Research Article | 12 Apr 2026

Molecular identification and phylogenetic profiling of African swine fever virus in Indonesia during 2021–2025 based on the B646L (p72) gene

Muharam Saepulloh1 , Ni Luh Putu Indi Dharmayanti1 , Aswin Rafif Khairullah1 , Harimurti Nuradji1 , Wiwiek Tyasningsih2 , Atik Ratnawati1 , Mustofa Helmi Effendi3 , Indrawati Sendow1 , Budiastuti Budiastuti4 , Susanti Susanti1 , Dian Ayu Permatasari3 , and Saifur Rehman5 Show more
VETERINARY WORLD | pg no. 1437-1446 | Vol. 19, Issue 4 | DOI: 10.14202/vetworld.2026.1437-1446
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Abstract

          
Background and Aim: African swine fever (ASF) is a highly contagious and often fatal viral disease of domestic pigs caused by African swine fever virus (ASFV), posing a serious threat to global swine production and food security. Since the first confirmed outbreak in Indonesia in 2019, molecular data on circulating strains remain limited, limiting the ability to trace viral transmission and evaluate long-term epidemiological patterns. The B646L gene encoding the major capsid protein p72 is widely used for ASFV genotyping and phylogenetic analysis. This study aimed to detect ASFV circulation in Indonesia between 2021 and 2025 and to characterize its phylogenetic relationships using partial sequencing of the B646L (p72) gene.
Materials and Methods: A cross-sectional molecular surveillance study was conducted from 2021 to 2025 using samples collected from slaughterhouses and pig-producing areas in several provinces of Indonesia. A total of 272 EDTA blood and serum samples were obtained through routine surveillance and risk-based sampling. DNA was extracted and screened using conventional polymerase chain reaction (PCR) targeting the B646L (p72) gene with primer pairs PPA1/PPA2 (257 bp) for detection and P72-U/P72-D (478 bp) for sequencing. Positive amplicons were subjected to bidirectional Sanger sequencing. Sequences were aligned with global reference strains representing ASFV genotypes I–XXIV and analyzed using the Neighbor-Joining method with the Kimura 2-parameter + Gamma model and 1,000 bootstrap replicates.
Results: Seven samples (2.6%) tested positive for ASFV, with detections recorded in North Sumatra, East Nusa Tenggara, Jakarta, and the Medan abattoir. Both blood and serum samples produced clear diagnostic amplicons. All sequence-positive samples clustered within the Eurasian genotype II lineage and showed >99% nucleotide identity with Georgia-2007–derived strains circulating in Asia. Phylogenetic analysis based on partial B646L (p72) gene sequences demonstrated strong bootstrap support and revealed no evidence of divergent genotypes, novel variants, or additional lineage introductions, indicating genetic stability of ASFV circulating in Indonesia during the study period. 
Conclusion: The findings confirm that ASFV genotype II continues to circulate in Indonesia several years after the initial outbreak and show that the virus has entered an endemic phase marked by low-level yet persistent transmission. Partial sequencing of the B646L (p72) gene remains useful for identifying genotypes; however, expanded genomic surveillance is necessary for detailed transmission tracking. Enhancing routine molecular monitoring and integrating phylogenetic analysis into national surveillance programs will be crucial for improving early detection and supporting long-term ASF control strategies. 
          
Keywords: African swine fever virus, B646L gene, genotype II, Indonesia, molecular surveillance, p72 gene, phylogenetic analysis, swine disease.