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Researchers from Basel and Spain have identified a new variant of SARS-CoV-2 that has spread widely across Europe in recent months, according to a non-peer-reviewed preprint released this week. While there is no evidence that this variant is more dangerous, its dissemination can give an idea of the effectiveness of travel policies adopted by European countries during the summer.
In Europe alone, hundreds of different variants of the new SARS-CoV-2 coronavirus are currently circulating, distinguished by mutations in their genomes. However, only a few of these variants have spread as successfully and become as prevalent as the recently identified variant, named 20A.EU1.
Researchers from the University of Basel, ETH Zürich in Basel, and the SeqCOVID-Spain consortium analyzed and compared virus genome sequences collected from Covid-19 patients across Europe to track the evolution and spread of the pathogen (see box). Their analysis suggests that the variant originated in Spain during the summer. The earliest evidence of the new variant is related to an event of overspread among agricultural workers in northeastern Spain. The variant moved into the local population, spreading rapidly throughout the country, and now accounts for almost 80% of sequences in Spain.
It is important to note that there is currently no evidence that the spread of the new variant is due to a mutation that increases transmission or affects the clinical outcome. ”
Dr Emma Hodcroft, lead author of the study from the University of Basel
The researchers believe that the expansion of the variant was facilitated by the relaxation of travel restrictions and social distancing measures in summer.
Pattern similar to that of spring in Spain
“We see a similar pattern with this variant in Spain to the one we saw in the spring,” advises Professor Iñaki Comas, co-author of the article and head of the SeqCOVID-Spain consortium. “A variant, with the help of an initial super spread event, can quickly become prevalent across the country.”
As of July, 20A.EU1 moved with travelers as borders were opened in Europe, and has now been identified in twelve European countries. It has also been transmitted from Europe to Hong Kong and New Zealand. While the initial introductions of the variant are likely to have come directly from Spain, the variant may have continued to spread from secondary countries.
Currently, 20A.EU1 represents 90% of the UK sequences, 60% of the Irish sequences and 30-40% of the sequences in Switzerland and the Netherlands. This makes this variant currently one of the most frequent in Europe. It has also been identified in France, Belgium, Germany, Italy, Latvia, Norway, and Sweden.
Traveling facilitated the spread
Genetic analysis indicates that the variant traveled at least tens and possibly hundreds of times between European countries. “We can see that the virus has been introduced several times in various countries and many of these introductions have spread through the population,” says Professor Tanja Stadler from ETH Zürich, one of the lead researchers on the study, “This is not a case. that an introduction just goes well. “
Although the increase in the prevalence of 20A.EU1 corresponds to the increasing number of cases seen in many European countries this fall, the study authors caution against interpreting the new variant as a cause of the increase in cases. “It is not the only variant circulating in recent weeks and months,” says Professor Richard Neher of the University of Basel, one of the lead researchers on the study. “In fact, in some countries with significant increases in Covid-19 cases, such as Belgium and France, other variants prevail.”
Analysis of the prevalence of SARS-CoV-2 in summer in Spain and travel data show that these factors may explain how 20A.EU1 spread so successfully. The relatively high number of cases and the popularity of Spain as a holiday destination may have allowed for multiple opportunities for introduction, some of which may have developed into larger outbreaks through risky behaviors after returning home.
The study authors highlight the importance of evaluating how border controls and travel restrictions functioned to contain SARS-CoV-2 transmissions during the summer, and the role travel has played. “Long-term border closures and severe travel restrictions are neither feasible nor desirable,” explains Hodcroft, “but from the spread of 20A.EU1 it seems clear that the measures put in place were often not enough to stop transmission. “of variants introduced. When countries have worked hard to reduce SARS-CoV-2 cases to low numbers, it is critical to identify better ways to ‘open up’ without risking an increase in cases.”
Evaluation of the phenotype of the new variant
The new variant was first identified by Hodcroft during a Swiss sequence analysis using the ‘Nextstrain’ platform, jointly developed by the University of Basel and the Fred Hutchinson Cancer Research Center in Seattle, Washington. 20A.EU1 is characterized by mutations that modify amino acids in the spike, nucleocapsid, and ORF14 proteins of the virus.
Although the current state of knowledge does not indicate that the spread of 20A.EU1 is due to a change in transmissibility, the authors are currently working with virology laboratories to examine any potential impact that the spike mutation, known as S: A222V, may have in SARS- CoV-2 virus phenotype. They also hope to receive early access to data that will allow them to assess the clinical implications of the variant.
Furthermore, the study authors emphasize the importance of closely monitoring the emergence of new variants such as 20A.EU1: “Only by sequencing the viral genome can we identify new variants of SARS-CoV-2 when they emerge and monitor their spread in and out. across countries, “Neher adds,” but the number of sequences we have varies a lot between countries, and we could identify the growing variants earlier with faster and more regular sequencing efforts across Europe. “
Source:
Magazine reference:
Hodcroft, EB, et al. (2020) Appearance and spread of a variant of SARS-CoV-2 in Europe in the summer of 2020. medRxiv. doi.org/10.1101/2020.10.25.20219063.
