Molecular and mathematical modeling analyses of inter-island transmission of rabies into a previously rabies-free island in the Philippines

Rabies shows how scale of transmission can enable acute infections to persist at low prevalence

How acute pathogens persist and what curtails their epidemic growth in the absence of acquired immunity remains unknown. Canine rabies is a fatal zoonosis that circulates endemically at low prevalence among domestic dogs in low- and middle-income countries. We traced rabies transmission in a population of 50,000 dogs in Tanzania from 2002 to 2016 and applied individual-based models to these spatially resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. Although rabies prevalence never exceeded 0.15%, the best-fitting models demonstrated appreciable depletion of susceptible animals that occurred at local scales because of clusters of deaths and dogs already incubating infection. Individual variation in rabid dog behavior facilitated virus dispersal and cocirculation of virus lineages, enabling metapopulation persistence. These mechanisms have important implications for prediction and control of pathogens that circulate in spatially structured populations.

One Health Surveillance for Rabies: A Case Study of Integrated Bite Case Management in Albay Province, Philippines

Canine rabies is a significant public health concern and economic burden in the Philippines. Animal Bite Treatment Centers (ABTCs) that provide post-exposure prophylaxis (PEP) to bite patients have been established across the country, but the incidence of bite patient presentations has grown unsustainably, whilst rabies transmission in domestic dogs has not been controlled. Moreover, weak surveillance leads to low case detection and late outbreak responses. Here we investigated the potential for Integrated Bite Case Management (IBCM) to improve rabies detection in Albay province. Using information obtained from animal bite histories combined with phone follow-ups and field investigations, we demonstrated that IBCM resulted in a fourfold increase in case detection over 13 months of study compared to the prior period. Bite patient incidence across Albay was very high (>600/100,000 persons/year) with PEP administered mostly indiscriminately. Clinic attendance reflected availability of PEP and proximity to ABTCs rather than rabies incidence (<3% of patient presentations were from “probable” or confirmed rabies exposures) and is therefore not a suitable indicator of rabies burden. Further analysis of the IBCM data suggests that rabies transmission is mostly localized with focal cases from the previous month and current cases in neighbouring villages being most predictive of future rabies occurrence. We conclude that investigations of suspicious biting incidents identified through IBCM have potential to foster intersectoral relationships, and collaborative investments between public health and veterinary services, enabling the One Health ethos to be applied in a more sustainable and equitable way. Triage of patients and investigations of suspect dogs offer an effective tool for improved PEP provisioning and reduction of unnecessary expenditure, whilst targeted field investigations should lead to increased and earlier detection of rabid dogs. Given the enduring risk of re-introductions from neighbouring populations, enhanced surveillance is critical to achieving and maintaining rabies freedom.

Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review

BACKGROUND

Rabies is a fatal yet vaccine-preventable disease. In the last two decades, domestic dog populations have been shown to constitute the predominant reservoir of rabies in developing countries, causing 99% of human rabies cases. Despite substantial control efforts, dog rabies is still widely endemic and is spreading across previously rabies-free areas. Developing a detailed understanding of dog rabies dynamics and the impact of vaccination is essential to optimize existing control strategies and developing new ones. In this scoping review, we aimed at disentangling the respective contributions of mathematical models and phylodynamic approaches to advancing the understanding of rabies dynamics and control in domestic dog populations. We also addressed the methodological limitations of both approaches and the remaining issues related to studying rabies spread and how this could be applied to rabies control.

METHODOLOGY/PRINCIPAL FINDINGS

We reviewed how mathematical modelling of disease dynamics and phylodynamics have been developed and used to characterize dog rabies dynamics and control. Through a detailed search of the PubMed, Web of Science, and Scopus databases, we identified a total of n = 59 relevant studies using mathematical models (n = 30), phylodynamic inference (n = 22) and interdisciplinary approaches (n = 7). We found that despite often relying on scarce rabies epidemiological data, mathematical models investigated multiple aspects of rabies dynamics and control. These models confirmed the overwhelming efficacy of massive dog vaccination campaigns in all settings and unraveled the role of dog population structure and frequent introductions in dog rabies maintenance. Phylodynamic approaches successfully disentangled the evolutionary and environmental determinants of rabies dispersal and consistently reported support for the role of reintroduction events and human-mediated transportation over long distances in the maintenance of rabies in endemic areas. Potential biases in data collection still need to be properly accounted for in most of these analyses. Finally, interdisciplinary studies were determined to provide the most comprehensive assessments through hypothesis generation and testing. They also represent new avenues, especially concerning the reconstruction of local transmission chains or clusters through data integration.

