Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase
Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase
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DOI：
10.1002/jmv.26447
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发表时间：
2020-09-29
影响因子：
12.7
通讯作者：
Gismondo, Maria R.
中科院分区：
文献类型：
--
作者：
Micheli, Valeria;Rimoldi, Sara G.;Gismondo, Maria R.
意大利米兰萨科医院临床微生物学、病毒学和生物紧急情况实验室于2020年2月20日记录了意大利首例本土传播SARS-CoV-2的病例，患者为一名38岁的男性患者，他在科尔多诺医院被发现肺炎阳性。此后，伦巴第报告了该国新冠肺炎病例的最高流行率，特别是在米兰、布雷西亚和贝加莫三省。这项研究的目的是评估伦巴第新冠肺炎病例涉及的六个主要省份是否存在不同的病毒群，以突出特定的省份依赖的病毒特征。对2020年2月20日至4月4日从伦巴第几家医院的患者那里获得的20个全长基因组进行了系统发育分析，并与截至2020年3月30日GISAID数据库中的41个意大利病毒基因组组合进行了比对：鉴定出两个主要的单系支系，分别包含8个和53个分离株。值得注意的是，贝加莫分离株被定位在含有M基因D3G突变的小分支内。分子时钟分析在第一个患者识别前大约一个月估计了集群差异，支持不同SARS-CoV-2毒株在不同时间在全球传播的假设，但它们的存在只有在2月下旬随着意大利疫情的出现才变得明显。因此，这一流行病学重建表明，病毒在伦巴第最初的传播归因于多次传入。然而，当有更多的基因组序列可用时，系统发育重建的稳健性将得到改善，以确保全面的流行病学监测。
The first identification of autochthonous transmission of SARS-CoV-2 in Italy was documented by the Laboratory of Clinical Microbiology, Virology and Bioemergencies of L. Sacco Hospital (Milano, Italy) on 20th February 2020 in a 38 years old male patient, who was found positive for pneumonia at the Codogno Hospital. Thereafter Lombardy has reported the highest prevalence of COVID-19 cases in the country, especially in Milano, Brescia and Bergamo provinces. The aim of this study was to assess the potential presence of different viral clusters belonging to the six main provinces involved in Lombardy COVID-19 cases in order to highlight peculiar province-dependent viral characteristics. A phylogenetic analysis was conducted on 20 full length genomes obtained from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020, aligned with 41 Italian viral genome assemblies available on GISAID database as of 30th March, 2020: two main monophyletic clades, containing 8 and 53 isolates, respectively, were identified. Noteworthy, Bergamo isolates mapped inside the small clade harbouring M gene D3G mutation. The molecular clock analysis estimated a cluster divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains had spread worldwide at different times, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, this epidemiological reconstruction suggests that virus initial circulation in Lombardy was ascribable to multiple introduction. The phylogenetic reconstruction robustness, however, will be improved when more genomic sequences are available, in order to guarantee a complete epidemiological surveillance.