Abstract
In the field of molecular epidemiology, genetic analyses of pathogens are used to complement traditional epidemiological methods in various ways. For instance, genetic analyses offer the possibility to infer linkages between infections that are not evident without analysing viral genomes. In particular, the development of phylogeographic methods has enabled to reconstruct dispersal history of epidemics in a discretised or on a continuous space, using only a relatively limited number of viral sequences sampled from known locations and times. Since the beginning of the COVID-19 pandemic, phylogeographic analyses have been conducted to reconstruct the dispersal history of SARS-CoV-2 lineages at global and more local spatial scales. I here illustrate the interest of phylogeographic inference by presenting analytical approaches that we implemented and applied to address some specific questions related to the epidemiology of SARS-CoV-2: the relative importance of introduction events to establish local transmission chains (e.g. at a country level), the impact of international travels during European summer holidays 2020 on the resurgence of COVID-19 in Europe, the invasion dynamic of the Alpha variant that emerged in England, and the variant-specific dispersal dynamics of SARS-CoV-2 in New York City. In these recent studies, we specifically aimed to go beyond historical reconstructions and further exploit phylogeographic reconstructions to formally test epidemiological hypotheses.
References
Dellicour, S., Durkin, K., Hong, S. L., Vanmechelen, B., Martí-Carreras, J., Gill, M. S., Meex, C., Bontems, S., André, E., Gilbert, M., Walker, C., Maio, N., Faria, N. R., Hadfield, J., Hayette, M. P., Bours, V., Wawina-Bokalanga, T., Artesi, M., Baele, G., & Maes, P. (2021). A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages. Molecular biology and evolution, 38(4), 1608–1613. https://doi.org/10.1093/molbev/msaa284
Lemey, P., Ruktanonchai, N., Hong, S. L., Colizza, V., Poletto, C., Van den Broeck, F., Gill, M. S., Ji, X., Levasseur, A., Oude Munnink, B. B., Koopmans, M., Sadilek, A., Lai, S., Tatem, A. J., Baele, G., Suchard, M. A., & Dellicour, S. (2021). Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature, 595(7869), 713–717. https://doi.org/10.1038/s41586-021-03754-2
Dellicour, S., Hong, S. L., Hill, V., Dimartino, D., Marier, C., Zappile, P., Harkins, G. W., Lemey, P., Baele, G., Duerr, R., & Heguy, A. (2023). Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron. PLoS pathogens, 19(4), e1011348. https://doi.org/10.1371/journal.ppat.1011348