Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus

Understanding the role of humans in the dispersal of predominately animal pathogens is essential for their control. We used newly developed Bayesian phylogeographic methods to unravel the dynamics and determinants of the spread of dog rabies virus (RABV) in North Africa. Each of the countries studied exhibited largely disconnected spatial dynamics with major geo-political boundaries acting as barriers to gene flow. Road distances proved to be better predictors of the movement of dog RABV than accessibility or raw geographical distance, with occasional long distance and rapid spread within each of these countries. Using simulations that bridge phylodynamics and spatial epidemiology, we demonstrate that the contemporary viral distribution extends beyond that expected for RABV transmission in African dog populations. These results are strongly supportive of human-mediated dispersal, and demonstrate how an integrated phylogeographic approach will turn viral genetic data into a powerful asset for characterizing, predicting, and potentially controlling the spatial spread of pathogens

Genomic Diversity and Evolution of the Lyssaviruses

Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial genome sequences, particularly of the nucleoprotein and glycoprotein genes, with little consideration of genome-scale evolution. Herein, we report the first genomic and evolutionary analysis using complete genome sequences of all recognised lyssavirus genotypes, including 14 new complete genomes of field isolates from 6 genotypes and one genotype that is completely sequenced for the first time. In doing so we significantly increase the extent of genome sequence data available for these important viruses. Our analysis of these genome sequence data reveals that all lyssaviruses have the same genomic organization. A phylogenetic analysis reveals strong geographical structuring, with the greatest genetic diversity in Africa, and an independent origin for the two known genotypes that infect European bats. We also suggest that multiple genotypes may exist within the diversity of viruses currently classified as ‘Lagos Bat’. In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses

Rhabdovirus Matrix Protein Structures Reveal a Novel Mode of Self-Association

The matrix (M) proteins of rhabdoviruses are multifunctional proteins essential for virus maturation and budding that also regulate the expression of viral and host proteins. We have solved the structures of M from the vesicular stomatitis virus serotype New Jersey (genus: Vesiculovirus) and from Lagos bat virus (genus: Lyssavirus), revealing that both share a common fold despite sharing no identifiable sequence homology. Strikingly, in both structures a stretch of residues from the otherwise-disordered N terminus of a crystallographically adjacent molecule is observed binding to a hydrophobic cavity on the surface of the protein, thereby forming non-covalent linear polymers of M in the crystals. While the overall topology of the interaction is conserved between the two structures, the molecular details of the interactions are completely different. The observed interactions provide a compelling model for the flexible self-assembly of the matrix protein during virion morphogenesis and may also modulate interactions with host proteins

Evolution et dynamique de la rage canine en Afrique

La diversité génétique des lyssavirus trouve son expression dans la capacité à coloniser de nombreuses niches écologiques et de nouveaux hôtes. Pendant la diffusion épidémique, les virus à ARN capables d évoluer rapidement, accumulent des mutations informatives au niveau de leur génome, la diffusion spatiale laisse donc son empreinte sur le génome. La reconstruction de l histoire de la diffusion spatiale basée sur les séquences génomiques permet donc de comprendre la dynamique d évolution de l épidémie.Dans ce travail, on a étudié la diversité génétique des lyssavirus, par la suite, on s'est spécifiquement intéressé à étudier l évolution et la dynamique la rage canine en Afrique. L analyse phylogénique de 22 génomes complets confirme la séparation des lyssavirus en 7 génotypes. La comparaison basée sur la totalité du génome nous amène à proposer de nouveaux critères de définition d'un nouveau génotype. L étude des virus rabiques canins en Afrique montre qu ils sont associés à l émergence récente de deux lignées: Africa 1 et Africa 2 il y a moins de 200 ans. L analyse de la dynamique spatiale des RABV montre que le mouvement des populations virales entre les pays de l Afrique du Nord et les régions subsahariennes est absent. Cette diffusion est plutôt caractérisée par des mouvements de migrations selon un axe est-ouest en Afrique de l Ouest et du Nord. Ces investigations permettent de mieux comprendre la structuration génétique et géographique des populations des RABV canins ainsi que la dynamique de la rage chez les chiens domestiques ce qui est crucial pour déterminer des stratégies d élimination efficaces de la rage.Genetic diversity of lyssaviruses is reflected in the ability of lyssavirus to colonize numerous ecological niches and new hosts. During the epidemic spread, RNA viruses evolve rapidly and can accumulate informative mutations in their genome, the spatial diffusion therefore, leaves its imprint on the genome. Reconstructing the history of the spatial distribution based on genomic sequences can therefore help to understand the epidemiological dynamic evolution.In this work, we first studied the genetic diversity of lyssavirus, and then we specifically addressed the question of the evolution and dynamics of dog rabies viruses in Africa. The phylogenetic analysis of 22 complete genomes confirms the separation of lyssavirus in 7 genotypes. The comparison based on the whole genome leads us to propose new criteria for defining a new genotype. The study of dog rabies virus in Africa shows that they are associated with the emergence of tow lineages: Africa 1 and Africa 2 introduced into this region only recently (probably <200 years ago). Spatial Dynamic analysis revealed that there was no spread of rabies between the countries of northern Africa and those of the sub-Saharan region.This distribution is rather characterized by east to west spread across west and north Africa. These investigations provide insight into the genetic structure and geographical populations of dog RABV and the dynamics of rabies in domestic dogs, which is crucial to identify effective strategies for eliminating rabies.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Frontespizio

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

Screening and Characterization of RAPD Markers in Viscerotropic <i>Leishmania</i> Parasites

<div><p>Visceral leishmaniasis (VL) is mainly due to the <i>Leishmania donovani</i> complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL <i>Leishmania</i> parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 <i>L. donovani</i>, <i>L. archibaldi</i> and <i>L. infantum</i> strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between <i>L. infantum</i> and <i>L. donovani</i>. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents.</p></div