Bioinformatic analysis of the emergence of SARS-CoV-2 in Libya

Abstract

This study aimed to identify the possible transmission pathways of SARS-CoV-2 into Libya and to determine the countries that were most likely to be sources of viral introduction into the country by analyzing the genetic and temporal relationships among viral isolates from Libya and selected neighboring countries. The study adopted a descriptive-analytical approach based on bioinformatics and phylogenetic analysis. SARS-CoV-2 spike protein sequences were retrieved from the NCBI Virus Hub using specific criteria for sequence completeness and quality. A total of 1,426 spike protein sequences were obtained, including 17 sequences from Libya, 86 from Tunisia, 29 from Morocco, 957 from Egypt, and 337 from Italy. Multiple sequence alignment was performed using the MAFFT program through the NGPhylogeny platform, followed by phylogenetic tree reconstruction to investigate the genetic relationships among viral isolates. The collection dates of closely related sequences were also compared to infer possible directions of viral transmission. The results showed that Libyan isolates repeatedly clustered genetically with isolates from Tunisia, Italy, and Morocco. In several clusters, Tunisian isolates had earlier collection dates than closely related Libyan isolates, indicating a likely transmission pathway from Tunisia to Libya. The findings suggest that Tunisia was the most likely major source of SARS-CoV-2 introduction into Libya during the period investigated, with limited evidence supporting transmission from Italy and Morocco to Libya. In contrast, the observed data indicated that viral transmission between Libya and Egypt was predominantly from Libya to Egypt. These findings demonstrate the value of integrating genetic, phylogenetic, and temporal analyses for investigating viral transmission pathways and supporting epidemiological surveillance and preparedness for future infectious disease outbreaks.