ULB - FNRS
" Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on Belgium, one of the countries with the highest spatial density of sequenced SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight an impact of the national lockdown of mid-March on both the long-distance dispersal events and the dispersal velocity of viral lineages. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement. "
Funding: FNRS, FWO, Région Wallonne
Publication References: Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, De Maio N, Hadfield J, Hayette MP, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P (submitted). A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages.
Comment: - This study will be submitted before Friday 08/03/20, and will also be put on a preprint server (bioRxiv) to be quickly and widely shared with other research teams from different countries. - This study is one of the active research projects led by the Spatial Epidemiology Lab (SpELL, ULB, spell.ulb.be) to fight the COVID-19 pandemic. A summary of the other research and analytical activities can be found here: https://spell.ulb.be/news/covid19_analyses/
Simon Dellicour, FNRS Postdoctoral Researcher
ULB - FNRS