Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia.
Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Viruses. 2022 Jun 7;14(6):1234. doi: 10.3390/v14061234.
Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage's genomic and epidemiological characteristics. However, in South America, this variant's arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.
对 SARS-CoV-2 的基因组监测是提供有关循环变体基因组信息的工具之一。鉴于奥密克戎（B.1.1.529）变体的最近出现，该工具提供了有关该谱系基因组和流行病学特征的数据。然而，在南美洲，这种变体的出现及其基因组多样性鲜为人知。因此，本研究确定了公共数据库中可用的 21615 个奥密克戎基因组的基因组多样性和系统发育关系。我们发现，在南美洲，BA.1（n = 15449，71%）和 BA.1.1（n = 6257，29%）是主要的亚谱系，具有有利于传播和逃避抗体的几种突变。此外，这些谱系在 2021 年 9 月底以隐匿传播的方式抵达该大陆。这一事件可能促成了奥密克戎亚谱系的传播和新突变的获得。考虑到这些谱系的基因组和流行病学特征，特别是那些基因组中存在大量突变的谱系，对这些谱系的动态进行研究和监测以确定突变获得的机制及其对公共卫生的影响非常重要。
