Oude Munnink Bas B, Worp Nathalie, Nieuwenhuijse David F, Sikkema Reina S, Haagmans Bart, Fouchier Ron A M, Koopmans Marion
Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
Nat Med. 2021 Sep;27(9):1518-1524. doi: 10.1038/s41591-021-01472-w. Epub 2021 Sep 9.
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
当前的2019冠状病毒病（COVID-19）大流行是首次近乎实时地应用全基因组测序，通过全球共享流感数据倡议组织（GISAID）平台已生成并共享了超过200万个严重急性呼吸综合征冠状病毒2（SARS-CoV-2）全基因组序列。这一基因组资源在整个大流行期间为公共卫生决策提供了信息；它还使得能够检测到可能影响病毒毒力、发病机制、宿主范围或免疫逃逸以及SARS-CoV-2诊断和治疗效果的突变。然而，无法以基因组测序的快速速度进行基因型到表型的预测。为了为大流行的下一阶段做好准备，需要一种系统的方法来将全球基因组监测与对新变种表型特征的及时评估联系起来，这将支持诊断、疫苗、治疗方法和非药物干预措施的开发与更新。本综述总结了关于关键病毒突变和变种的当前知识，并展望了不断演变的大流行监测的下一阶段。
