The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

Abstract

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.

Keywords: B.1.398; Lebanon; SARS-CoV-2; dispersal; lineages.

Figure A1

Correlation between sampling dates and the root-to–tip distance of the maximum likelihood tree of lineage B.1.398 when including sequences from GISAID prior to June, 2020 (red points). These sequences were removed for the final analysis.

Figure A2

Maximum likelihood phylogeny of SARS-CoV-2 sequences sampled in Lebanon. Colored tip points show the newly-sequenced genomes and their attributed lineage.

Figure A3

Temporal distribution of intercontinental (red) and within-continent (blue) dispersal of B.1.398 lineage.

Figure 1

Epidemics of COVID-19 in the first two years of the pandemic in Lebanon. In (A), we see the relative frequency of SARS-CoV-2 lineages sampled in Lebanon between February 2020 and December 2021. Lineages belonging to the variants of concern Alpha, Delta, and Omicron are grouped under these labels. The numbers of COVID-19 cases and deaths are described in (B,C).

Figure 2

International dispersal of the B.1.398 lineage. In (A), all the international transmission routes are represented, with the left bar being the countries of origin of dispersal, the right bar their destinations, and the color of dispersal representing the originating country. In (B), the temporal distribution of countries receiving B.1.398 that originated in Lebanon is displayed. The legend for both graphs is located at the bottom.

Figure 3

Phylodynamics of the B.1.398 lineage in Lebanon. In (A), we see the time tree of B.1.398, indicating divergence times between genomic sequences, with colors representing the districts in Lebanon. The Tripoli district acted as a dispersal hub in the country, as displayed in (B). Colors in (B) indicate the time at which dispersal started.