by Alezandra Patriz Aragon (Fosmid)
Photo from The Pirbright Institute
African Swine Fever (ASF), a highly contagious and deadly disease affecting pigs, continues to pose a serious threat to the Philippines. Since its first detection in 2019, ASF has spread rapidly, prompting scientists to improve detection, monitoring, and control through genome analysis.
Understanding the African Swine Fever
ASF is caused by a large, double-stranded DNA virus from the Asfarviridae family. While it does not infect humans, its proliferation is devastating to both farm and wild pig populations. The virus spreads through direct and indirect contact with infected pigs via their fluids, contaminated tools, vehicles, feed, and even farm workers. Biggest contributors to this outbreak include swill feeding and illegal movement of pigs and pork products. Studies have also identified poor farm biosecurity and lack of awareness among locals also hindered the containment of the virus.
Impact of ASF in the Philippines
ASF was first confirmed in Rizal province in 2019. Since then, ASF has spread to multiple provinces, leading to the culling of over 300,000 pigs and a 20.8% decrease in the pig population by 2021. The outbreak caused economic losses, exceeding PHP 100 billion, which caused the surge in pork prices. As of December 2024, active ASF cases were reported in 21 provinces.
Enhancing ASF Surveillance with Genome Technology
The Philippines relies on PCR-based testing for ASF detection. While accurate, this method is costly and labor-intensive. To address these limitations and improve rapid detection, the Department of Agriculture has supported the development of a Nanogold Biosensor test kit. This tool uses loop-mediated isothermal amplification (LAMP) and nanotechnology, offering a quicker and more cost-efficient way to screen samples at border points.
Beyond detection, controlling the spread of ASF requires a deeper understanding on the mechanism of how the virus spreads and evolves. This is where molecular characterization and whole-genome sequencing of local African swine fever virus (ASFV) strains come in. These methods help map where and how different strains emerge, supporting better outbreak management. Through molecular tools, scientists can assess the transmissibility of the virus and potential changes in virus behavior.
New Insights from Recent ASFV Genome Studies
As an initiative to contribute to global ASF knowledge and monitoring, researchers have begun sequencing the local ASFV and uploaded their results in online public databases. For instance, Montecillo et al. (2025) examined ten ASFV strains collected from outbreaks in various provinces in the Philippines between 2021 and 2023. The team utilized a multi-gene-based approach to analyze several key genetic regions known for their role in determining the virus’ phylogenetic relationships, transmission pattern, and virulence.
To investigate the genetic characteristics of ASFV strains circulating in the Philippines, suspected ASF outbreak samples from various regions were collected. Viral DNA was isolated and verified using quantitative PCR. The researchers used a modified tiled amplicon sequencing strategy with Oxford Nanopore technology to generate high-coverage, coding-complete viral genomes. Subsequent genome assembly and annotation were performed using established bioinformatics pipelines, referencing the ASFV Georgia 2007/1 strain to facilitate comparative genomic analysis and variant identification. The Georgia 2007/1 reference strain is a well-documented ASFV strain from the 2007 outbreak in Georgia.
The study outlined the following key findings:
- The strains were discovered to match important genetic markers with the Georgia 2007/1 reference strain.
- While most regions remained conserved, minor variations were found in intergenic regions, including a novel C-to-T substitution in 2023 strains from Negros Occidental and Mindoro Oriental, suggesting a potential link.
- A 2022 Bataan strain showed a 1.9 kb deletion in the genes, which are thought to help the virus replicate in specific cells including macrophages. Despite this genetic change, the virus’s virulence was not affected.
- Overall, there were no indications of genotype I recombination and the strains remained closely related to Georgia 2007/1, underscoring the importance of genome analysis in tracking viral evolution, improving surveillance, and combating emerging ASFV variants in the country.
Genome Analysis: A Vital Tool in Strengthening ASF Control Efforts
Genome analysis is a key tool in enhancing ASF surveillance in the Philippines. By studying the ASFV genome, researchers can track strains and their spread, helping to monitor the virus' evolution and design containment strategies. These insights are crucial for surveillance strategies, vaccine development, and improving disease control efforts.
SOURCES
Department of Agriculture, Environment and Rural Affairs. (n.d.). African swine fever. https://www.daera-ni.gov.uk/articles/african-swine-fever
Fernandez-Colorado, C. P., Kim, W. H., Flores, R. A., & Min, W. (2024). African swine fever in the Philippines: A review on surveillance, prevention, and control strategies. Animals, 14(12), 1816. https://doi.org/10.3390/ani14121816
Hsu, C. H., Montenegro, M., & Perez, A. (2023). Space–time dynamics of African swine fever spread in the Philippines. Microorganisms, 11(6), 1492. https://doi.org/10.3390/microorganisms11061492
Lagare, J. (2025, January 4). ASF cases slightly up by end of December 2024 – BAI. Inquirer.net. https://business.inquirer.net/499781/asf-cases-slightly-up-by-end-of-december-2024-bai
Montecillo, A. D., Baybay, Z. K., Ferrer, J. B. C., Cariaso, W., Pantua, A., Jose, J. P., Madera, R., Shi, J., Doysabas, K. C., Dargantes, A., Dargantes, K. A. T., Boongaling, A. R. A., Manglicmot, A. P., Villegas, L. C., & Pantua, H. D. (2025). Genetic profiles of ten African swine fever virus strains from outbreaks in select provinces of Luzon, Visayas, and Mindanao, Philippines, between 2021 and 2023. Viruses, 17(4), 588. https://doi.org/10.3390/v17040588
U.S. Food and Drug Administration. (n.d.). African swine fever. U.S. Department of Health and Human Services. https://www.fda.gov/animal-veterinary/safety-health/african-swine-fever
This article was originally published in the GENEWS May 2025 Issue.
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