Genome sequencing of SARS-Co-V-2 reveals mutations including F559I and V781D in S protein and LI123-124L in the nsp6 in 21K and 21L clades

Contagious and virulent virus variants like B.1.1.529 have complicated the 2019 global COVID-19 pandemic from Wuhan, China. Omicron, with extensive mutations and high transmissibility, is replacing Delta in some regions. Remarkably, Omicron exhibits reduced disease severity and resistance to certain vaccines and treatments. Our research sought to identify Egypt-specific variants of concern (VOCs) and their mutation patterns, aiming to provide critical insights for tailored public health strategies. We also looked at vaccine compatibility with these VOCs, as well as the efficacy of current treatments against new SARS-CoV-2 variants. We collected 103 PCR-confirmed COVID-19 cases from an Egyptian army hospital and used next-generation sequencing technology to sequence the entire viral genome. The viral genome was then assembled and reconstructed. Nextclade tools aided in clade assignment and Phylogenetic analysis, allowing classification, and understanding of these genomes' Phylogenetic relationships. Our findings reveal that the dominant VOCs in Egypt are the 21K clade, mainly Pango lineages BA.1 (34%), BA.1.1 (30.1%), and BA.1.17 (6.8%), and the 21L clade represented by Pango lineages BA.2. We also identified novel mutations, including F559I in the S protein (consistent in the 21K clade), V781D in the S protein (present in > 50% of both 21K and 21L clades), and LI123-124L in the nsp6 gene (found in both 21K and 21L clades). Finally, our research provides important insights into Egypt's evolving COVID-19 landscape, allowing for tailored responses and risk mitigation strategies for emerging variants in the region.