SARS-CoV-2 Variants in Lebanon

Abstract

COVID-19 has caused more than 7 million deaths and 775 million positive cases, ranging from asymptomatic to deadly. The causative agent, SARS-CoV-2, has a positive single-stranded RNA genome. The spike protein, expressed on the surface, binds to host cells. Mutations, especially in the S gene, defined viral fitness and caused the emergence and worldwide spread of variants. Variants of concern (VOC) included Alpha, Beta, Delta, Gamma, and most recently Omicron. Co-infections of SARS-CoV-2 with influenza viruses were detected and led to increased infectivity and SARS-CoV-2 viral load. This study’s aim was to track the variants circulating in Lebanon over the 2022-2023 flu season to assess the trajectory of the pandemic. A total of 222 RNA samples were collected, reverse transcribed, amplified, and sequenced using the Nanopore MinION sequencing platform. Genomes were generated using the artic nCoV-2019 bioinformatics protocol. We detected 53 Omicron subvariants, with XBB.1.5 (17.59%), XBB.1.42 (10.05%), and XBB.1.42.1 (9.05%), being the most common. Apart from the most frequently detected clades, which were 22F (22.97%), 23A (22.07%), and 23D (17.57%), the prevalence of subvariants and clades varied over time. There was a notable emergence and dominance of XBB subvariants starting in February 2023. A27S (99.1%), D614G and D796Y (96.85%) were the top three most detected S gene mutations, while S135R and P3395H in ORF1a, and P314L in ORF1b, were seen in all sequenced genomes. XAY.1, a Delta-Omicron recombinant, had mutations not typically detected in other subvariants. Phylogenetic analysis was done for the subvariants that had very low worldwide prevalence including BN.4, XAY.1 and XCC, and for XBB.1.42.1, which formed a high proportion of the sequenced genomes in this study despite low worldwide prevalence. The phylogenetic analysis revealed travel transmission of XAY.1 and XCC, and local introductions of mutations upon circulation. This study is significant for its role in detecting and analyzing the variants and mutations that have influenced the course of the pandemic. Consistent sequencing and surveillance are essential for identifying circulating variants and mutations, which in turn facilitate more effective spread prevention, treatment options, and vaccination strategies.