CONCLUSIONS/SIGNIFICANCE

Despite advances in rabies knowledge, substantial uncertainty remains regarding the mechanisms of local spread, the role of wildlife in dog rabies maintenance, and the impact of community behavior on the efficacy of control strategies including vaccination of dogs. Future integrative approaches that use phylodynamic analyses and mechanistic models within a single framework could take full advantage of not only viral sequences but also additional epidemiological information as well as dog ecology data to refine our understanding of rabies spread and control. This would represent a significant improvement on past studies and a promising opportunity for canine rabies research in the frame of the One Health concept that aims to achieve better public health outcomes through cross-sector collaboration.

Genome-based local dynamics of canine rabies virus epidemiology, transmission, and evolution in Davao City, Philippines, 2018-2019

Rabies is a fatal zoonotic and neglected tropical disease caused by the rabies virus (RABV) and is associated with neuronal dysfunction and death, with dogs as the predominant carrier. The Philippines plans to eradicate rabies by 2022, but this is challenged with sub-optimal coverage of vaccination programs coupled with sustained transmission chains, making it unable to eradicate the disease. We investigated the dynamics of canine rabies in the highly urbanized Davao City of the Philippines and its neighboring localities by assessing genetic relationships, transmission patterns, selection pressure, and recombination events using the whole genome sequence of 49 RABV cases from June 2018 to May 2019, majority of which (46%) were from the district of Talomo, Davao City. Although phylogeographic clustering was observed, local variants also exhibited genetic sub-lineages. Phylogenetic and spatial transmission analysis provided evidence for intra- and inter-city transmission predominantly through the Talomo district of Davao City. Around 84% of the cases were owned dogs, but the genetic similiarity of RABVs from stray and owned dogs further alluded to the role of the former as transmission vectors. The high rate of improper vaccination among the affected dogs (80%) was also a likely contributor to transmission. The RABV population under Investigation is generally under strong purifying selection with no evidence of vaccine evasion due to the genetic homogeneity of viruses from vaccinated and improperly vaccinated dogs. However, some homologous recombination (HR) events were identified along the G and L genes, also predominantly associated with viruses from Talomo. The complementary findings on epidemiology, transmission, and recombination for Talomo suggest that high incidence areas can be seeds for virus dispersal and evolution. We recommend further Investigations on the possibility of HR in future large-scale genome studies. Finally, districts associated with these phenomena can be targeted for evidence-based local strategies that can help break RABV transmission chains and prevent emergence of novel strains in Davao City.

Modeling transmission dynamics of rabies in Nepal

Even though vaccines against rabies are available, rabies still remains a burden killing a significant number of humans as well as domestic and wild animals in many parts of the world, including Nepal. In this study, we develop a mathematical model to describe transmission dynamics of rabies in Nepal. In particular, an indirect interspecies transmission from jackals to humans through dogs, which is relevant to the context of Nepal, is one of the novel features of our model. Our model utilizes annual dog-bite data collected from Nepal for a decade long period, allowing us to reasonably estimate parameters related to rabies transmission in Nepal. Using our model, we calculated the basic reproduction number ( R 0 = 1.16 ) as well as intraspecies basic reproduction numbers of dogs ( R 0 D = 1.14 ) and jackals ( R 0 J = 0.07 ) for Nepal, and identified that the dog-related parameters are primary contributors to R 0 . Our results show that, along with dogs, jackals may also play an important role, albeit lesser extent, in the persistence of rabies in Nepal. Our model also suggests that control strategies may help reduce the prevalence significantly but the jackal vaccination may not be as effective as dog-related preventive strategies. To get deeper insight into the role of intraspecies and interspecies transmission between dog and jackal populations in the persistence of rabies, we also extended our model analysis into a wider parameter range. Interestingly, for some feasible parameters, even though rabies is theoretically controlled in each dog and jackal populations ( R 0 D < 1 , R 0 J < 1 ) if isolated, the rabies epidemic may still occur ( R 0 > 1 ) due to interspecies transmission. These results may be useful to design effective prevention and control strategies for mitigating rabies burden in Nepal and other parts of the world.

Towards the elimination of dog-mediated rabies: development and application of an evidence-based management tool

BACKGROUND

International organizations advocate for the elimination of dog-mediated rabies, but there is only limited guidance on interpreting surveillance data for managing elimination programmes. With the regional programme in Latin America approaching elimination of dog-mediated rabies, we aimed to develop a tool to evaluate the programme's performance and generate locally-tailored rabies control programme management guidance to overcome remaining obstacles.

METHODS

We developed and validated a robust algorithm to classify progress towards rabies elimination within sub-national administrative units, which we applied to surveillance data from Brazil and Mexico. The method combines criteria that are easy to understand, including logistic regression analysis of case detection time series, assessment of rabies virus variants, and of incursion risk. Subjecting the algorithm to robustness testing, we further employed simulated data sub-sampled at differing levels of case detection to assess the algorithm's performance and sensitivity to surveillance quality.

