Tegally Houriiyah, Wilkinson Eduan, Martin Darren, Moir Monika, Brito Anderson, Giovanetti Marta, Khan Kamran, Huber Carmen, Bogoch Isaac I, San James Emmanuel, Tsui Joseph L-H, Poongavanan Jenicca, Xavier Joicymara S, Candido Darlan da S, Romero Filipe, Baxter Cheryl, Pybus Oliver G, Lessells Richard, Faria Nuno R, Kraemer Moritz U G, de Oliveira Tulio
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
medRxiv. 2022 Nov 27:2022.11.22.22282629. doi: 10.1101/2022.11.22.22282629.
In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance.
Global phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs)Omicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCsOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travelAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs.
在世界许多地区，2020年至2021年期间，阿尔法、贝塔和伽马严重急性呼吸综合征冠状病毒2变异株（VOC）共同传播，引发了多轮感染浪潮。2021年期间，这些变异株几乎完全被德尔塔变异株取代，导致全球范围内的第三波感染。2021年末，当奥密克戎变异株在全球传播时，这种全球病毒谱系替代现象再次出现。在本研究中，我们使用系统发育和系统地理学方法重建了严重急性呼吸综合征冠状病毒2变异株在全球的传播模式。我们发现，严重急性呼吸综合征冠状病毒2的源 - 汇动态因变异株而异，并确定了作为变异株传播全球枢纽的国家，而其他国家则成为特定变异株出口的区域贡献者。我们证明了VOC假定起源国对其全球传播的作用在下降：我们估计印度对其他国家的德尔塔全球出口贡献不到15%，南非对全球奥密克戎全球出口贡献不到1 - 2%。我们进一步估计，在奥密克戎推断出现日期后的100天内，超过80个国家引入了奥密克戎BA.1，而阿尔法变异株出现时，只有略超过25个国家引入。这种全球传播速度的加快与奥密克戎出现之前航空旅行量的反弹以及奥密克戎相对于阿尔法更高的传播性有关。
全球系统发育分析揭示了航空旅行与严重急性呼吸综合征冠状病毒2变异株（VOC）传播速度之间的关系
奥密克戎变异株出现后100天内传播到的国家数量是所有其他变异株的5倍
在全球航空旅行增加期间，德尔塔和奥密克戎变异株的进一步传播和扩散主要来自二级枢纽，而非最初检测到的国家
分析突出了被确定为VOC主要全球和区域出口国的高度连通国家。
