Jeewandara Chandima, Jayathilaka Deshni, Ranasinghe Diyanath, Hsu Nienyun Sharon, Ariyaratne Dinuka, Jayadas Tibutius Thanesh, Panambara Arachchige Deshan Madhusanka, Lindsey Benjamin B, Gomes Laksiri, Parker Matthew D, Wijewickrama Ananda, Karunaratne Malika, Ogg Graham S, de Silva Thushan I, Malavige Gathsaurie Neelika
Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
Department of Infection, Immunity and Cardiovascular Diseases, Medical School, University of Sheffield, Sheffield, United Kingdom.
Front Microbiol. 2021 Sep 16;12:722838. doi: 10.3389/fmicb.2021.722838. eCollection 2021.
In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.
为了解严重急性呼吸综合征冠状病毒2（SARS-CoV-2）在斯里兰卡的分子流行病学情况，自2020年3月起，我们在现有流行病学数据基础上开展了基因组测序，直至2021年4月。对373例新冠肺炎患者的诊断性痰液或鼻咽拭子进行了全基因组测序。进行了分子钟系统发育分析以进一步探索优势谱系。B.1.411谱系最为普遍，该谱系在斯里兰卡出现，并在2021年3月前在全国引发了多起疫情。该谱系最近共同祖先（tMRCA）的估计时间为2020年6月1日（95%置信区间下限为3月30日，上限为7月27日），这表明在2020年10月开始大规模疫情之前可能已经发生了隐匿传播。归国旅行者被检测出感染了B.1.258谱系以及传播性更强的B.1.1.7谱系，后者已取代B.1.411谱系，推动了该国目前正在发生的大规模疫情。始于10月初的大规模疫情是由单一病毒谱系B.1.411传播所致，直到2021年3月底B.1.1.7谱系出现并成为优势谱系。
