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

ABSTRACT:

Background

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.

Methods

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

SUBMITTER: Feghali R 

PROVIDER: S-EPMC8447710 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature