On September 15 2021 by Dan Schar
Antibiotic-resistant bacteria are on the rise globally, threatening animal and human health. The aquaculture and fisheries industry is experiencing rapid growth–with aquatic animals now the fastest growing food animal sector globally. Yet, antimicrobial resistance (AMR) in aquatic animals destined for human consumption is seldom documented, limiting the application of targeted interventions. Addressing this gap, we reviewed current evidence on AMR in farmed and wild-caught aquatic food animals over two decades in Asia, the world’s most productive aquaculture and fisheries region. Read more...
On July 22 2021 by Simon Dellicour
Understanding the causes and consequences of the emergence of SARS-CoV-2 variants of concern is crucial to pandemic control yet difficult to achieve, as they arise in the context of variable human behaviour and immunity. We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analysing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B. Read more...
On June 30 2021 by Simon Dellicour
Following the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting late summer. Although it appears clear that travel had a significant impact on the circulation of the virus, it remains challenging to assess how it may have restructured and reignited the epidemic in the different European countries. In our new study published in Nature, we built a phylogeographic model to assess how newly introduced viral lineages, as opposed to persisting ones, contributed to the resurgence of COVID-19 in Europe. Read more...
On June 15 2021 by Simon Dellicour
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 measures. However, this type of analysis is often not possible because of the lack of spatially-explicit health data and spatial uncertainties associated with infection. Read more...
On June 01 2021 by Simon Dellicour & Guy Baele
The continuing accumulation of SARS-CoV-2 infections across the world continues to pose a significant threat to public health, with the different variants of concern (VOCs) being the primary focus, especially those that originated in South Africa (lineage B.1.351) and Brazil (lineage P.1) due to their potential of escaping vaccine-induced immunity, a pressing concern now that vaccination campaigns are being deployed around the world. Additionally, many countries are trying to avoid or control a next wave of infections by maintaining public health measures (including social distancing and partial or complete lockdowns) to avoid flooding hospitals with patients and to keep medical care facilities from collapsing. Read more...
On May 26 2021 by Simon Dellicour
Our new study on the dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City has been published in PLoS Pathogens. In this study, we performed phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak, during which the city rapidly became the epicenter of the pandemic in the United States. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. Read more...
On September 21 2020 by Simon Dellicour
Our new study on landscape phylogeography has been accepted for publication in Nature Communications. In this study, we illustrate how phylogeographic and phylodynamic and analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. In our new study, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. Read more...
On June 16 2020 by Simon Dellicour
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on Belgium, one of the countries with the highest spatial density of sequenced SARS-CoV-2 genomes. Read more...
On April 19 2020 by Simon Dellicour & Marius Gilbert
The Spatial Epidemiology Lab is actively involved in several real-time analyses dedicated to the COVID-19 epidemic in Belgium. Here is an overview of ongoing analyses and preliminary results. All the scripts written and used to perform these analyses are available on the following GitHub repo. Please note that the content of this page (and GitHub repo) will be regularly updated to rapidly share updated or new results. Spatial analyses are performed in collaboration with the research teams of Catherine Linard (UNamur), Sophie Vanwambeke (UCL), and Niel Hens (UHasselt), and phylogenetic analyses are performed in collaboration with the research teams of Piet Maes and Guy Baele from the Rega Institute (KU Leuven), as well as the teams of Marie-Pierre Hayette, Vincent Bours and Keith Durkin (ULiège). Read more...
On April 17 2020 by Simon Dellicour
Our new study on the dispersal dynamics and ecological drivers of the African swine fever outbreak in Belgium has been accepted for publication in Journal of Applied Ecology. In this study, we present and apply a novel analytical framework that uses occurrence data to investigate the impact of environmental factors on the wavefront progression of epidemics and biological invasions.
African swine fever is a devastating disease of domestic pigs and wild boars caused by African swine fever virus (ASFV). Read more...