Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus

Journal
Journal of Virology
Date Issued
2023-11-30
Author(s)
Van Borm, Steven
Dellicour, Simon
Martin, Darren P
Lemey, Philippe
Agianniotaki, Eirini I
Chondrokouki, Eleni D
Vidanovic, Dejan
Vaskovic, Nikola
Petroviċ, Tamaš
Laziċ, Sava
Koleci, Xhelil
Vodica, Ani
Vandenbussche, Frank
Haegeman, Andy
De Clercq, Kris
Mathijs, Elisabeth
DOI
10.1128/jvi.01394-23
Abstract
Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we provide the first fine-grained whole genome sequence sampling of a constrained LSDV outbreak (southeastern Europe, 2015-2017), which we analyze along with global publicly available genomes. We formally evaluate the past occurrence of recombination events as well as the temporal signal that is required for calibrating molecular clock models and subsequently conduct a time-calibrated spatially explicit phylogeographic reconstruction. Our study further illustrates the importance of accounting for recombination events before reconstructing global and regional dynamics of DNA viruses. More LSDV whole genomes from endemic areas are needed to obtain a comprehensive understanding of global LSDV dispersal dynamics.
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