Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies
Authors: Lushasi Kennedy , Brunker Kirstyn , Rajeev Malavika , Ferguson Elaine A , Jaswant Gurdeep , Baker Laurie , Biek Roman , Changalucha Joel , Cleaveland Sarah , Czupryna Anna , Fooks Anthony R , Govella Nicodemus , Haydon Daniel T , Johnson Paul , Kazwala Rudovick , Lembo Tiziana , Marston Denise , Masoud Msanif , Maziku Mathew , Mbunda Eberhard , Mchau Geofrey , Mohamed Ally Z , Mpolya Emmanuel , Ngeleja Chanasa , Ng’abhi Kija , Nonga Hesron , Omar Khasim , Rysava Kristyna , Sambo Maganga , Sikana Lwitiko , Steenson Rachel , Hampson Katie 
Published: November 2022

AbstractBackgroundDog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle.MethodsWe combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010-2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data we inferred transmission chains, estimated case detection and quantified the public health burden to evaluate these interventions.ResultsWe resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were highly cost-effective ($405 per death averted), their accessibility was limited and only dog vaccination interrupted transmission. A combined One Health approach rapidly eliminated rabies, was highly cost-effective ($1865 per death averted) and saved 20-120 families from rabid dog bites annually.ConclusionsA One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere.FundingWellcome [207569/Z/17/Z, 095787/Z/11/Z, 103270/Z/13/Z], the UBS Optimus Foundation, and the DELTAS Africa Initiative [Afrique One-ASPIRE/DEL-15-008] comprising a donor consortium of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), the New Partnership for Africa’s Development Planning and Coordinating (NEPAD) Agency, Wellcome [107753/A/15/Z] and the UK government. The rabies elimination demonstration project from 2010-2015 was supported by the Bill & Melinda Gates Foundation (OPP49679) and whole-genome sequencing was partially supported at APHA by Defra grant SE0421.