An analysis of the genomic diversity of SARS-CoV-2 has identified more than 500 entries into the country at the beginning of the pandemic, but only a few lineages became massively spread thanks to super-dispersal events, such as soccer games and funerals. One of the genotypes generated 30% of all cases, reaching 60% in the first week of March.
A single coronavirus genotype generated 60% of cases in the first week of March, according to a report showing the map of the genomic diversity of SARS-CoV-2, which causes Covid-19, during the first three months of the epidemic, from February to April. The research carried out by the SeqCovid-Spain consortium, led by the Higher Council for Scientific Research (CSIC), has collected samples of the virus genome from 30 hospitals throughout Spain and has identified the genotype that generated 30% of all sequenced cases and accounted for 60% in early March.
“Among the sequences analyzed, a genotype has been identified that generated 30% of all sequenced cases, reaching 60% in the first week of March,”indicates the CSIC researcher who is co-leading the work, Iñaki Comas, from the Institute of Biomedicine of Valencia (IBV-CSIC).
The study has observed that the genomic diversity of the coronavirus in Spain is unique in Europe, and closer to the genotypes of the virus circulating in Asia between the end of 2019 and the beginning of 2020. This is consistent with the early introduction of the virus, especially from the second half of February, and with a very rapid expansion at the end of the month.
“A detailed reconstruction of this genotype shows that it was introduced multiple times and simultaneously from Italy, at least in Madrid and Valencia, before the transalpine country sounded the alarm,”explains the researcher.
The analyses identify a minimum of 519 entries in the country within the 2,170 sequences of the beginning of the epidemic analyzed but only a few came to generate a substantive number of cases and had great weight. Spain is the second country in Europe with the most samples of the virus genome collected, and the fourth in the world, with 4,244, of which the consortium has sequenced 3,800.
“Superdispersion events contributed to the success of these introductions,” he adds, “such as a funeral in Vitoria, which helped this specific genotype to maintain and expand rapidly. The high mobility between Spanish provinces did the rest for the genotype to become the most successful of the first wave in Spain.”
The work is led by the CSIC researcher Iñaki Comas, from the València Institute of Biomedicine, the virologist Mireia Coscolla, from the Institute for Integrative Systems Biology of the CSIC and the University of Valencia, and Fernando González Candelas, head of the Mixed Unit of Research on Infection and Public Health of the Fisabio Foundation of the Generalitat Valenciana.