The lockdown removed variants of coronavirus circulating during the first wave in Spain, according to a work carried out by the SeqCOVID consortium, which includes more than 50 Spanish institutions led by the University of Valencia, the Institute of Biomedicine of València (IBV, CSIC) and the Fisabio Foundation.
A year and a half after the outbreak of the Covid-19 pandemic, the most complete scientific study on the variants of the coronavirus that circulated in Spain during the ‘first wave’ has been published, which identifies nine variants of the virus that dominated the pandemic among the months of March and June 2020.
Between them, the two most common came from a SARS-CoV-2 lineage abundant in Asian countries at the timeAlthough the virus came mainly through contacts from European countries with more than 500 introductions, according to the study published by ‘Nature Genetics’. The work concludes that the confinement imposed served to “drastically” reduce the transmission of these variants, even the most contagious, which were replaced by others as of the summer of 2020 when control measures were relaxed.
The study used 2,500 samples from patients diagnosed in Spain during the first wave of the pandemic, collected by 40 hospitals and sequenced by the SeqCOVID consortium, a research team made up of more than 50 Spanish institutions and hundreds of researchers who lead the University of Valencia, the Institute of Biomedicine of Valencia (IBV, CSIC) and the Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (Fisabio). The samples analyzed account for 1 percent of all cases diagnosed in the first wave (14% before confinement).
The research team identified 9 virus variants (known as SEC, from the English Spanish Epidemic Clades), which were the ones that dominated this first wave in Spain. Two of them (SEC7 and SEC8) were the first detected in the country and the predominant during that period, and are associated with at least two known super-dispersion events: the Atalanta-Valencia match of the Champions League and a funeral in Vitoria, although Early foci are identified in other parts of the country.
There was not a single introduction of the virus in Spain but “multiple independent entries” (at least 500), from different international origins, which occurred mainly during February and March 2020, before the implementation of the control measures.
“Most of the first wave infections before confinement in Spain were caused by coronavirus lineage A strains. These were abundant in Asian countries at that time, but they had less presence in the rest of European countries, where B lineage strains dominated. This does not mean that the introductions of SARS-CoV-2 in our country were mainly Asian “, explains Álvaro Chiner, one of the CSIC researchers at the IBV in Valencia who participated in the study.
According to Chiner, actually, “Most introductions come from European countries, but A lineage strains were established earlier and, thanks to super-dispersal events, they quickly expanded in our country. ”
The researchers observed a similar pattern for the variant that dominated in the second wave (called 20E (EU1)), which they just published in ‘Nature’. This variant expanded rapidly in Spain helped by super-dispersion events and ended up dominating the second wave in Spain and much of Europe, associated with summer mobility.
“This is a lesson that we have not learned from last summer” affirms Fernando González Candelas, professor at the University of Valencia, researcher at the Institute of Integrative Systems Biology (UV-CSIC) and at Fisabio, and one of the coordinators of SeqCOVID .
In addition, the first wave work published in ‘Nature Genetics’ quantifies the effectiveness of the measures implemented to control the virus during the first wave: all the identified variants reduced their prevalence and transmission significantly from the state of alarm. They practically disappeared at the end of the first wave and were replaced by new variants that emerged in the summer, when containment measures were relaxed.
“Confinement was highly effective in stopping the transmission of the virus. Not only for the dominant variants SEC7 and SEC8, but for all those that were circulating at that time, including those that contained the S gene mutation called D614G, which was the first that it was shown to increase the transmissibility of the virus “, remarks Mariana López, CSIC researcher at IBV and co-author of the study.
“We are seeing something similar through the waves. We are detecting more transmissible variants, but their impact can be controlled with the appropriate control measures. Where those measures have not existed or are more relaxed, the variants have aggravated the outbreaks. It happened in the UK with the Alpha variant and is happening in Spain with the Delta“, indicates Iñaki Comas, CSIC researcher at the IBV coordinator of SeqCOVID.
According to the research team of the SeqCOVID consortium, the results of this work, as well as that of the second wave published recently in ‘Nature’, demonstrate the need to incorporate genomic epidemiology as one more public health tool to track the virus and identify the variants with the greatest impact.
“Active surveillance of viral mutations must continue to be able to evaluate the threat of new variants with potential risks to control the epidemic. That is one of the objectives that we have set ourselves within the Interdisciplinary Thematic Platform of Global Health of the CSIC”, says Mireia Coscollá, a researcher at the University of Valencia at the Institute for Integrative Systems Biology (I2SysBio, UV-CSIC) and one of the coordinators of the study.
The work of SeqCOVID has contributed to the creation of a National Genomic Surveillance Network directed by the Center for the Coordination of Health Alerts and Emergencies (CCAES) and coordinated by the Carlos III Health Institute (ISCIII). This network is fully integrated into the care work of the hospitals.
Eddie is an Australian news reporter with over 9 years in the industry and has published on Forbes and tech crunch.