Disease surveillance remains a challenge in the Philippines due to its limited resources. Integration of genomic-based surveillance in the National Rabies Control Program provides additional insights into rabies virus (RABV) evolution and transmission dynamics and can, therefore, inform public health decisions. This pilot study used the previously reported 49 RABV sequences in Davao City and some neighboring provinces to evaluate the utility of targeted sequencing as an inexpensive alternative to whole genome sequencing. We applied different tree distance metrics to compare RABV whole genome (WG) and individual RABV genes. Phylogenetic trees reconstructed using IQTree2 and BEAST were used to compare differences in phylogenetic signals, tree topology, and evolutionary patterns. There were no significant differences in the phylogenetic signals of the three major clades in the trees, with strong support values for sampling variance and underlying variances at the gene and site levels. A comparison of the Bayesian phylogenetic tree of WG and individual genes showed that there were no significant differences in the substitution rate and divergence time. Moreover, patristic distances (PDs) of all individual gene trees were positively correlated and congruent to the RABV WG of identical strains, with correlation values above 99%, which ruled out the possibility of missing out on relevant findings on evolutionary dynamics using only individual genes. Based on the results of our detailed genetic analyses, RNA-dependent RNA polymerase (L) and phosphoprotein (P) segments were identified as the best biomarkers to investigate the evolutionary analysis of locally circulating RABV variants in Davao City due to the close PDs of their trees relative to the WG. Less expensive options such as gene-based surveillance will enable the local government to trace and monitor the actual genetic diversity and spread of the virus, which could lead to the design and implementation of focused strategies.

Rabies is a neglected tropical disease that continues to be a public health threat despite the government’s intention to eliminate it by 2022. Specifically, Davao City has implemented the Intensified Rabies Control Program (IRCP), but animal rabies remains endemic, primarily due to canine transmission. Understanding the dynamics of rabies and its control is critical in formulating strategies to hasten disease eradication. This study utilized hotspot analysis on reported canine rabies cases in Davao City from 2005–2017 to determine the spatiotemporal behavior of the disease pre- and post-IRCP. Around 42% of the barangays have had at least one reported case of canine rabies, most of which were owned dogs (82.0%) and unvaccinated or non-updated vaccination (80.1%). Using the Getis-Ord statistic, five hotspot clusters were detected during pre-IRCP, which was reduced to three new clusters in post-IRCP – all of which were highly populated barangays (> 9,000 residents). The hotspot clusters shifted to neighboring areas with recurrent hotspot barangays located at the junction of this shift, suggesting spillover mediated by the hotspots. The number of rabies cases (mean per barangay of 0.797 pre-IRCP and 0.610 post-IRCP), proportion of affected barangays (33.5% pre-IRCP and 30.2% postIRCP), and rate of improper vaccination (mean per barangay of 31.8% pre-IRCP and 28.8% post-IRCP) did not significantly decrease post-IRCP, suggesting the need to boost the vaccination program and responsible pet ownership. There was no systematic geographical distribution of rabies control programs, hence prioritizing high-risk areas through hotspot analysis provides an efficient alternative to addressing the problem

Despite the control programs of the City Veterinarian’s Office (CVO), rabies is still geographically widespread across Davao City. Hence, a modified SEIV model incorporating different control strategies and adding population compartments focusing on reported rabies cases was formulated to understand dog rabies transmission dynamics. The model was fitted to the datasets of CVO from 2006–2020, such as the cumulative monthly positive rabies cases and the number of examined positive rabies samples in Talomo, Buhangin, and Poblacion districts. Results showed that the Talomo district had the highest rabies transmission rate but the lowest castration rate. On the other hand, the Poblacion district had the highest impounding rate and castration rate but the lowest birth and vaccination rate. Finally, the Buhangin district had the highest birth rate and vaccination rate but the lowest impounding rate and transmission rate. Sensitivity analysis (SA) was performed on over 10,000 samples of parameter space by the LHS method to obtain PRCC values. Results of the SA revealed that dog vaccination had a significantly strong influence among many interventions in mitigating rabies transmission – consistently in Talomo, Poblacion, and Buhangin districts. The results obtained in this study support the CVO’s ongoing mass canine rabies vaccination campaign in the city as a method of rabies control. Despite this, dog population control strategies (i.e. castration and impounding) must still be implemented in addition to intensifying vaccination strategy, as the birth rate also strongly contributes to increasing rabies transmission. Through the model and data fitting approaches, this study has provided information on the level of control measures implemented in three districts and can also be utilized to develop future rabies epidemiological models in Davao City and other locations.