Phylogenetic and evolutionary analysis of VP1 coding sequences of foot-and-mouth disease virus serotypes A, O, and...

Foot-and-mouth disease (FMD) is a highly infectious viral disease caused by the foot-and-mouth disease virus (FMDV), which has seven serotypes requiring serotype-specific vaccines due to the absence of cross-protection. Understanding the genetic evolution of circulating strains is crucial for effective disease control and vaccine design. This study provides the first comprehensive evolutionary analysis of FMDV serotypes A, O, and SAT2 circulating in Egypt (1972-2022), integrating molecular clock modeling and structural analysis to uncover recent viral diversification. This study focused on analyzing the viral protein 1 (VP1) coding sequences from Egyptian field strains of serotypes A, O, and SAT2 using in silico approaches.

The nucleotide and amino acid sequences of VP1 for FMDV serotypes A, O, and SAT2 circulating in Egypt were retrieved from GenBank. Multiple sequence alignment was performed using ClustalW in MEGA 11, followed by phylogenetic tree construction using the maximum likelihood method with 1,000 bootstrap replicates. Pairwise identity matrices were generated to assess nucleotide similarities among isolates. Time-calibrated phylogenetic analyses were conducted using BEAST v2.6 to estimate substitution rates per site per year. Mutational analysis of the VP1 protein, particularly within the RGD (Arg-Gly-Asp) motif, was performed to identify novel amino acid substitutions with potential functional significance.

Multiple sequence alignment, phylogenetic analysis, and identity matrix comparisons were conducted to evaluate genetic relationships, while time-calibrated phylogenetic analysis estimated substitution rates per site per year. Serotype A strains clustered within Asia and Africa topotypes, with the first detection of a novel Europe-South America (Europe-SA) topotype in Egypt. Serotype O strains were grouped into East Africa (EA-3), Middle East-South Asia (ME-SA), and another new Euro-SA topotype was identified in Sharqia Governorate. Serotype SAT2 strains consistently aligned with topotype VII, with clustering patterns noted in 2012 and 2018 isolates. Importantly, a novel G136S mutation was identified within the conserved RGD motif of the Menoufia strain (MG552839), representing the first report of this substitution. The estimated mean evolutionary rates were 2.23 × 10⁻³, 1.85 × 10⁻³, and 4.48 × 10⁻⁶ substitutions per site per year for serotypes A, O, and SAT2, respectively.

This study extends previous molecular investigations by including recent isolates from nearly all Egyptian governorates and integrating quantitative evolutionary rate estimation with structural analysis. The detection of new topotypes and unique mutations provides novel insights into FMDV evolution in Egypt and emphasizes the need for continuous molecular surveillance and periodic vaccine updates to maintain protection against emerging lineages.