A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

Published on May 11, 2020, by Simon Dellicour

Since the early days of the COVID-19 pandemic, there has been an important mobilisation of the scientific community to understand its epidemiology and help providing a real-time response. To this end, research teams around the world have massively sequenced and publicly released viral genome sequences to study the origin of the virus, or to allow evolutionary analyses to link worldwide infectious cases and retrace the dispersal history of the virus. 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. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages. 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 a global impact of the national lockdown on 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.

Figure Map

Figure 3: Spatially-explicit phylogeographic reconstruction of the dispersal history of SARS-CoV-2 lineages in Belgium. A: Continuous phylogeographic reconstruction performed along each Belgian clade (cluster) identified by the initial discrete phylogeographic analysis. For each clade, we mapped the maximum clade credibility (MCC) tree and overall 80% highest posterior density (HPD) regions reflecting the uncertainty related to the phylogeographic inference. MCC trees and 80% HPD regions are based on 1,000 trees subsampled from each post burn-in posterior distribution. MCC tree nodes were coloured according to their time of occurrence, and 80% HPD regions were computed for successive time layers and then superimposed using the same colour scale reflecting time. Continuous phylogeographic reconstructions were only performed along Belgian clades linking at least three sampled sequences for which the geographic origin was known (see the Methods section for further details). Besides the phylogenetic branches of MCC trees obtained by continuous phylogeographic inference, we also mapped sampled sequences belonging to clades linking less than three geo-referenced sequences. Furthermore, when a clade only gathers two geo-referenced sequences, we highlighted the phylogenetic link between these two sequences with a dashed curve connecting them. Sub-national province borders are represented by white lines. B: Evolution of the weighted lineage dispersal velocity through time, with the surrounding polygon representing the 95% credible interval. C: MCC tree branches occurring before the 18 March 2020 (beginning of the Belgian lockdown. D: MCC tree branches occurring after the 18 March 2020. E: MCC tree branches occurring before the 18 March 2020 in the province of Liège. F: MCC tree branches occurring after the 18 March 2020 in the province of Liège. G: Estimates of the weighted lineage dispersal velocity for different subsets of phylogenetic branches [and corresponding 95% HPD intervals].

Reference: 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. biorXiv 2020.05.05.078758; doi: https://doi.org/10.1101/2020.05.05.078758