Complete genome analysis of African swine fever virus strains in Thailand

African Swine Fever Virus (ASFV) is a large double-stranded DNA virus responsible for the highly contagious and lethal African Swine Fever (ASF), affecting the global porcine industry. The virus has a genome length of 170-194 kb and is broadly categorized into the left variable region (LVR), the right variable region (RVR), and the central conserved region (CCR). In Thailand, ASF was officially confirmed in January 2022 and identified as genotype II, which is primarily responsible for the current Eurasian swine pandemic. To date, due to the absence of a globally accepted vaccine against ASFV, culling and quarantine remain the primary control strategies. This highlights the importance of genomic surveillance to understand viral evolution, strain diversity, and the potential emergence of novel variants. Therefore, this study aims to classify and investigate the genomic diversity and evolutionary relationships of ASFV strains from outbreaks in Thailand. In this study, the genomic data from 2 Thai ASFV isolates, retrieved from the National Institute of Animal Health (NIAH), were used and aligned with 175 complete genotype II genomes from Asia and Europe for comparative analysis. The study reveals that the Thai isolates, namely TH_21/RB1 and TH_21/RB2, were classified as genotype II, serogroup 8, IGR-II, and CVR-I. The isolates share over 99.9% nucleotide similarity with both the reference Georgia 2007/1 strain and Thailand’s first characterized strain, TH1_22/CR. Bayesian phylogenetic analysis placed the Thai isolates within the clade I.2.1.2, with substitution rates estimated at approximately 1 × 10-5 substitutions/site/year, as observed in the TH_21/RB2 isolate. Mutation analysis identified a total of 6 unique variation events across the isolates, comprising both synonymous and non-synonymous mutations, indicating that the Thai isolates are genetically diverse on a molecular level. MGF 110-4L, a member of the MGF 110 family, exhibited up to 3 variations in the TH_21/RB2 isolate, highlighting it as a mutational hotspot consistent with observations from other genomes analyzed in this study. Additionally, three potential molecular signatures were detected across the isolates, suggesting a common geographic origin and co-circulation of closely related variants within the country. These findings contribute to ongoing efforts in ASFV molecular surveillance and provide a genomic baseline for future outbreak investigations.