In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese–Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants.

This study aimed to investigate the SARS-CoV-2 infection prevalence among >18-year-old students in the Faculty of Public Health and Faculty of Sciences at the Lebanese University in Tripoli, Northern Lebanon, in June 2023 and to characterize the circulating Omicron subvariants. Out of 357 participants, only 2 (0.56%) tested positive by qPCR, corresponding to 0.61% (2/326) of asymptomatic students. One case tested positive with a qPCR targeting the Omicron BA.2 variant. These findings indicate a low incidence at that time and emphasize the interest of SARS-CoV-2 surveillance among students.