In-depth genomic characterisation of SARS-CoV-2 variants from Egypt exhibited heterogeneous lineages.

Background: Genetic variation of SARS-CoV-2 remains a public health challenge worldwide because of it influences the pathogenicity and transmissibility of the virus.

Aims: To determine the genomic mutations of SARS-CoV-2 isolated in Egypt.

Methods: This was an in silico cross-sectional study of 200 SARS-CoV-2 variants of concern, which were retrieved from the National Centre for Biotechnology Information on 11 January 2021 and aligned with the original Wuhan strain (NC_045512). Nucleotide basic local alignment search tool (BLASTN) was used to identify the nucleotide variations. Corresponding proteins were identified using protein basic local alignment search tool (BLASTP). A phylogenetic tree was constructed to study the evolutionary relationships using the neighbour-joining method.

Results: The variants of concern belonged to 26 species and there were 4 non-classified variants. All variants of concern showed 99.47-99.98% homology with the original Wuhan strain and demonstrated up to 60 mutations per variant. There were 1101 mutations identified among the variants of concern, with 458 synonymous and 583 nonsynonymous mutations. Specific mutations that were characteristically present in various SARS-CoV-2 lineages were identified, showing the microevolutionary genetic variations.

Conclusion: This study showed vast genetic variations of the Egyptian SARS-CoV-2 with characteristic mutations for the A, B and C lineages. The study contributes to a better understanding of the epidemiological and demographic variations of COVID-19 in Egypt based on SARS-CoV-2 genomic evolution and supports further investigation of SARS-CoV-2 contextbased vaccine development and preventive measures.