Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Abstract

Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of the virus to be tracked via phylogenetic analysis (Worobey et al., 2020; Hadfield et al., 2018; Pybus et al., 2020). While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced, allowing continent-specific variants to emerge. However, within Europe travel resumed in the summer of 2020, and the impact of this travel on the epidemic is not well understood. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread to multiple locations in Europe. We find no evidence of increased transmissibility of this variant, but instead demonstrate how rising incidence in Spain, resumption of travel across Europe, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions and quarantine requirements, we estimate 20E (EU1) was introduced hundreds of times to countries across Europe by summertime travellers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.

FIG. 1

Phylogenetic overview of SARS-CoV-2 in Europe through the end of November. The tree shows a representative sample of isolates from Europe colored by clade and by the variants highlighted in this paper. A novel variant (orange; 20E (EU1)) with mutation S:A222V on a S:D614G background emerged in early summer and is common in most countries with recent sequences. A separate variant (20A.EU2, blue) with mutation S:S477N is prevalent in France. On the right, the proportion of sequences belonging to each variant (through the duration of the pandemic) is shown per country. Tree and visualization were generated using the Nextstrain platform (Hadfield et al., 2018) as described in methods.

FIG. 2. Frequency of submitted samples are 20E (EU1) in selected countries, with quarantine-free travel dates shown above.

We include the eight countries which have at least 200 sequences from 20E (EU1), as well as Norway and France, to illustrate points in the text. The symbol size indicates the number of available sequence by country and time point in a non-linear manner. Travel restrictions from selected countries are shown to/from Spain, as this is the probable origin of the cluster. Most European countries allowed quarantine-free travel to other (non-Spanish) countries in Europe for a longer period. When the last data point included only very few sequences, it has been dropped for clarity. Frequencies are smoothing using a Gaussian with σ = 1w.

FIG. 3. Collapsed genotype phylogeny.

The phylogeny shown is the subtree of the 20E (EU1) cluster using data from samples collected before 30 Sept 2020 and available on GISAID as of Jan 2021, with sequences carrying all six defining mutations. Pie charts show the representation of sequences from selected countries at each node. Size of the pie chart indicates the total number of sequences at each node. Pie chart fractions scale non-linearly with the true counts (fourth root) to ensure all countries are visible and branch lengths are jittered to reduce overlap.

FIG. 4. Travel volume and contribution of imported infections.

Travel from Spain to other European countries resumed in July (though low compared to previous years). Assuming that travel returnees are infected at the average incidence of Spanish province they visited and transmit the virus at the rate of their resident population, imports from Spain are expected to account between 2 and 12% of SARS-CoV-2 cases after the summer. Traveler incidence is calculated using case and travel data at the level of provinces. Note that this model only accounts for contribution of summer travel and that stochastic fluctuations and other variants after the summer will results in further variation in the frequency of 20E (EU1). See Methods and Fig. S8.