Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon

• DOI: 10.7717/peerj.11015
• Publication Date: 2021-03-16T11:09:05Z
• Authors: Rita Feghali; Georgi Merhi; Aurelia Kwasiborski; Veronique Hourdel; Nada Ghosn; Sima Tokajian
• Keywords: Lineage (genetic); Pandemic; Pangolin

Background In December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases unknown origin in city Wuhan, China. Presently, it has almost reached 94 million worldwide. Lebanon on brink economic collapse and its healthcare system thrown into turmoil, previously managed to cope with initial SARS-CoV-2 wave. this study, we sequenced 11 viral genomes positive isolated between 2 February 2020 15 March 2020. Methods Sequencing data was quality controlled, consensus sequences generated, maximum-likelihood tree generated IQTREE v2. Genetic lineages were assigned Pangolin v1.1.14 single nucleotide variants (SNVs) called read files manually curated sequence alignment through JalView v2.11 genomic mutational interference molecular diagnostic tools assessed CoV-GLUE pipeline. Phylogenetic analysis whole genome confirmed multiple introduction scenario due international travel. Results Three major identified be circulating studied period. The B.1 (20A clade) most prominent, followed by B.4 lineage (19A B.1.1 (20B clade). SNV showed novel mutations which only one observed spike region.