Data_Sheet_1_Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.ZIP

Background: 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.Methods: 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.Results: 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.Conclusions: 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.

背景：为深入探究斯里兰卡严重急性呼吸综合征冠状病毒-2（SARS-CoV-2）的分子流行病学，自2020年3月起，本研究在现有流行病学数据的基础上，对至2021年4月期间373名COVID-19患者的诊断性痰液或鼻咽拭子样本进行了全基因组测序。方法：通过分子钟系统发育分析，进一步解析了优势谱系。结果：B.1.411谱系在斯里兰卡最为普遍，该谱系起源于该国并导致全国范围内至2021年3月的大规模疫情爆发。该谱系最近共同祖先（tMRCA）的估计时间为2020年6月1日（95%置信区间为3月30日至7月27日），暗示可能存在隐匿性传播，发生在2020年10月开始的大规模疫情爆发之前。此外，还确定了感染B.1.258谱系以及更具传染性的B.1.1.7谱系归国的旅行者，B.1.1.7谱系已取代B.1.411，成为推动该国持续大规模疫情爆发的主导谱系。结论：始于10月初的大规模疫情爆发，直至2021年3月底，由单一病毒谱系B.1.411传播所致，随后B.1.1.7谱系出现并成为主导谱系。