Feghali Rita, Merhi Georgi, Kwasiborski Aurelia, Hourdel Veronique, Ghosn Nada, Tokajian Sima
Department of Laboratory Medicine, Rafik Hariri University Hospital, Beirut, Lebanon.
Department of Natural Sciences, Lebanese American University, Byblos, Lebanon.
PeerJ. 2021 Mar 16;9:e11015. doi: 10.7717/peerj.11015. eCollection 2021.
In December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases of unknown origin in the city of Wuhan, China. Presently, it has almost reached 94 million cases worldwide. Lebanon on the brink of economic collapse and its healthcare system thrown into turmoil, has previously managed to cope with the initial SARS-CoV-2 wave. In this study, we sequenced 11 viral genomes from positive cases isolated between 2 February 2020 and 15 March 2020.
Sequencing data was quality controlled, consensus sequences generated, and a maximum-likelihood tree was generated with IQTREE v2. Genetic lineages were assigned with Pangolin v1.1.14 and single nucleotide variants (SNVs) were called from read files and manually curated from consensus sequence alignment through JalView v2.11 and the genomic mutational interference with molecular diagnostic tools was assessed with the CoV-GLUE pipeline. Phylogenetic analysis of whole genome sequences confirmed a multiple introduction scenario due to international travel.
Three major lineages were identified to be circulating in Lebanon in the studied period. The B.1 (20A clade) was the most prominent, followed by the B.4 lineage (19A clade) and the B.1.1 lineage (20B clade). SNV analysis showed 15 novel mutations from which only one was observed in the spike region.
2019年12月，新冠疫情最初在中国武汉市由一组不明原因的肺炎病例爆发。目前，全球病例数已近9400万例。黎巴嫩濒临经济崩溃，其医疗系统陷入混乱，此前已成功应对了最初的新冠病毒浪潮。在本研究中，我们对2020年2月2日至2020年3月15日期间分离出的11例阳性病例的病毒基因组进行了测序。
对测序数据进行质量控制，生成一致序列，并使用IQTREE v2生成最大似然树。使用Pangolin v1.1.14指定遗传谱系，从读取文件中调用单核苷酸变异（SNV），并通过JalView v2.11从一致序列比对中手动挑选，使用CoV-GLUE管道评估基因组突变对分子诊断工具的干扰。全基因组序列的系统发育分析证实了由于国际旅行导致的多次引入情况。
在研究期间，黎巴嫩确定有三个主要谱系在传播。B.1（20A分支）最为突出，其次是B.4谱系（19A分支）和B.1.1谱系（20B分支）。SNV分析显示有15个新突变，其中只有一个在刺突区域被观察到。
