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Genomic Study Highlights Summer Travel Role in SARS-CoV-2 Variant Spread in Europe

NEW YORK – A new genomic study has highlighted the role that international travel can play in transmitting a variant version of SARS-CoV-2, even when travel is relatively restricted.

In a paper published in Nature on Monday, researchers in Switzerland, the US, and elsewhere described a variant known as 20E (EU1) — marked by a characteristic spike protein-coding sequence substitution — that appeared in Spain during the pandemic's first summer in 2020 and subsequently spread to Switzerland, the UK, France, the Netherlands, and other parts of western Europe alongside travelers visiting the countries or returning from trips abroad.

"[W]e report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread across Europe," first and co-corresponding author Emma Hodcroft, a researcher with the University of Basel, the Swiss Institute of Bioinformatics, and the University of Bern, and her colleagues wrote, noting that "[d]espite travel restrictions, we estimate 20E (EU1) was introduced hundreds of times to European countries by summertime travelers, likely undermining local efforts to keep SARS-CoV-2 cases low."

Because SARS-CoV-2 isolates have been subjected to ongoing genome sequencing and phylogenetic analyses since not long after the virus began circulating in late 2019, the investigators explained, it has been possible to tap into this vast collection of genetic data to retrace SARS-CoV-2 movement and evolution.

"In addition to tracking the viral spread," they wrote, "these sequences have been used to monitor mutations which might change the transmission, pathogenesis, or antigenic properties of the virus."

The team detected 20E (EU1) with the help of a phylogenetic analysis that included SARS-CoV-2 sequences submitted to GISAID from isolates collected before the end of September 2020, digging into the genetic data to retrace its emergence and spread within Spain and beyond. In particular, the phylogenetic clusters provided a relatively refined look at the ways travel between different regions increased the movement of the strain as some borders began opening to travel late last spring.

"Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings," the authors reported, adding that "[g]enomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes."

Although the team's subsequent antibody binding and functional experiments indicated that the EU1 version of SARS-CoV-2 is no more transmissible than the original strain behind the COVID-19 pandemic, the available genomic, anonymized mobile phone roaming data and other clues suggested that the variant was able to become common by reaching high rates in Spain before hitchhiking with vacationing Europeans to other locations that appeared to lack the level of screening and containment needed to curb its further spread.

Indeed, the researchers noted that the 20E (EU1) variant — and a related variant known as 20A.EU2, which contained an additional spike protein-coding mutation — went on to become the most common circulating strains in western Europe by the time fall rolled around.

"While long-term travel restrictions and border closures are not tenable or desirable," the authors concluded, "identifying better ways to reduce the risk of introducing variants, and ensuring that those which are introduced do not go on to spread widely, will help countries maintain often hard-won low levels of SARS-CoV-2 transmission."

In a statement, Hodcroft noted that "20E (EU1) did not need to be more transmissible to spread rapidly across Europe but took advantage of loosening restrictions and increasing travel." She called the findings "a timely reminder that not all rises in variant frequencies are due entirely to changes in the virus."

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