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Introduction
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Publications
Publications (36)
Abstract The circulation of mammarenaviruses in rodent populations of the Mekong region has recently been established, with a genetic variant of Wēnzhōu virus, Cardamones virus, detected in two Rattus species. This study tests the potential teratogenic effects of Wēnzhōu infection on the development of a Murid rodent, Rattus exulans. Using direct v...
In the last two decades, two important avian influenza viruses infecting humans emerged in China, the highly pathogenic avian influenza (HPAI) H5N1 virus in the late nineties, and the low pathogenic avian influenza (LPAI) H7N9 virus in 2013. China is home to the largest population of chickens (4.83 billion) and ducks (0.694 billion), representing,...
The highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Asia since 2003 and diversified into several genetic lineages, or clades. Although the spatial distribution of its outbreaks was extensively studied, differences in clades were never previously taken into account. We developed models to quantify associations over time a...
In this study, we present a comprehensive analysis of the key spatial risk factors and predictive risk maps for HPAI infection in France, with a focus on the 2016–17 and 2020–21 epidemic waves. Our findings indicate that the most explanatory spatial predictor variables were related to fattening duck movements prior to the epidemic, which should be...
Since 2014, highly pathogenic avian influenza (HPAI) H5 viruses of clade 2.3.4.4 have been dominating the outbreaks across Europe, causing massive deaths among poultry and wild birds. However, the factors shaping these broad‐scale outbreak patterns, especially those related to waterbird community composition, remain unclear. In particular, we do no...
Driven by population growth and rising incomes, the demand for animal source foods in low and middle-income countries is increasing rapidly. Pork is one of the most commonly consumed animal-based food, with the highest demand being in China due to its largest population and changing dietary habits linked to increasing wealth. Here, we show the chan...
Background
The COVID-19 pandemic is affecting nations globally, but with an impact exhibiting significant spatial and temporal variation at the sub-national level. Identifying and disentangling the drivers of resulting hospitalisation incidence at the local scale is key to predict, mitigate and manage epidemic surges, but also to develop targeted m...
Various interventions for live poultry markets (LPMs) have emerged to control outbreaks of avian influenza A(H7N9) virus in mainland China since March 2013. We assessed the effectiveness of various LPM interventions in reducing transmission of H7N9 virus across 5 annual waves during 2013-2018, especially in the final wave. With the exception of wav...
Motivation:
The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences are geo-referenced at broad spatial scale...
In winter 2016–2017, Highly Pathogenic Avian Influenza (HPAI) H5N8 virus spread across Europe, causing unprecedented epizootics. France was massively affected, resulting in the culling of over 6 million poultry. Boosted regression tree (BRT) models were used to quantify the association between spatial risk factors and HPAI H5N8 infection in poultry...
Species distribution models (SDMs) have been increasingly used over the past decades to characterise the spatial distribution and the ecological niche of various taxa. Validating predicted species distribution is important, especially when producing broad-scale models (i.e. at continental or oceanic scale) based on limited and spatially aggregated...
Background:
The Avian Influenza A (H5N1) virus is endemic in poultry in Egypt. The winter of 2014/2015 was particularly worrying as new clusters of HPAI A (H5N1) virus emerged, leading to an important number of AI A (H5N1) outbreaks in poultry farms and sporadic human cases. To date, few studies have investigated the distribution of HPAI A (H5N1)...
Over the years, the emergence of novel H5 and H7 highly pathogenic avian influenza viruses (HPAI) has been taking place through two main mechanisms: first, the conversion of a low pathogenic into a highly pathogenic virus, and second, the reassortment between different genetic segments of low and highly pathogenic viruses already in circulation. We...
The fifth epidemic wave of avian influenza A(H7N9) virus in China during 2016-2017 demonstrated a geographic range expansion and caused more human cases than any previous wave. The factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry, and wetland variables on...
Technical Appendix. Additional information about the methods and databases used in study of 5 waves of influenza A(H7N9) infection in China.
In the last few years, several reassortant subtypes of highly pathogenic avian influenza viruses (HPAI H5Nx) have emerged in East Asia. These new viruses, mostly of subtype H5N1, H5N2, H5N6, and H5N8 belonging to clade 2.3.4.4, have been found in several Asian countries and have caused outbreaks in poultry in China, South Korea, and Vietnam. HPAI H...
The 5 th epidemic wave in 2016-2017 of avian influenza A(H7N9) virus in China caused more human cases than any previous waves but the factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry and wetland information and of market closures on all epidemic waves (1-...
p>BACKGROUND: The avian influenza A H7N9 virus has caused infections in human beings in China since 2013. A large epidemic in 2016-17 prompted concerns that the epidemiology of the virus might have changed, increasing the threat of a pandemic. We aimed to describe the epidemiological characteristics, clinical severity, and time-to-event distributio...
Suitability predictions for the HPAI H5N1 best model (GeoTiff format).DOI:
http://dx.doi.org/10.7554/eLife.19571.010
Suitability predictions for the H5Nx clade 2.3.4.4 best model (GeoTiff format).DOI:
http://dx.doi.org/10.7554/eLife.19571.011
R script implementing the cross validations (CV); namely, partition into geographic folds, running the BRT models with standard CV, standard CV accounting for the spatial sorting bias (SSB), and the spatial CV.
DOI:
http://dx.doi.org/10.7554/eLife.19571.017
Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global suitability model of highly pathogenic avian influenza (HPAI) H5N1 and demonstrate that reliable predictions can be obtained at global scale. Best predictions are obtained using spatial predictor variables des...
Forest, in particular deciduous forest, is a key element in determining areas with a high probability of tick presence. The way forest is generally monitored may be ill suited to some landscapes where Ixodes ricinus is found, as forest is usually characterised using crisp land cover classes. However, tree vegetation can be found outside of forests...
SUMMARY Leptospira interrogans, hantaviruses (particularly Seoul virus), hepatitis E virus (HEV), and Toxoplasma gondii are rat-associated zoonoses that are responsible for human morbidity and mortality worldwide. This study aimed to describe the infection patterns of these four pathogens in wild rats (Rattus norvegicus) across socioeconomic levels...