Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
Viruses. 2021 Jun 9;13(6):1098. doi: 10.3390/v13061098.
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island.
严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）的传播导致了一场非凡的全球公共卫生危机。2020 年初，塞浦路斯与其他欧洲国家一样，受到 SARS-CoV-2 疫情的影响，并于 2020 年 3 月采取封锁措施，以限制该岛的疫情初始爆发。在这项研究中，我们对 2020 年 4 月至 2021 年 1 月塞浦路斯的 SARS-CoV-2 分离株进行了全面的回顾性分子流行病学分析（遗传、系统发育、系统发生和系统地理学分析），涵盖了该岛 SARS-CoV-2 感染流行的头十个月。本研究的主要目的是评估 SARS-CoV-2 谱系在塞浦路斯的传播能力。从社区诊断检测中心和住院患者获得的 596 份临床样本（鼻咽拭子）中生成了完整的 SARS-CoV-2 基因组序列。系统发育分析显示，塞浦路斯共有 34 种不同的谱系，B.1.258、B.1.1.29、B.1.177、B.1.2、B.1 和 B.1.1.7（指定为 202012/01 关注变异株，VOC）是研究期间该岛最流行的谱系。系统发生分析显示，SARS-CoV-2 感染的疫情非常活跃，连续出现了三次疫情高峰，具有特定的谱系（2020 年 4 月至 6 月的 B.1.1.29；2020 年 9 月至 2021 年 1 月的 B.1.258；以及 2020 年 12 月至 2021 年 1 月的 B.1.1.7）。对上述谱系的完整 SARS-CoV-2 基因组序列的遗传分析显示，S 蛋白内存在突变（L18F、ΔH69/V70、S898F、ΔY144、S162G、A222V、N439K、N501Y、A570D、D614G、P681H、S982A 和 D1118H），这些突变赋予了病毒更高的传染性和/或抗体逃逸（免疫逃避）能力。系统地理学分析表明，大部分输入和输出都是来自英国（UK），尽管还确定了许多其他地区/国家（东南亚、南欧、东欧、德国、意大利、巴西、智利、美国、丹麦、捷克共和国、斯洛文尼亚、芬兰、瑞士和巴基斯坦）。综上所述，这些发现表明，塞浦路斯的 SARS-CoV-2 感染疫情是由来自多个国家的谱系不断涌入维持的，导致该岛不断出现进化和多系病毒。
