Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders.
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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DOI：
10.24272/j.issn.2095-8137.2020.217
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发表时间：
2020-11-18
影响因子：
4.9
通讯作者：
Salas A
中科院分区：
文献类型：
--
作者：
Gómez-Carballa A;Bello X;Pardo-Seco J;Pérez Del Molino ML;Martinón-Torres F;Salas A
西班牙一直是2019冠状病毒病（COVID-19）全球主要流行中心之一。在这里，我们分析了从GISAID库下载的>41 000个基因组（包括>26 000个高质量（HQ）基因组），其中包括在西班牙采样的1 245个（922个HQ）。本研究的目的是调查新型严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的基因组变异，并重建西班牙的地理分布和传播模式。系统地理学分析表明，在疫情爆发之初，至少有34个SARS-CoV-2独立传入西班牙。六个谱系在西班牙传播得非常成功，可能受到超级传播者的青睐，即A2 a4（7.8%），A2 a5（38.4%），A2 a10（2.8%），B3 a（30.1%）和B 9（8.7%），占西班牙数据库中所有基因组的87.9%。西班牙SARS-CoV-2基因组的一个显著特征是B谱系的频率（39.3%，主要是B3 a + B 9）高于任何其他欧洲国家。虽然B3 a、B 9（以及A2 a5的一个重要亚系，即A2 a5 c）最有可能起源于西班牙，但其他三个单倍型群是从欧洲其他地区进口的。B3 a菌株可能起源于巴斯克地区，来自不确定地理来源的B3祖先，而B 9可能出现在马德里。SARS-CoV-2的最近共同祖先（TMRCA）的时间表明，第一种冠状病毒在2020年2月11日左右进入该国，这是根据该国检测到的第一个谱系B3 a的TMRCA估计的。此外，与其他疾病发病率较低但这种突变频率高得多的国家相比，早期声称D 614 G突变与更高的传播性相关，这与西班牙的COVID-19非常高的患病率不一致（西班牙为56.4%，欧洲其他地区为82.4%）。相反，这些数据支持遗传漂变在模拟全国病毒株的微地理分层以及SARS-CoV-2超级传播者的作用中发挥重要作用。
Spain has been one of the main global pandemic epicenters for coronavirus disease 2019 (COVID-19). Here, we analyzed >41 000 genomes (including >26 000 high-quality (HQ) genomes) downloaded from the GISAID repository, including 1 245 (922 HQ) sampled in Spain. The 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 Spain. Phylogeographic analysis suggested at least 34 independent introductions of SARS-CoV-2 to Spain at the beginning of the outbreak. Six lineages spread very successfully in the country, probably favored by super-spreaders, namely, A2a4 (7.8%), A2a5 (38.4%), A2a10 (2.8%), B3a (30.1%), and B9 (8.7%), which accounted for 87.9% of all genomes in the Spanish database. One distinct feature of the Spanish SARS-CoV-2 genomes was the higher frequency of B lineages (39.3%, mainly B3a+B9) than found in any other European country. While B3a, B9, (and an important sub-lineage of A2a5, namely, A2a5c) most likely originated in Spain, the other three haplogroups were imported from other European locations. The B3a strain may have originated in the Basque Country from a B3 ancestor of uncertain geographic origin, whereas B9 likely emerged in Madrid. The 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 B3a, the first lineage detected in the country. Moreover, earlier claims that the D614G 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.
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DOI：
10.4137/ebo.s9738
发表时间：
2012
期刊：
Evolutionary bioinformatics online
影响因子：
--
作者：
Norström MM;Prosperi MC;Gray RR;Karlsson AC;Salemi M
通讯作者：
Salemi M
影响因子：
5.1
作者：
Conrad, O.;Bechtel, B.;Boehner, J.
通讯作者：
Boehner, J.
影响因子：
20.6
作者：
Tang, Xiaolu;Wu, Changcheng;Lu, Jian
通讯作者：
Lu, Jian
影响因子：
3.4
作者：
Heled, Joseph;Drummond, Alexei J.
通讯作者：
Drummond, Alexei J.
影响因子：
6.6
作者：
Leigh, Jessica W.;Bryant, David
通讯作者：
Bryant, David