Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants.
Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants.
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DOI：
10.1038/s43856-022-00168-7
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Munoz-Jordan, Jorge L
中科院分区：
文献类型：
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作者：
Santiago, Gilberto A;Flores, Betzabel;Gonzalez, Glenda L;Charriez, Keyla N;Huertas, Limari Cora;Volkman, Hannah R;Van Belleghem, Steven M;Rivera-Amill, Vanessa;Adams, Laura E;Marzan, Melissa;Hernandez, Lorena;Cardona, Iris;O'Neill, Eduardo;Paz-Bailey, Gabriela;Papa, Riccardo;Munoz-Jordan, Jorge L
波多黎各经历了COVID-19大流行的全面影响。自2020年3月首次在岛上发现导致COVID-19的病毒SARS-CoV-2以来，它在岛上的人口中迅速传播，成为对公共卫生的严重威胁。我们通过与卫生机构和学术机构的伙伴关系进行了一项基因组监测研究，以了解该病毒在岛上的出现和分子流行病学。我们在19个月内每月对COVID-19病例进行采样，并在2020年3月至2021年9月期间对总共753个SARS-CoV-2基因组进行测序，利用系统发育推断在区域背景下重建当地疫情。我们的分析显示，在整个研究期间，多个输入事件推动了该病毒的出现和传播，包括在世界范围内检测到的大多数SARS-CoV-2变体的引入和传播。观察到在当地流行的各个阶段的谱系更替周期，在当地流行约4个月后，主要谱系被下一个竞争谱系或变体所取代。我们还发现了B.1.588谱系的出现，这是一种本地谱系，于2020年9月至12月在波多黎各占主导地位，随后传播到美国。这种合作方法的结果突出了及时收集和分析SARS-CoV-2基因组监测数据的重要性，以便为公共卫生应对提供信息。2019冠状病毒病大流行于2020年3月抵达波多黎各。为了了解SARS-CoV-2对波多黎各的影响，我们与大学和当地政府建立了合作伙伴关系，研究2020年3月至2021年9月期间从感染者身上采集的病毒基因序列。我们的研究结果表明，当地的流行病是由频繁输入各种各样的SARS-CoV-2谱系和变体引发和维持的，其中一些在岛上流传了一段时间。我们还发现了一种名为B.1.588的SARS-CoV-2谱系，它首先在波多黎各被发现，随后传播到美国。这项研究强调了研究病毒遗传数据对告知公共卫生反应的重要性。Santiago等人对2020年3月至2021年9月期间在波多黎各采样的SARS-CoV-2基因组进行了测序。系统发育分析发现，多次输入增加了感染，变异的更替动态与美国相似。
Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island’s population and became a critical threat to public health. We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Our analyses reveal that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after ~4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated in Puerto Rico from September to December 2020 and subsequently spread to the United States. The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses. The COVID-19 pandemic reached Puerto Rico in March 2020. To understand the impact of SARS-CoV-2 on Puerto Rico, we formed a partnership with universities and local government to study the genetic sequence of viruses sampled from infected people between March 2020 and September 2021. Our results show that the local epidemic was initiated and sustained by frequent importation of a wide diversity of SARS-CoV-2 lineages and variants, some of which circulated for some time in the island. We also detected a lineage of SARS-CoV-2, named B.1.588, that was first detected in Puerto Rico and subsequently spread to the United States. This study highlights the importance of the study of viral genetic data to inform public health responses. Santiago et al. sequenced SARS-CoV-2 genomes sampled in Puerto Rico between March 2020 and September 2021. Phylogenetic analyses found multiple importations that increased infections and that variant turnover dynamics were similar to those seen in the USA.