Fig 1.
Time-resolved phylogeny from the discrete phylogeographic analysis of Florida Clade 1.
MCC tree obtained from the analysis of the HA-only dataset. Branches are coloured according to the most probable location of the parental node of each lineage (colour codes are shown in the lower left) across the five defined global regions. Tips representing European sequences are coloured based on their country of origin. Diamonds on nodes represent posterior probability support ≥ 0.9, with grey horizontal bars representing the 95% HPD estimates for node age.
Fig 2.
Time-resolved phylogeny of EIV viruses from the UK.
The tips in the maximum clade credibility tree are coloured according to the viral clusters, while singletons and low-support clusters are shown in grey. Nodes with posterior probability ≥ 0.9 are labelled with a diamond.
Table 1.
Characteristics of the viral clusters detected in the UK during the 2019 epizootic.
Fig 3.
Phylodynamics of viruses isolates during the FC1 EI epizootic in the United Kingdom.
(A) Time-resolved phylogeny of UK viruses with the summary of the phylogeographic ancestral state reconstruction. Colours on tips and branches correspond to the regions outlined in the upper-right inset. Nodes with posterior probability ≥ 0.9 are labelled with diamonds. (B) Supported lineage dispersal events between locations. The thickness of the arrows indicates the corresponding standard BF; only transitions with strong support BF ≥ 20 are plotted. Base UK map shapefile sourced from Natural Earth (https://www.naturalearthdata.com/) public domain. (C) Contribution of each region in seeding viral lineages to (any) other locations through time measured as the mean count of Markov jumps per day across all trees in the posterior distribution and smoothed using a 7-day centred rolling mean. (D) Between-region circular migration flow plot as estimated from the Markov jumps analysis. Arrows indicate the direction of the migration and thickness is relative to the number of jumps. Only migration events associated with a BF support ≥3 are reported.
Fig 4.
Comparison of EIV HA and NA protein sequences.
(A) Amino acid changes on surface glycoproteins between A/equine/Lincolnshire/00620/2019 (UK/2019) and the vaccine strains commonly used: A/equine/South Africa/4/2003 (SA/2003) and A/equine/Richmond/1/2007 (UK/2007), and a more recent FC2 strain A/equine/Kent/2015 (UK/2015). (B) Viral shedding in vaccinated and unvaccinated horses affected during the 2019 epizootic in the UK. Viral load (determined by qPCR) in vaccinated (n = 74) and unvaccinated horses (n = 297) stratified by day since the onset of clinical signs.
Fig 5.
Phylodynamics of the H3N8 EIV lineage between 1963 and 2022.
(A) Supported lineage dispersal events between locations. The thickness of the arrows indicates the corresponding standard BF; only transitions with positive support BF ≥ 3 are plotted. Base map shapefile sourced from Natural Earth (https://www.naturalearthdata.com/) public domain. (B) Between-region circular migration flow plot as estimated from the Markov jumps analysis. Arrows indicate the direction of the migration and thickness is relative to the number of jumps. Only migration events associated with a BF support ≥3 are reported. (C) Markov reward times per region. The boxplot of each region depicts the density distribution of the total time (boxes show the median and HPD80 interval).