Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel.
Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel.
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值得关注的 SARS-CoV-2 变体的全球扩张：传播模式和航空旅行的影响。
DOI：
10.1101/2022.11.22.22282629
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
R
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文献类型：
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作者：
Tegally,Houriiyah;Wilkinson,Eduan;Martin,Darren;Moir,Monika;Brito,Anderson;Giovanetti,Marta;Khan,Kamran;Huber,Carmen;Bogoch,IsaacI;San,JamesEmmanuel;Tsui,JosephL-H;Poongavanan,Jenicca;Xavier,JoicymaraS;Candido,DarlandaS;R
在世界许多地区，2020 - 2021年期间，甲型、乙型和伽型SARS-CoV-2关注变体（voc）共同传播，引发了感染浪潮。在2021年期间，这些变体几乎完全被Delta变体所取代，在全球范围内引发了第三波感染。2021年底，当Omicron变体在全球传播时，再次观察到这种全球病毒谱系位移现象。在这项研究中，我们使用系统发育和系统地理学方法重建了SARS-CoV-2挥发性有机物在全球的传播模式。我们发现SARS-CoV-2的源汇动态因VOC而有很大差异，并确定了充当变体传播全球中心的国家，而其他国家则成为特定变体出口的区域贡献者。我们证明了VOCs的假定原产国对其全球扩散的作用正在下降：我们估计印度对达美航空对其他国家的全球出口的贡献小于15%，南非对欧米克隆全球出口的贡献小于1-2%。我们进一步估计，80个国家在其推测的出现日期100天后收到了Omicron BA.1的介绍，相比之下，只有超过25个国家收到了Alpha变体。全球传播速度的加快与Omicron出现之前航空运输量的反弹有关，此外，Omicron的传播率相对于Alpha更高。我们的研究强调了全球和区域中心在VOC传播中的重要性，以及高传染性变异通过这些中心传播的速度，甚至在通过基因组监测检测和表征它们之前。
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.