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.

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.

Rabies is an endemic disease in the Philippines. Addressing the disease at source, massive efforts towards dog vaccination and public awareness on rabies have been pursued by various Local Government Units (LGUs) in the country. While marked improvements have been seen, rabies continues to persist where it exists, largely owing to poor surveillance of the disease in animals and weak coordination between the human and animal health sectors. To bridge these critical gaps, the BAI-OIE STANDZ Rabies Project in the Philippines, together with the key rabies stakeholders in Bicol Region, developed the "Practical Inter-sectoral Linking"-an operational protocol and practical network of local key players (human health, animal health and LGUs) involved in rabies detection, reporting and implementation of appropriate interventions. It is initiated by recognized triggers such as detection of confirmed or probable rabies cases and is closely linked with early detection in animals, case investigation, quarantine, diagnosis, reporting and post-exposure prophylaxis. People down to the village level are informed about the routine, protocol and contact details of relevant people in responding to bite victims with the flowchart provided by the tool. This tool was initially rolled out in pilot provinces in the Bicol Region and to date has already documented success in initiating timely actions to 31 laboratory confirmed rabies cases being investigated, which actually saved 46 human lives upon further investigation. With this established at the LGU level, the goal to timely detect suspect or probable rabies cases and promptly implement appropriate interventions are expected to improve, while local officials are empowered with their roles as frontline workers in the prevention and control of rabies.

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.

Rabies is endemic in the Philippines. To support the rabies campaign in the Bicol region at the southeastern part of Luzon, the BAI-OIE Stop Transboundary Animal Diseases and Zoonoses (STANDZ) Rabies project was implemented in the pilot provinces of Camarines Norte, Camarines Sur, Albay, and Masbate. A community awareness survey was conducted with the residents of these provinces to determine their knowledge, attitude, and practices (KAP) on rabies during the start and end of the project. Qualitative, descriptive research was done with a structured KAP questionnaire. Pet owners in the pilot provinces were chosen as respondents. Results showed that respondents know that they can acquire rabies in animals through the bite of a rabid dog (pre-project implementation (PRI): 19.6%, post-project implementation (POI): 38.0%). Vaccination was the top rabies preventive measure (PRI: 61.8%, POI: 92.8%). Biting incidents were noted in some respondents, and observing the dog and killing it immediately were some of the actions taken by bite victims. If a supposed rabid dog was seen, respondents would either: immediately kill the dog (PRI: 20.3%, POI: 13.7%), report it to authorities (PRI: 26.3%, POI: 63.1%), and capture and observe the dog concerned (PRI: 13.5%, POI: 6.0%). Pet owners increased their KAP about rabies prevention and control as compared to the pre-implementation study. However, certain gaps in their KAP need to be given attention; thus continuous education of pet owners must be done.