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

Rita Feghali; Georgi Merhi; Aurelia Kwasiborski; Veronique Hourdel; Nada Ghosn; Sima Tokajian

doi:10.7717/peerj.11015

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

PeerJ. 2021 Mar 16:9:e11015. doi: 10.7717/peerj.11015. eCollection 2021.

Authors

Rita Feghali^#¹, Georgi Merhi^#², Aurelia Kwasiborski³, Veronique Hourdel³, Nada Ghosn⁴, Sima Tokajian²

Affiliations

¹ Department of Laboratory Medicine, Rafik Hariri University Hospital, Beirut, Lebanon.
² Department of Natural Sciences, Lebanese American University, Byblos, Lebanon.
³ Laboratory: Environment and Infectious Risks, Pasteur Institute, Paris, France.
⁴ Epidemiological Surveillance Unit, Ministry of Public Health, Beirut, Lebanon.

^# Contributed equally.

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 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.

Results: 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.

Keywords: B.1 (20A clade); B.4 (19A clade); COVID-19; Lebanon; SASR-CoV-2; SNV analysis.

Grants and funding

The sequencing of the SARS-CoV-2 samples was financed by the MediLabSecure project, founded by the European Commission (DEVCO: IFS/2018/402-247). This study was also funded by the Strategic Research Review Committee (Grant #SRRC-R-2019-38) at the Lebanese American University and by the National Council for Scientific Research (Grant #00993). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.