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Comparative Study
. 2025 Jul;122(26):e2506743122.
doi: 10.1073/pnas.2506743122. Epub 2025 Jun 26.

Comparative performance of viral landscape phylogeography approaches

Simon Dellicour  1   2   3 , Fabiana Gámbaro  1 , Maude Jacquot  4 , Sebastian Lequime  5 , Guy Baele  2 , Marius Gilbert  1 , Oliver G Pybus  6   7 , Marc A Suchard  8   9   10 , Philippe Lemey  2
Affiliations
Comparative Study

Comparative performance of viral landscape phylogeography approaches

Simon Dellicour et al. Proc Natl Acad Sci U S A. 2025 Jul.

Abstract

The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.

Keywords: continuous phylogeography; landscape phylogeography; molecular epidemiology; viruses.

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Conflict of interest statement

Competing interests statement:The authors declare no competing interest.

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