Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Department of Zoology, University of Oxford, Oxford, UK.
Nature. 2022 Oct;610(7930):154-160. doi: 10.1038/s41586-022-05200-3. Epub 2022 Aug 11.
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
新冠病毒德尔塔(Pango 谱系 B.1.617.2)变异株在全球范围内传播,导致全球 COVID-19 疫情再次爆发。德尔塔变异株在英国的出现是在免疫异质性和非药物干预措施放松的背景下发生的。在这里,我们分析了来自英格兰的 52992 个 SARS-CoV-2 基因组和来自世界其他地区的 93649 个基因组,以重建德尔塔的出现,并在不断变化的旅行和社会限制背景下量化其在英格兰的引入和区域传播。利用人类活动、接触者追踪和病毒基因组数据分析,我们发现德尔塔变异株扩展的地理重点从印度转移到 2021 年 5 月初更具全球性的模式。在英格兰,德尔塔谱系被引入超过 1000 次,并随着非药物干预措施的放松而在全国范围内传播。我们发现,对旅行者的酒店隔离减少了进口病例的传播;然而,后来在英格兰主导德尔塔浪潮的传播链是在旅行限制出台之前出现的。英格兰内部区域间旅行的增加推动了德尔塔在全国范围内的传播,一些城市从其他地方接收了 2000 多次可观察到的谱系引入。随后,当地人口混合程度的增加——而不是进口数量的增加——与德尔塔的相对传播速度加快有关。德尔塔的入侵动态取决于接触模式的空间异质性,我们的研究结果将为减少当前和未来关注变体(如奥密克戎(Pango 谱系 B.1.1.529))的传播提供最佳的空间干预措施。