![]() ![]() Rabies virus can infect many mammalian species but has established sustained transmission cycles in only a few host species. It is important to not only identify the presence of rabies in a region but also to characterize the circulating variants, determine which host species are responsible for virus maintenance, and identify the geographic distribution of rabies across different regions and borders. As rabies elimination efforts progress, continued surveillance is necessary to determine the impact of control efforts, confirm canine rabies elimination, and promptly identify re-emergence. Good surveillance data are required to gain an accurate estimate of the rabies prevalence so resources can be allocated in the most effective way possible. Rabies surveillance using validated laboratory tests is a critical component of rabies control and elimination efforts. The absence of reliable surveillance data makes it challenging to estimate the rabies burden, procure funding and plan control strategies, and lack of data has been a major factor in the low prioritization of rabies in endemic countries. The number of rabid dogs and human rabies deaths is likely underreported in many canine rabies endemic countries. However, many countries with endemic canine rabies are in the early stages of planning control efforts and face barriers including limited understanding of rabies prevalence, logistical challenges, and competition for limited resources. The World Health Organization (WHO), the World Organization for Animal Health (OIE) and the Food and Agriculture Organization (FAO) have set a goal to eliminate dog-mediated human rabies deaths by 2030. Canine rabies has been effectively controlled and even eliminated in several countries through coordinated surveillance and canine vaccination campaigns. More than 99% of human rabies cases are caused by rabid dogs, and control of rabies in dogs can reduce human cases. Current estimates suggest over 59,000 people die of rabies each year across the world. The vast majority of human rabies deaths are caused by a virus in the species Rabies lyssavirus, commonly referred to as rabies virus. Rabies is a progressive, fatal encephalitis caused by members of 17 different viral species within the Lyssavirus genus of rhabdoviruses. Taken together, our evaluation highlights the MinION’s potential for low-cost, high volume sequencing of pathogens in locations with limited resources. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination.
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