RESULTS

Our tool demonstrated clear epidemiological transitions in Mexico and Brazil: most states progressed rapidly towards elimination, but a few regressed due to incursions and control lapses. In 2015, dog-mediated rabies continued to circulate in the poorest states, with foci remaining in only 1 of 32 states in Mexico, and 2 of 27 in Brazil, posing incursion risks to the wider region. The classification tool was robust in determining epidemiological status irrespective of most levels of surveillance quality. In endemic settings, surveillance would need to detect less than 2.5% of all circulating cases to result in misclassification, whereas in settings where incursions become the main source of cases the threshold detection level for correct classification should not be less than 5%.

CONCLUSION

Our tool provides guidance on how to progress effectively towards elimination targets and tailor strategies to local epidemiological situations, while revealing insights into rabies dynamics. Post-campaign assessments of dog vaccination coverage in endemic states, and enhanced surveillance to verify and maintain freedom in states threatened by incursions were identified as priorities to catalyze progress towards elimination. Our finding suggests genomic surveillance should become increasingly valuable during the endgame for discriminating circulating variants and pinpointing sources of incursions.

A cointegration analysis of rabies cases and weather components in Davao City, Philippines from 2006 to 2017

Rabies is a lethal viral disease and dogs are the major disease reservoir in the Philippines. Spatio-temporal variations in environmental factors are known to affect disease dynamics. Some rabies-affected countries considered investigating the role of weather components in driving rabies cases and it has helped them to strategize their control efforts. In this study, cointegration analysis was conducted between the monthly reported rabies cases and the weather components, such as temperature and precipitation, to verify the effect of weather components on rabies incidence in Davao City, Philippines. With the Engle-Granger cointegration tests, we found that rabies cases are cointegrated into each of the weather components. It was further validated, using the Granger causality test, that each weather component predicts the rabies cases and not vice versa. Moreover, we performed the Johansen cointegration test to show that the weather components simultaneously affect the number of rabies cases, which allowed us to estimate a vector-error correction model for rabies incidence as a function of temperature and precipitation. Our analyses showed that canine rabies in Davao City was weather-sensitive, which implies that rabies incidence could be projected using established long-run relationship among reported rabies cases, temperature, and precipitation. This study also provides empirical evidence that can guide local health officials in formulating preventive strategies for rabies control and eradication based on weather patterns.

Zero human deaths from dog-mediated rabies by 2030: perspectives from quantitative and mathematical modelling

Dog-mediated rabies continues to kill tens of thousands of people every year in low- and middle-income countries despite being an entirely vaccine-preventable disease. WHO and partners have launched a global campaign to reach zero human deaths from dog-mediated rabies by 2030. The primary tools for reaching this target are mass dog vaccination to interrupt transmission in domestic dog populations that maintain infection, appropriate post-exposure prophylaxis (PEP) for rabies-exposed persons to prevent the fatal onset of disease, together with education to support their effective uptake. Models have been developed to assess the feasibility, impact and cost-effectiveness of these measures. From these models, we argue that the 2030 target of zero human rabies deaths is achievable, but will require concerted effort, engagement and investment. A proposed Gavi investment in human rabies vaccines has potential to drive progress towards the 2030 target; however, concomitant investment is needed to scale up mass dog vaccination or this target will be missed. Predicted economic benefits of mass dog vaccination vary according to national PEP provisioning and healthcare access. Integrated Bite Case Management can enhance surveillance and rationalize PEP use, but needs adapting to and integrating within local health systems and international reporting systems to improve PEP accountability, monitor impacts and support verification of disease freedom. Modelling approaches need refining to project realistic and geographically specific timelines for achieving targets. Model iterations informed by data on the implementation of interventions can be used to evaluate progress and guide future strategies. Critically such models are needed to advocate for investment, since the greatest risk to the ‘Zero by 30’ strategy is the limited long-term cross-sectoral or targeted financing to support countries to deliver and sustain mass dog vaccination.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Zero human deaths from dog-mediated rabies by 2030: perspectives from quantitative and mathematical modelling

