Beijing Center for Disease Prevention and Control, Beijing, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China.
Lancet. 2023 Feb 25;401(10377):664-672. doi: 10.1016/S0140-6736(23)00129-0. Epub 2023 Feb 8.
BACKGROUND: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic. METHODS: We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study. FINDINGS: We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022. INTERPRETATION: The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility. FUNDING: National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences. TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section.
背景：由于中国全国动态清零的防疫策略，2022 年 12 月之前北京没有持续的本地传播的 SARS-CoV-2。然而，在过去的 3 年中，进口病例时有发现。随着中国 COVID-19 病例数量的飙升，人们担心可能会出现新型 SARS-CoV-2 变体。在过去的 3 年中，北京一直在对病毒基因组进行常规监测。对最近的病毒基因组序列与全球汇集数据和本地数据进行时空分析，对于全球应对持续的 COVID-19 大流行至关重要。
方法：我们常规地收集了过去 3 年中北京的进口和本地病例的呼吸道样本（本研究涉及 2022 年 1 月至 12 月采集的样本），然后随机选择样本进行分析。使用下一代测序生成 SARS-CoV-2 基因组。在本研究中，使用高质量的完整序列进行了系统发育和种群动态分析。
结果：我们共获得了 2994 株完整的 SARS-CoV-2 基因组序列，其中 2881 株为高质量序列，用于进一步分析。从 2022 年 11 月 14 日至 12 月 20 日，我们共测序了 413 个新样本，包括 350 个本地病例和 63 个输入性病例。所有这些基因组都属于现有的 123 个 Pango 谱系，表明没有持续占主导地位的变体或新谱系。然而，BA.5.2 和 BF.7 目前在北京占主导地位，占自 2022 年 11 月 14 日以来北京本地病例的 90%（本研究中测序的 350 个本地病例中有 315 个）。2022 年 11 月 14 日之后，BA.5.2 和 BF.7 的北京有效种群数量均有所增加。
结论：自 2022 年 11 月 14 日以来，北京当前疫情中同时存在 BF.7 和 BA.5.2 的循环，没有证据表明出现了新型变体。尽管我们的数据仅来自北京，但由于频繁的人口流动以及高传播力的流行株的存在，这些结果可以被认为是中国的一个快照。
资助：国家重点研发计划和中国科学院战略性先导科技专项。
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