Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology

Abstract

Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved phylogenies with 69 local and 3,894 global genome sequences. Furthermore, we investigated specific clades associated with the UAE cohort and, their global diversity, introduction events and inferred domestic and international virus transmissions between January and June 2020. The study comprehensively characterized the genomic aspects of the virus and its spread within the UAE and identified that the prevalence shift of the D614G mutation was due to the later introductions of the G-variant associated with international travel, rather than higher local transmissibility. For clades spanning different emirates, the most recent common ancestors pre-date domestic travel bans. In conclusion, we observe a steep and sustained decline of international transmissions immediately following the introduction of international travel restrictions.

Fig 1. Phylogenetic tree of the 69 UAE genome sequences in the context of global data.

A subsampled tree displaying 8 Abu Dhabi clades with multiple UAE descendants in ovals. Samples collected for this study are from Abu Dhabi (green) and Dubai (green with bold outline). Samples from Tayoun et al. are shown in orange.

Fig 2. Abu Dhabi’s largest cluster (clade 5).

A. Time tree for UAE clade 5. B. Divergence tree for the same clade. We identify four identical UAE strains that appear along a vertical line (with 2 mutations with respect to the clade ancestor).

Fig 3. Comparison of international and domestic transmissions over time.

The dotted and dash-dotted vertical lines mark the time of the travel ban to/from China and globally, on March 18 and March 25, 2020, respectively. A nearly instantaneous steep drop in international transmissions (blue) can be observed. We also observe that domestic transmissions (orange) continued to occur.

Fig 4. A shift of prevalence of strains with D614G mutations.

We measure the accumulated fraction of G-variants vs D-variants over time, while distinguishing international (blue) and domestic (orange) transmissions. The y-axis holds the total accumulated fraction of the G-variant. If the G-variant was substantially more transmissable, we would expect the domestic G/D ratio to clearly and increasingly dominate the international G/D ratio, in particular in light of the stronger domestic epidemiology after April 2020.