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Phylogeography of SARS-CoV-2 pandemic in Spain:a story of multiple introductions,micro-geographic stratification,founder effects,and super-spreaders

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Zoological Research 2020年第6期41卷 605-620页

作者： Alberto Gomez-Carballa Xabier Bello Jacobo Pardo-Seco Maria Luisa Perez del Molino Federico Martinon-Torres Antonio Salas unidade de xendtica Instituto de Ciencias Forenses(I NCI FOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstituto de Investigaci6n Sanitaria(IDIS)Hospital Clinico Universitario de Santiago(SERGAS)Galicia 15706Spain Genetics Vaccines and Pediatric Infectious Diseases Research Group(GENVIP)Instituto de Investigacion Sanitaria de Santiago(IDIS)and Universidade de Santiago de Compostela(USC)Galicia 15706Spain Translational Pediatrics and Infectious Diseases Department of PediatricsHospital Clinico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain Servicio de Microbiologia y Parasitologia Complejo Hospitalario Universitario de Santiago de CompostelaSantiago de CompostelaGalicia15706 Spain

Spain has been one of the main global pandemic epicenters for coronavirus disease 2019(COVID-19).Here,we analyzed>41000 genomes(including>26000 high-quality(HQ)genomes)downloaded from the GISAID repository,including 1245(922 HQ)sampled in *** aim of this study was to investigate genome variation of novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and reconstruct phylogeographic and transmission patterns in *** analysis suggested at least 34 independent introductions of SARS-CoV-2 to Spain at the beginning of the *** lineages spread very successfully in the country,probably favored by super-spreaders,namely,A2 a4(7.8%),A2 a5(38.4%),A2 a10(2.8%),B3 a(30.1%),and B9(8.7%),which accounted for 87.9% of all genomes in the Spanish *** distinct feature of the Spanish SARS-Cov-2 genomes was the higher frequency of B lineages(39.3%,mainly B3 a+B9)than found in any other European *** B3 a,B9,(and an important sub-lineage of A2 a5,namely,A2 a5 c)most likely originated in Spain,the other three haplogroups were imported from other European *** B3 a strain may have originated in the Basque Country from a B3 ancestor of uncertain geographic origin,whereas B9 likely emerged in *** time of the most recent common ancestor(TMRCA)of SARS-CoV-2 suggested that the first coronavirus entered the country around 11 February 2020,as estimated from the TMRCA of B3 a,the first lineage detected in the ***,earlier claims that the D614 G mutation is associated to higher transmissibility is not consistent with the very high prevalence of COVID-19 in Spain when compared to other countries with lower disease incidence but much higher frequency of this mutation(56.4% in Spain vs.82.4% in rest of Europe).Instead,the data support a major role of genetic drift in modeling the micro-geographic stratification of virus strains across the country as well as the role of SARS-CoV-2 super-spreaders.

关键词： Covid-19 SARS-CoV-2 Genomics Phylogeny Phylogeography

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