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

PLoS Pathogens

Andrew Rambaut¹  Anthony Lepelletier¹  Pierre Nouvellet¹  Philippe Lemey²  Simon Cauchemez³  Emmanuel Nakouné⁴  Edward C. Holmes⁵  Laurence Watier⁵  Hervé Bourhy⁵  Matthew Hall⁶  Christl A. Donnelly⁷  Chiraz Talbi⁸ 

[1] Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom;Faculté de Médecine Paris Ile de France-Ouest, Université de Versailles–Saint-Quentin, Versailles, France;INSERM, UMR 1181 and Institut Pasteur, B2PHI, Paris, France;Institut Pasteur de Bangui, Bangui, République Centrafricaine;Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France;Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom;Marie Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, Sydney, Australia;Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom

关键词: Dogs;    Rabies;    Rabies virus;    Infectious disease epidemiology;    Infectious disease control;    Phylogenetic analysis;    Sequence analysis;    Spatial epidemiology;   

DOI  :  10.1371/journal.ppat.1005525

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

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.

【 授权许可】

CC BY