decide what it’s going to do in terms of sequencing. Some could do it if they wanted but it costs money and needs infrastructure.”
Experts have meanwhile said the government should not be encouraging travel in the summer due to the threat posed by the Indian variant. “From a more altruistic perspective, we should not be going on holiday and spreading B.1.617.2 to other places,” said Prof Pagel.
Prof Gupta said that “on balance” the prevalence of the Indian variant in the UK meant British holidaymakers pose more of a “major risk” to the rest of Europe, “rather the other way around.”
