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© Pierre Gounon
Virus influenza purifié, agent de la grippe. Ce virus enveloppé possède un génome fragmenté : 8 segments d'ARN négatif protégés par une nucléocapside.
Publication : PeerJ

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in PeerJ - 16 Mar 2021

Feghali R, Merhi G, Kwasiborski A, Hourdel V, Ghosn N, Tokajian S

Link to Pubmed [PMID] – 34611501

Link to HAL – pasteur-03720775

Link to DOI – 10.7717/peerj.11015

PeerJ 2021 ; 9(): e11015

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.