Abstract
Following its emergence in late 2019, the spread of SARS-CoV-21,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail3-5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes.
Highlights
In addition to tracking viral spread, these sequences have been used to monitor mutations that might change the transmission, pathogenesis, or antigenic properties of the virus
We report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe
We report on SARS-CoV-2 variant 20E (EU1), with an A222V mutation in the spike protein, which first rose in frequency in Spain in early summer 2020 and subsequently spread to multiple locations in Europe, rising in frequency in parallel
Summary
In addition to tracking viral spread, these sequences have been used to monitor mutations that might change the transmission, pathogenesis, or antigenic properties of the virus. D614G in the spike protein (Nextstrain clade 20A and its descendants), seeded large outbreaks in Europe in early 2020 and subsequently dominated outbreaks in the Americas, thereby largely replacing previously circulating lineages. This rapid rise led to the suggestion that this variant is more transmissible, which has since been corroborated by phylogenetic[7,8] and experimental evidence[9,10]. We report on SARS-CoV-2 variant 20E (EU1), with an A222V mutation in the spike protein, which first rose in frequency in Spain in early summer 2020 and subsequently spread to multiple locations in Europe, rising in frequency in parallel. Updated phylogenies and further analyses of these and other variants are available at https:// covariants.org/
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