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.

当前的冠状病毒病 2019 (COVID-19) 大流行是首次近乎实时地应用全基因组测序，通过以下方式生成和共享了超过 200 万个严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 全基因组序列GISAID 平台。这一基因组资源为整个大流行期间的公共卫生决策提供了信息；它还允许检测可能影响毒力、发病机制、宿主范围或免疫逃逸以及 SARS-CoV-2 诊断和治疗有效性的突变。然而，基因型到表型的预测不能以基因组测序的快速速度进行。为了为大流行的下一阶段做好准备，需要一种系统的方法将全球基因组监测与及时评估新变异的表型特征联系起来，这将支持诊断、疫苗、治疗和非药物干预措施的开发和更新。本综述总结了当前关于关键病毒突变和变体的知识，并展望了下一阶段对不断演变的大流行病的监测。