Gardezi Syeda Anam Masood, Rabbani Masood, Mushtaq Muhammad Hassan, Shabbir Muhammad Zubair
Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan.
Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan.
Arch Virol. 2025 May 25;170(7):137. doi: 10.1007/s00705-025-06319-0.
Foot-and-mouth disease virus (FMDV) causes a highly infectious transboundary disease in cloven-hoofed animals. However, there is limited information on comparative genomic and evolutionary analysis of FMDV strains reported in Pakistan. In the current study, we investigated a few disease outbreaks in Pakistan and determined the complete genome sequences of three isolates belonging to different serotypes: O, A, and Asia-1. Comparative genomic analysis showed a close relationship between the FMDV strains from this study and those reported in neighboring Asian countries. Phylogenetic analysis based on the complete genome and VP1 gene sequences revealed that serotype O clustered within the Pak-98 lineage, serotype A within genotype I, and serotype Asia-1 within group 5, grouping with strains from Pakistan, India, and China. Potential negatively selected sites were identified in the region encoding the structural proteins VP4, VP3, VP2, and VP1, with the most episodic diversifying section observed in the VP1 and VP3 regions. Substantial variation was observed in polymorphic and monomorphic sites, with the highest diversity observed in the VP1 protein of serotype O viruses. No evidence of recombination events was found in the FMDV strains from this study. Our findings indicate the cocirculation of multiple serotypes and sublineages of FMDV in Pakistan, underscoring the potential for the emergence of new variants. This study adds to the existing knowledge on the genetic variation and evolutionary dynamics of FMDV serotypes in Pakistan, providing valuable insights for the development of effective vaccines and improved disease control strategies.
口蹄疫病毒（FMDV）在偶蹄动物中引发一种具有高度传染性的跨界疾病。然而，关于巴基斯坦报道的FMDV毒株的比较基因组和进化分析的信息有限。在本研究中，我们调查了巴基斯坦的几起疾病暴发事件，并确定了属于不同血清型（O型、A型和亚洲1型）的三株分离株的全基因组序列。比较基因组分析表明，本研究中的FMDV毒株与亚洲邻国报道的毒株关系密切。基于全基因组和VP1基因序列的系统发育分析显示，O型血清型聚集在Pak - 98谱系内，A型血清型在基因型I内，亚洲1型血清型在第5组内，与来自巴基斯坦、印度和中国的毒株归为一类。在编码结构蛋白VP4、VP3、VP2和VP1的区域中鉴定出潜在的负选择位点，在VP1和VP3区域观察到最明显的多样化区段。在多态性和单态性位点观察到大量变异，在O型血清型病毒的VP1蛋白中观察到最高的多样性。本研究的FMDV毒株中未发现重组事件的证据。我们的研究结果表明，FMDV的多种血清型和亚谱系在巴基斯坦共同传播，凸显了新变种出现的可能性。本研究增加了关于巴基斯坦FMDV血清型遗传变异和进化动态的现有知识，为开发有效的疫苗和改进疾病控制策略提供了有价值的见解。
