Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, China.
Key Laboratory of Public Health Safety, Fudan University, Ministry of Education, Shanghai, China.
Nat Genet. 2022 Apr;54(4):499-507. doi: 10.1038/s41588-022-01033-y. Epub 2022 Mar 28.
Genomic surveillance has shaped our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. We performed a global landscape analysis on SARS-CoV-2 genomic surveillance and genomic data using a collection of country-specific data. Here, we characterize increasing circulation of the Alpha variant in early 2021, subsequently replaced by the Delta variant around May 2021. SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 45 countries performing a high level of routine genomic surveillance and 96 countries with a high availability of SARS-CoV-2 sequencing. We also observed a marked heterogeneity of sequencing percentage, sequencing technologies, turnaround time and completeness of released metadata across regions and income groups. A total of 37% of countries with explicit reporting on variants shared less than half of their sequences of variants of concern (VOCs) in public repositories. Our findings indicate an urgent need to increase timely and full sharing of sequences, the standardization of metadata files and support for countries with limited sequencing and bioinformatics capacity.
基因组监测改变了我们对严重急性呼吸综合征冠状病毒 2 型（SARS-CoV-2）变异株的认识。我们利用特定国家的数据收集，对 SARS-CoV-2 基因组监测和基因组数据进行了全球景观分析。在这里，我们描述了 2021 年初 Alpha 变异株传播的增加，随后在 2021 年 5 月左右被 Delta 变异株取代。各国之间的 SARS-CoV-2 基因组监测和测序可用性差异显著，45 个国家进行了高水平的常规基因组监测，96 个国家具有高可用性的 SARS-CoV-2 测序。我们还观察到，不同地区和收入群体的测序百分比、测序技术、周转时间和发布元数据的完整性存在显著差异。在明确报告变异体的国家中，有 37%的国家在公共存储库中共享的关注变异体（VOCs）序列不到一半。我们的研究结果表明，迫切需要增加及时和全面的序列共享，规范元数据文件，并为测序和生物信息学能力有限的国家提供支持。