Dog-mediated rabies continues to kill tens of thousands of people every year in low- and middle-income countries despite being an entirely vaccine-preventable disease. WHO and partners have launched a global campaign to reach zero human deaths from dog-mediated rabies by 2030. The primary tools for reaching this target are mass dog vaccination to interrupt transmission in domestic dog populations that maintain infection, appropriate post-exposure prophylaxis (PEP) for rabies-exposed persons to prevent the fatal onset of disease, together with education to support their effective uptake. Models have been developed to assess the feasibility, impact and cost-effectiveness of these measures. From these models, we argue that the 2030 target of zero human rabies deaths is achievable, but will require concerted effort, engagement and investment. A proposed Gavi investment in human rabies vaccines has potential to drive progress towards the 2030 target; however, concomitant investment is needed to scale up mass dog vaccination or this target will be missed. Predicted economic benefits of mass dog vaccination vary according to national PEP provisioning and healthcare access. Integrated Bite Case Management can enhance surveillance and rationalize PEP use, but needs adapting to and integrating within local health systems and international reporting systems to improve PEP accountability, monitor impacts and support verification of disease freedom. Modelling approaches need refining to project realistic and geographically specific timelines for achieving targets. Model iterations informed by data on the implementation of interventions can be used to evaluate progress and guide future strategies. Critically such models are needed to advocate for investment, since the greatest risk to the 'Zero by 30' strategy is the limited long-term cross-sectoral or targeted financing to support countries to deliver and sustain mass dog vaccination.

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

On the path to rabies elimination: The need for risk assessments to improve administration of post-exposure prophylaxis

BACKGROUND

Costs of rabies post-exposure prophylaxis (PEP) often remain high in regions where rabies has been controlled in dogs, presenting a challenge for sustaining rabies elimination programmes. We investigated the potential for bite patient risk assessments to improve PEP provision and surveillance in settings approaching elimination of dog-mediated rabies.

METHODS

We conducted a longitudinal study of patients presenting to animal bite treatment centres (ABTCs) on the island province of Bohol in the Philippines to investigate the health status of biting dogs and to quantify current expenditure on PEP.

RESULTS

Incidence of bite patients presenting to ABTCs was high (>300/100,000 persons/year) and increasing, resulting in substantial health provider costs. Over $142,000 was spent on PEP in 2013 for a population of 1.3 million. From follow up of 3820 bite patients we found that  >92% were bitten by healthy dogs (alive 14 days after the bite) and just 1.4% were bitten by probable or confirmed rabid dogs. The status of dogs that bit 6% of patients could not be determined. During the course of investigations of bites by suspect dogs, we were able to obtain samples for case confirmation, identify exposed persons who had not sought PEP as well as in-contact dogs at risk of developing rabies. We calculate that expenditure on PEP could at least be halved through more judicious approaches to provision of PEP, based on the histories of biting animals determined through risk assessments with bite patients.

CONCLUSIONS

We conclude that a One Health approach to surveillance based on Integrated Bite Case Management could improve the sustainability and effectiveness of rabies elimination programmes while also improving patient care by identifying those genuinely in need of lifesaving PEP.

One million dog vaccinations recorded on mHealth innovation used to direct teams in numerous rabies control campaigns

Background

Canine transmitted rabies kills an estimated 59,000 people annually, despite proven methods for elimination through mass dog vaccination. Challenges in directing and monitoring numerous remote vaccination teams across large geographic areas remain a significant barrier to the up-scaling of focal vaccination programmes to sub-national and national level. Smartphone technology (mHealth) is increasingly being used to enhance the coordination and efficiency of public health initiatives in developing countries, however examples of successful scaling beyond pilot implementation are rare. This study describes a smartphone app and website platform, “Mission Rabies App”, used to co-ordinate rabies control activities at project sites in four continents to vaccinate over one million dogs.

Methods

Mission Rabies App made it possible to not only gather relevant campaign data from the field, but also to direct vaccination teams systematically in near real-time. The display of user-allocated boundaries on Google maps within data collection forms enabled a project manager to define each team’s region of work, assess their output and assign subsequent areas to progressively vaccinate across a geographic area. This ability to monitor work and react to a rapidly changing situation has the potential to improve efficiency and coverage achieved, compared to regular project management structures, as well as enhancing capacity for data review and analysis from remote areas. The ability to plot the location of every vaccine administered facilitated engagement with stakeholders through transparent reporting, and has the potential to motivate politicians to support such activities.

Results

Since the system launched in September 2014, over 1.5 million data entries have been made to record dog vaccinations, rabies education classes and field surveys in 16 countries. Use of the system has increased year-on-year with adoption for mass dog vaccination campaigns at the India state level in Goa and national level in Haiti.

Conclusions

Innovative approaches to rapidly scale mass dog vaccination programmes in a sustained and systematic fashion are urgently needed to achieve the WHO, OIE and FAO goal to eliminate canine-transmitted human deaths by 2030. The Mission Rabies App is an mHealth innovation which greatly reduces the logistical and managerial barriers to implementing large scale rabies control activities. Free access to the platform aims to support pilot campaigns to better structure and report on proof-of-concept initiatives, clearly presenting outcomes and opportunities for expansion. The functionalities of the Mission Rabies App may also be beneficial to other infectious disease interventions.