Philippines’ unique RABV lineages found to have limited inter-island transmission

In particular, rabies continues to be a significant public concern in the Philippines, with over 200 human deaths reported yearly. A study published by Zhang et al. in 2025 investigated the epidemiology, evolution, and spread of the rabies virus (RABV) in the country to obtain significant insights for targeted control and prevention. [Mol Biol Evol. 2025;42(2):msaf007. Doi: 10.1093/molbev/msaf007]

The research involved collecting whole genomes of RABV from animal rabies cases between 2018 and 2022, targeting animals exhibiting abnormal behavior, clinical signs of rabies, or a history of biting. Brain tissues from 35,700 animals across seventeen regions were obtained, with 10,225 samples testing positive for rabies, dogs reportedly being the primary carriers. Positive brain tissue samples from different outbreaks in separate locations from this period were collected in FTA (Flinders Technology Associates) cards (specialized filter paper cards for stable storage and analysis of DNA and RNA for forensic and genetic studies) for RABV genome sequencing. From this, 353 complete rabies virus genomes were sequenced and analyzed.

Phylogenetic and spatial-temporal evolutionary analyses showed that RABV in the Philippines is part of the SEA4 subclade within the Asian clade and is unique in the world. This subclade is classified into three main geographically specific lineages: SEA4-L in Luzon, SEA4-V in Visayas, and SEA4-M in Mindanao. Rabies transmission occurs within these major island regions, with limited inter-island transmission, which may be due to ocean barriers. The few instances of inter-island transmission suggested that the movement of dogs by humans contributed to the spread of specific lineages of RABV among islands.

The study also looked at the temporal dynamics and spread of RABV. The average rate of nucleotide substitution was estimated, and the time to the most recent common ancestor (TMRCA) of the SEA4 subclade was determined to be between 1923 and 1956. Analysis of significant translocation pathways indicated that rabies primarily spreads within islands, with rare occurrences of inter-island transmission. 

Zhang et al. reviewed the several risk factors associated with rabies incidence. An elevated temperature and humidity create favorable conditions for rabies in dogs. Chiroptera richness correlated with increased RABV-positive rates, which suggested a potential role for bats in rabies transmission. A higher percentage of agricultural land and increased travel time to healthcare institutions suggested that rabies transmission in dogs may be higher in areas where assorted crops are planted, and the community has poor medical and health conditions.

The study supported previous work linking climatic conditions and access to healthcare with rabies spread. This emphasizes the need for continuous monitoring and updating genetic data to track new rabies virus variants. This ongoing surveillance is said to be important for effective public health responses and containment strategies as this enables researchers and public health officials to stay ahead of viral evolution. Given the limited spread of rabies between islands due to geographical barriers, Zhang et al. noted that implementing island-based rabies control strategies is a workable and potentially cost-saving approach. 

The Philippines’ archipelagic nature, with major islands separated by bodies of water, resulted in a distinct pattern of rabies transmission, with limited inter-island spread and a tendency for each island to have its dominant viral lineage. This geographical separation, Zhang et al. said, offers an opportunity for targeted, island-specific rabies control and elimination programs. By understanding the evolutionary dynamics and transmission patterns of RABV, public health authorities can develop more effective strategies to combat this deadly disease and progress to its eventual elimination.