Yakovleva Anna, Kovalenko Ganna, Redlinger Matthew, Liulchuk Mariia G, Bortz Eric, Zadorozhna Viktoria I, Scherbinska Alla M, Wertheim Joel O, Goodfellow Ian, Meredith Luke, Vasylyeva Tetyana I
University of Oxford.
University of Cambridge.
Res Sq. 2021 Nov 30:rs.3.rs-1044446. doi: 10.21203/rs.3.rs-1044446/v1.
Since spring 2020, Ukraine has experienced at least two COVID-19 waves and has just entered a third wave in autumn 2021. The use of real-time genomic epidemiology has enabled the tracking of SARS-CoV-2 circulation patterns worldwide, thus informing evidence-based public health decision making, including implementation of travel restrictions and vaccine rollout strategies. However, insufficient capacity for local genetic sequencing in Ukraine and other Lower and Middle-Income countries limit opportunities for similar analyses. Herein, we report local sequencing of 24 SARS-CoV-2 genomes from patient samples collected in Kyiv in July 2021 using Oxford Nanopore MinION technology. Together with other published Ukrainian SARS-COV-2 genomes sequenced mostly abroad, our data suggest that the second wave of the epidemic in Ukraine (February-April 2021) was dominated by the Alpha variant of concern (VOC), while the beginning of the third wave has been dominated by the Delta VOC. Furthermore, our phylogeographic analysis revealed that the Delta variant was introduced into Ukraine in summer 2021 from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. This study highlights the need to urgently integrate affordable and easily-scaled pathogen sequencing technologies in locations with less developed genomic infrastructure, in order to support local public health decision making.
自2020年春季以来，乌克兰至少经历了两波新冠疫情，2021年秋季刚刚进入第三波。实时基因组流行病学的应用使得追踪全球范围内严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的传播模式成为可能，从而为基于证据的公共卫生决策提供信息，包括实施旅行限制和疫苗推广策略。然而，乌克兰以及其他低收入和中等收入国家的本地基因测序能力不足，限制了进行类似分析的机会。在此，我们报告了2021年7月在基辅采集的患者样本中24个SARS-CoV-2基因组的本地测序情况，采用的是牛津纳米孔MinION技术。结合其他主要在国外测序的已发表的乌克兰SARS-CoV-2基因组，我们的数据表明，乌克兰第二波疫情（2021年2月至4月）主要由关注的阿尔法变异株（VOC）主导，而第三波疫情开始时则主要由德尔塔变异株主导。此外，我们的系统地理学分析显示，德尔塔变异株于2021年夏季从全球多个地点传入乌克兰，大多数传入来自中欧和东欧国家。这项研究强调，迫切需要在基因组基础设施欠发达的地区整合经济实惠且易于扩展的病原体测序技术，以支持当地的公共卫生决策。
