The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013-2014 Has Significant Implications for the Epidemiology of the Virus in the Region

Abstract

Molecular surveillance of FMD epidemiology is a fundamental tool for advancing our understanding of virus biology, monitoring virus evolution, and guiding vaccine design. The accessibility of genetic data will facilitate a more comprehensive delineation of FMDV phylogeny on a global scale. In this study, we investigated the FMDV strains circulating in Russia during the 2013-2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences. Phylogenetic analysis showed congruence in the topology of the phylogenetic trees constructed using the complete genome and VP1 gene sequence, clearly demonstrating that the isolates analyzed belong to two distinct genetic lineages: A/SEA97 in the Far East and Iran-05 in the North Caucasus. The A/SEA97 isolates exhibited a close genetic identity to those from China and Mongolia, whereas the Iran-05 isolates demonstrated clusterization with those from Turkey. The vaccine-matching studies with isolates from the Far East and North Caucasus revealed no antigenic homology with A/SEA-97 (r₁ = 0.015-0.29) and A/Iran 05 (r₁ = 0.009-0.17). The close genetic relationship of FMDV in the reported outbreak waves to those from neighboring countries indicates that animal movement could contribute to spillover and virus dispersal. The phylogenetic data reported here provide insight into the molecular epidemiology of FMD in the Eurasia region, elucidating the circulation pattern, molecular evolution, and genetic diversity, which is highly valuable for guiding vaccine designs and improving regional eradication policies.

Keywords: FMDV outbreak; Iran-05; Russia; SEA97; foot-and-mouth disease; molecular epidemiology; phylogeny; serotype A; vaccine matching.

Figure 1

Map illustrating foot-and-mouth disease outbreaks in Russia over the period 2013–2014. Outbreaks of A serotype are shown as red circles; outbreaks of O serotype are shown as blue circles.

Figure 2

Maximum likelihood unrooted phylogenetic tree of the whole genome sequences of 52 serotype A FMDV isolates. The tree was constructed using RAXML-NG software with 1000 bootstraps [26]. The isolates described in this study are labeled with green. The nodes with bootstrap support less than 50% are marked with red. The topotype distribution is illustrated by light gray sectors. Genetic lineages within topotype ASIA (as referenced by https://www.wrlfmd.org/, accessed on 19 December 2024) are indicated by dark gray arcs.

Figure 3

Maximum likelihood unrooted phylogenetic tree of the VP1 gene sequences of 79 FMDV isolates. The tree was constructed using RAXML-NG software with 1000 bootstraps [26]. The nodes with bootstrap support less than 50% are marked with red. The isolates described in this study are labeled with green. The topotype distribution is illustrated by light gray sectors. Genetic lineages within topotype A (as referenced by https://www.wrlfmd.org/, accessed on 19 December 2024) are indicated by dark gray arcs.

Figure 4

The pairwise comparisons of the whole genome FMDV serotype A sequences of SEA-97 (A) and Iran-05 (B) genetic lineages. The percentage of identical nucleotides is displayed in the bottom left half of each heatmap. The color scale varies from blue (minimum) to red (maximum). The top right half depicts the number of differences between the two sequences, including both gaps and single nucleotide polymorphisms (SNPs).