SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation

SIMPLE SUMMARY: Thanks to whole genome sequencing approaches, the proteins that compose the SARS-CoV-2 virus that causes COVID-19 are compared, and mutations and differences highlighted. This allows strains to be classified into clades or lineages, according to marker mutations in their proteins as well as relatedness to certain epidemiological events. In this study, 58 SARS-CoV-2 Lebanese strains were analyzed. They were classified into four GISAID clades and 11 Pango lineages. Moreover, the mutational survey revealed several mutations in the encoded proteins, particularly the structural ones, in which 22 uncommon mutations were found, 21 of which were in strains sequenced within this study. The latter also showed an interesting combination of mutations in their spike protein, the key element in the virus’ interaction with cellular receptors. In summary, this study highlights the key features of sequenced Lebanese SARS-CoV-2 genomes, including their classification, phylogenetic relationship, and mutations. ABSTRACT: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen a worldwide spread since its emergence in 2019, including to Lebanon, where 534,968 confirmed cases (8% of the population) and 7569 deaths have been reported as of 14 May 2021. With the genome sequencing of strains from various countries, several classification systems were established via genome comparison. For instance, the GISAID clades classification highlights key mutations in the encoded proteins that could potentially affect the virus’ infectivity and transmission rates. In this study, 58 genomes of Lebanese SARS-CoV-2 strains were analyzed, 28 of which were sequenced for this study, and 30 retrieved from the GISAID and GenBank databases. We aimed to classify these strains, establish their phylogenetic relationships, and extract the mutations causing amino acid substitutions within, particularly, the structural proteins. The sequenced Lebanese SARS-COV-2 strains were classified into four GISAID clades and 11 Pango lineages. Moreover, 21 uncommon mutations in the structural proteins were found in the newly sequenced strains, underlining interesting combinations of mutations in the spike proteins. Hence, this study constitutes an observation and description of the current SARS-CoV-2 genetic and clade situation in Lebanon according to the available sequenced strains.