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Research Article | 27 May 2026

Molecular detection and VP1-based phylogenetic characterization of Foot-and-mouth disease virus serotype O circulating in cattle in Aceh, Indonesia

M. Daud AK1, Mahdi Abrar1, Teuku Reza Ferasyi2,3, Darniati Darniati1, Erina Erina1, Tongku Nizwan Siregar4, and Surachmi Setiyaningsih5 Show more
VETERINARY WORLD | Article No. 28 | pg no. 2221-2232 | Vol. 19, Issue 5 | DOI: 10.14202/vetworld.2026.2221-2232
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ABSTRACT

                      
Background and Aim: Foot-and-mouth disease (FMD) remains a major transboundary animal disease affecting livestock production and trade worldwide. Following the re-emergence of FMD virus (FMDV) in Indonesia in 2022, repeated outbreaks have continued to occur in several provinces, including Aceh. However, molecular information regarding circulating strains in Aceh remains limited. This study aimed to detect FMDV in clinically affected cattle in Aceh, Indonesia, using serological and molecular approaches and to characterize the phylogenetic relationship of the detected virus based on the VP1 gene. 
Materials and Methods: Serum and swab samples were collected from clinically suspected cattle in Aceh Besar District, Aceh Province, Indonesia, during 2024. Antibodies against FMDV non-structural proteins were detected using non-structural protein enzyme-linked immunosorbent assay. Viral RNA was extracted from nasopharyngeal and oral swabs and examined using reverse transcription polymerase chain reaction targeting the 5′ untranslated region and 3D gene. Positive samples were further analyzed using serotype O-specific VP1 primers. Amplicons were sequenced using the Sanger method, and phylogenetic analysis was performed using the Neighbor-Joining method with the Kimura 2-parameter model and 1,000 bootstrap replicates in MEGA version 12. 
Results: Non-structural protein antibody detection showed positive or weak-positive reactions in a subset of clinically affected cattle, while all clinically uninfected cattle were negative. Reverse transcription polymerase chain reaction confirmed FMDV RNA in 70% of tested swab samples, producing the expected 328 bp and 644 bp amplicons. VP1 amplification generated an approximately 1,135 bp fragment, with 56°C identified as the optimal annealing temperature. Phylogenetic analysis demonstrated that the representative isolate, O/AcehBesar/ 01A/2024, clustered within the Middle East-South Asia topotype, Ind-2001e sub-lineage, together with Indonesian outbreak strains reported during 2022. The isolate shared 96% nucleotide identity with Indonesian serotype O isolates and showed close genetic relationships with strains from several Asian and trans-regional countries. 
Conclusion: The study confirmed the continued circulation of FMDV serotype O belonging to the Middle East-South Asia/Ind-2001e sub-lineage in Aceh, Indonesia. The findings provide updated VP1-based molecular evidence from Aceh and emphasize the importance of integrating serological and molecular surveillance for outbreak investigation, lineage monitoring, and future vaccine-matching studies. 
                      
Keywords: Aceh, cattle, foot-and-mouth disease virus, Ind-2001e, molecular epidemiology, phylogenetic analysis, serotype O, VP1 gene.