Denis Fargette
Rivers and landscape ecology of a plant virus; Rice yellow mottle virus along the Niger Valley
A regular sampling of isolates of Rice yellow mottle virus (RYMV) along 500 km of the Niger Valley in the Republic of Niger was conducted and complemented by additional sampling in neighboring countries in West Africa and in Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework earlier applied to reconstruct the phylogeography in West Africa, East Africa and Madagascar. The spatial resolution along this section of the Niger River is the highest implemented for RYMV and possibly for a plant virus. We benefited from results of early field surveys of the disease for the validation of the phylogeographic reconstructions, and from the well documented history of rice cultivation along the Niger River for their interpretation. The role of the hydrographic network of the Niger Basin in RYMV spread was examined. Rice cultivated as floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from the south-west of the country where rice is increasingly grown. It was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometers, and led to the development of severe epidemics. There was no evidence of long distance dissemination through natural water. This study which concentrates detailed information on the virus, the disease and its hosts over the Middle Niger reveals links between river valleys, rice cultivation and virus spread not apparent at wider spatial scales. RYMV along the Niger River is an informative example of how river networks differentially shaped plant virus epidemiology.
Julien Thézé
Genomic epidemiology of Zika virus in the Americas
The use of next-generation sequencing technologies has revolutionized the study of viral infectious diseases. The possibility to generate, rapidly and accurately, full viral genomes combined with phylodynamic inference enables to analyse in more detail the dynamics of viral epidemics. To illustrate this, I will present in this talk the case study of the recent epidemic of Zika virus in the Americas. I will show our main findings on the timescale of the establishment and spread of the outbreak. I will also demonstrate that varying local environmental conditions for mosquito vectors along with human movements and herd immunity have driven spatial and temporal heterogeneities of Zika virus transmission in the Americas. This work highlights the importance of integrating epidemiological and ecological data to genetic-based findings, and vice-versa.
Gonché Danesh
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with ‘new’ and ‘classical’ hosts, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the ‘classical’ HCV epidemics and that its doubling time is ten times lower (0.44 years versus 4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.
Stéphane Guindon
Bayesian phylogeography along a continuum: sampling its way in a random walk
Statistical phylogeography provides useful tools to characterize and quantify the spread of organisms including, most notably, viral pathogens, during the course of evolution. In fact, geo-referenced genetic sequences convey signal about rates of migration and population densities. Yet, analysing these data rely on mathematical models that generally make simplifying assumptions about the way sequences were collected throughout space. We hereby show that violation of these assumptions may lead to serious overconfidence and bias in migration rates and population size estimates. A new approach based on recent advances in statistical computing is then described that is most suited to modelling data where sequences are preferentially collected at specific locations. We argue that this last situation applies when an epidemic is no longer under control, making our approach particularly relevant to the analysis of the most serious forms of viral pandemics.
Debapriyo Chakraborty
Phylodynamic investigation of control measures for the highly pathogenic avian influenza A H5N8 epidemic in France
Between November 2016 and March 2017, France experienced its largest and most devastating epidemic yet of the highly pathogenic avian influenza (HPAI; H5N8), which was concentrated in the large foie gras-growing region of the southwest. Using 196 viral genomes, we conducted a computationally-efficient, structured-coalescent-based phylodynamics analysis that combined viral genomic data with epidemiological data and allowed us to test specific hypothesis about control measures. We showed that the large- scale culling of ducks that was initiated in the region on 4 Jan. 2017 reduced the viral spread between départements (French administrative regions akin to Districts or Counties). We however did not find significant links between duck transport between farms and viral spread. Additionally, we showed that the virus was probably introduced only once into the region and thereafter it spread in short-distances from one département to the adjacent one, east to west. Lastly, we found that the number of infected farms and density of duck farms predicted the viral effective population size Ne. Many of our results agreed with or complimented findings of epidemiological modelling studies. Our methods also successfully investigated both the broad viral spread patterns and hypotheses related to specific control measures. These two facts together highlight the usefulness and versatility of our phylodynamics analysis, which can be adapted to investigate many other viral epidemics.