Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.

Hervé Bourhy (1, 2) , Emmanuel Nakouné (3) , Matthew Hall (4, 5) , Pierre Nouvellet (5, 6) , Anthony Lepelletier (1, 2) , Chiraz Talbi (1, 2) , Laurence Watier (7) , Edward C Holmes (8) , Simon Cauchemez (5, 6, 9) , Philippe Lemey (10) , Christl A Donnelly (5, 6) , Andrew Rambaut (4, 11)

1 CC-OMS - Centre Collaborateur de l'OMS pour la Rage - Dynamique des lyssavirus et adaptation à l'hôte
2 CNR - Centre National de Référence de la Rage-Dynamique des Lyssavirus et adaptation à l'hôte
3 Institut Pasteur de Bangui
4 Edin. - University of Edinburgh
5 DIDE - Department of Infectious Disease Epidemiology [London]
6 Medical Research Council Centre for Outbreak Analysis and Modelling
7 B2PHI - Biostatistique, Biomathématique, Pharmacoépidémiologie et Maladies Infectieuses
8 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia,
9 Modélisation mathématique des maladies infectieuses
10 Department of Microbiology and Immunology
11 Fogarty International Center

The development of novel approaches that combine epidemiological and genomic data provides new opportunities to reveal the spatiotemporal dynamics of infectious diseases and determine the processes responsible for their spread and maintenance. Taking advantage of detailed epidemiological time series and viral sequence data from more than 20 years reported by the National Reference Centre for Rabies of Bangui, the capital city of Central African Republic, we used a combination of mathematical modeling and phylogenetic analysis to determine the spatiotemporal dynamics of rabies in domestic dogs as well as the frequency of extinction and introduction events in an African city. We show that although dog rabies virus (RABV) appears to be endemic in Bangui, its epidemiology is in fact shaped by the regular extinction of local chains of transmission coupled with the introduction of new lineages, generating successive waves of spread. Notably, the effective reproduction number during each wave was rarely above the critical value of 1, such that rabies is not self-sustaining in Bangui. In turn, this suggests that rabies at local geographic scales is driven by human-mediated dispersal of RABV among sparsely connected peri-urban and rural areas as opposed to dispersion in a relatively large homogenous urban dog population. This combined epidemiological and genomic approach enables development of a comprehensive framework for understanding disease persistence and informing control measures, indicating that control measures are probably best targeted towards areas neighbouring the city that appear as the source of frequent incursions seeding outbreaks in Bangui.

Domaines: Sciences du Vivant [q-bio]; Santé publique et épidémiologie

Hervé Bourhy, Emmanuel Nakouné, Matthew Hall, Pierre Nouvellet, Anthony Lepelletier, et al.. Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.. PLoS Pathogens, 2016, 12 (4), pp.e1005525. ⟨10.1371/journal.ppat.1005525.s001⟩. ⟨pasteur-01429570⟩