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.
Highlights
COVID-19 is an emerging disease caused by a novel beta coronavirus, SARS-CoV-2 [1]
Our analysis identified transmissions across the Emirates, since the most recent common ancestor, MRCA of clades comprising Dubai and Abu Dhabi samples are estimated to be of United Arab Emirates (UAE) origin with a confidence of 66% or higher
We show that even though multiple international introductions happened (Fig 1), import events declined drastically in the UAE during the period of international travel restrictions, while domestic transmissions persisted (Fig 3)
Summary
COVID-19 is an emerging disease caused by a novel beta coronavirus, SARS-CoV-2 [1]. The first cases of the disease were described in patients from Wuhan, China [2]. It has affected most countries of the world, causing 900,000 deaths and infecting nearly 30 million people by early October 2020 [3]. Understanding the pandemic at the molecular level through viral genome sequencing is paramount for tracing the epidemic spread, and for diagnostics as well as vaccine and antiviral drug development since regional differences in viral sequences may affect both the drug and vaccine efficacy. The first COVID-19 case in the United Arab Emirates (UAE) was reported on the 29th of January 2020. As of September 2020, the UAE has registered 74,454 cases of SARS-CoV-2 (around 48,000 during this study period) [4]
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