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

Simon Dellicour, Keith Durkin, Samuel L Hong, Bert Vanmechelen, Joan Martí-Carreras, Mandev S Gill, Cécile Meex, Sébastien Bontems, Emmanuel André, Marius Gilbert, Conor Walker, Nicola De Maio, Nuno R Faria, James Hadfield, Marie-Pierre Hayette, Vincent Bours, Tony Wawina-Bokalanga, Maria Artesi, Guy Baele, Piet Maes

Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated. These sequences provide a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a computational hurdle if analysed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyse the spatio-temporal dispersal history and dynamics of SARS-CoV-2 lineages. The analytical workflow has the potential to be rapidly applied to study the dispersal history and dynamics of SARS-CoV-2 lineages.

Published November 2020 in Molecular Biology and Evolution