Emma B. Hodcroft
Moira Zuber
Sarah Nadeau
Iñaki Comas
Fernando González Candelas
8SeqCOVID-SPAIN consortium
Tanja Stadler
Richard A. Neher
Abstract
A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and has since spread to multiple European countries. The variant was first observed in Spain in June and has been at frequencies above 40% since July. Outside of Spain, the frequency of this variant has increased from very low values prior to 15th July to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about other European countries because few recent sequences are available. Sequences in this cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this variant was exported from Spain to other European countries multiple times and that much of the diversity of this cluster in Spain is observed across Europe. It is currently unclear whether this variant is spreading because of a transmission advantage of the virus or whether high incidence in Spain followed by dissemination through tourists is sufficient to explain the rapid rise in multiple countries.
CAVEATS
- This variant rose in frequency in multiple countries, but we have no direct evidence that it spreads faster. The rise in frequency could also be due to epidemiological factors.
- There are currently no data to evaluate whether this variant affects the severity of the disease.
- While dominant in some countries, 20A.EU1 has not taken over everywhere and diverse variants of SARS-CoV-2 continue to circulate across Europe.
Competing Interest Statement
The authors have declared no competing interest.
Funding Statement
This work was supported by the SNF through grant numbers 31CA30_196046 (to RAN, EBH) and 31CA30_196267 and core funding by the University of Basel. SeqCOVID-SPAIN is funded by the Instituto de Salud Carlos III project COV20/00140, Spanish National Research Council and ERC StG 638553 to IC.
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This is an analysis of publicly available data and no IRB approval is needed.
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Data Availability
All sequence data is available on GISAID (gisaid.org), and the code for the analyses performed is available on Github and linked in the manuscript text.
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