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

作     者：Alberto Gomez-Carballa Xabier Bello Jacobo Pardo-Seco Maria Luisa Perez del Molino Federico Martinon-Torres Antonio Salas Alberto Gómez-Carballa;Xabier Bello;Jacobo Pardo-Seco;María Luisa Pérez del Molino;Federico Martinón-Torres;Antonio Salas

作者机构：Unidade de XendticaInstituto 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 GeneticsVaccines 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 DiseasesDepartment of PediatricsHospital Clinico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain Servicio de Microbiologia y ParasitologiaComplejo Hospitalario Universitario de Santiago de CompostelaSantiago de CompostelaGalicia15706 Spain 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2020年第41卷第6期

页      面：605-620页

核心收录：

学科分类：0710[理学-生物学] 0830[工学-环境科学与工程（可授工学、理学、农学学位）] 1004[医学-公共卫生与预防医学(可授医学、理学学位)] 0905[农学-畜牧学] 0906[农学-兽医学] 100401[医学-流行病与卫生统计学] 0833[工学-城乡规划学] 0713[理学-生态学] 0834[工学-风景园林学（可授工学、农学学位）] 10[医学] 

基　　金：supported by the Instituto de Salud Carlos Ⅲ project Ge PEM(Instituto de Salud Carlos Ⅲ(ISCⅢ)/PI16/01478/Cofinanciado FEDER) DIAVIR(Instituto de Salud Carlos Ⅲ(ISCⅢ)/DTS19/00049/Cofinanciado FEDER Proyecto de Desarrollo Tecnológico en Salud) Resvi-Omics(Instituto de Salud Carlos Ⅲ(ISCⅢ)/PI19/01039/Cofinanciado FEDER) project BI-BACVIR(PRIS-3 Agencia de Conocimiento en Salud(ACIS)—Servicio Gallego de Salud(SERGAS)—Xunta de Galicia Spain)given to A.S project Re SVinext(Instituto de Salud Carlos Ⅲ(ISCⅢ)/PI16/01569/Cofinanciado FEDER) Enterogen(Instituto de Salud Carlos Ⅲ(ISCⅢ)/PI19/01090/Cofinanciado FEDER)given to F.M.-T 

主　　题：Covid-19 SARS-CoV-2 Genomics Phylogeny Phylogeography 

摘      要：Spain has been one of the main global pandemic epicenters for coronavirus disease 2019(COVID-19).Here,we analyzed41000 genomes(including26000 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.