Research Sophie Gryseels

Abstract

Hybridisation between wild species and their domestic counterparts poses a large risk for the wild population. It may lead to the introduction of deleterious alleles that have been artificially selected for in the domestic species and even lead to complete genetic swamping of the wild genotype, resulting in a de facto extinction of the wild species. Conversely, hybridisation may also result in the introduction of adaptive alleles that provide a fitness advantage in the wild species context. Contact between the two species may also lead to an exchange of viruses, which could have severe health and epidemiological consequences in a non-natural host. The European wildcat (Felis silvestris) lives in close contact with, and is subject to hybridisation and potential virus exchange with its domestic congener (Felis catus). Understanding the patterns and drivers of introgression between these two species and the role of virus exchange will be vital for informing conservation efforts of the wildcat. To investigate this, I will collect whole-genome sequencing data from wildcats and apply statistical genomic algorithms to identify regions of adaptive introgression and purifying selection. Furthermore, I will characterise viral genomes from wildcats and use phylodynamics to test for virus exchange between the two species. To accomplish these goals, I will set up a collaboration between labs at the University of Antwerp and University of Liège that specialise in these types of analyses.

Researcher(s)

• Promoter: Svardal Hannes
• Co-promoter: Gryseels Sophie
• Fellow: Meeus Michaël

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

The Congo basin is a biodiversity hotspot for various plant and animal taxa, but also for infectious diseases. Several zoonotic infections naturally circulate in the region and frequently emerge from wildlife reservoirs. Many of these are transmitted via arthropod vectors such as ticks. Domestic animals like dogs can relatively easily transport ticks and their infections from natural to human-dominated habitats. Tick-borne infections that normally circulate among wildlife thus have an important ecological potential to emerge in human populations. To be able to mitigate the risk of emergence of tick-borne infections, we identify two major needs in Tshopo province, Democratic Republic of Congo: (1) increased capacity of carrying out laboratory tests for the (early) detection, identification and characterization of zoonotic infectious diseases, and (2) increased awareness of the risks posed to both humans and domestic animals themselves by ticks infesting domestic animals. In this Short Initiatives project, we propose to leverage the past and ongoing research on biodiversity, zoonoses and tick ecology at the Centre de Surveillance de la Biodiversité of the University of Kisangani to (1) include the laboratory skills and capacity to detect and characterize zoonotic and tick-borne infections locally, and (2) to increase awareness and the capacity to mitigate tick-borne infections in the local communities. Our actor of change will be Steve Ngoy, an expert in tick ecology, biosafety procedures and mammal sampling. He will undergo extensive training at UAntwerp and KU Leuven to conduct advanced molecular laboratory assays on ticks collected from domestic animals. Additionally, he will work alongside master students to raise awareness of tick-borne infections in local communities and educate them on safe tick removal techniques, while increasing his collection of ticks from domestic animals. The laboratory skills will next be propagated to other researchers at CSB-UNIKIS through a local laboratory training workshop. Taken together, we foresee that this project will significantly contribute to the epidemic and pandemic preparedness in Tshopo, DRC.

Researcher(s)

• Promoter: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Arthropod borne viruses (arboviruses) rely on hematophagous arthropods as a vector for the transmission to a vertebrate host, either an animal or human. During enzootic transmission periods, arboviruses survive in sylvatic cycles using a variety of vertebrate species of which many are currently not identified. This project aims to gain more insight in the ecology and life cycle of these viruses and their vertebrate hosts. I will focus the research on the African continent, since several zoonotic viruses originated in West-, Central- and East Africa. I will mainly target small animal wildlife, such as rodents and bats, with the intention to determine their contribution to the persistence and spread of arboviruses. I hypothesize that these small, but high density and turnover rate, species are an important reservoir that supports sylvatic cycles during epizootic periods. These species often live in proximity to humans, creating spillover opportunities. To examine the hypotheses, I will screen wildlife samples across Africa and perform genetic analyses on the arboviral RNA. Additionally, host species, distribution ranges, phylogeographical relations and transmission models will be determined and created. The results will contribute to a better understanding of arbovirus occurrence and spread in wildlife, leading to an improved prediction, prevention, and control of arbovirus epidemics in wildlife and to a certain extent in humans.

Researcher(s)

• Promoter: Gryseels Sophie
• Fellow: De Kesel Wim

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Many important zoonotic viruses in humans such as Ebola, Zika and the HIV-precursors have emerged, and continue to do so, from Afrotropical mammals in the Congo basin. This region also holds one of the highest mammal diversities in the world, of which thousands of specimens are stored in the museum collections of RBINS, RMCA and CSB-UNIKIS. From the same region, KU Leuven stores thousands of archived pathology specimens of human origin. These are not just collections of mammal tissues and human biopsies: the genomic material of the viruses that these hosts had been carrying have been stored safely in these tissue collections as well. The main objective of the proposed project is to estimate the emergence potential of zoonotic viruses from the Afrotropics. We will do so through reconstructing virus evolutionary histories in relation to their hosts, based on virus genomic data generated from our tissue collections. We will test whether particular taxonomic or ecological groups of mammals hold a higher diversity of viruses, and/or viruses with higher cross-species emergence potential. This project connects a consortium of expert virologists, evolutionary biologists, phylogeneticists, museum curators and taxonomists. We believe that through working together, the proposed project will lead to ground-breaking new insights into the relationships between host taxonomy, host traits and the relative probabilities for different viruses to emerge in new host species – such as humans.

Researcher(s)

• Promoter: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

RNA viruses have a profound impact on human health and society. In particular, viruses that were previously unknown and that newly emerge in humans from an animal source can have catastrophic impact on the global human population. Virologists are well aware that most of the virus diversity that infects non-human animals is unknown to us, but the extent of the discrepancy between our assumed knowledge on RNA virus diversity and what remains to be discovered has recently become starkly clear through the characterization of relatives of well-known mammalian and human viruses – such as Influenza, Filoviruses, Coronaviruses – in very different vertebrate groups such as reptiles and fish. In this doctoral project, I propose for a PhD student to search for RNA viruses in sequence datasets both publicly available and that we generate ourselves using our extensive vertebrate sample collections. To accomplish this search efficiently, we will leverage on recent advances in sequencing technologies to optimize protocols for unbiased detection of diverse members of important virus families such as Arenaviridae, Coronaviridae, Hantaviridae, Paramyxoviridae, and Retroviridae, in archived animal specimens. We aim to demonstrate that (potentially divergent) relatives of known members of these common virus families also infect vertebrate phylogroups that are usually neglected in virus surveillance efforts. Using the novel vertebrate virus diversity data, we aim to update our understanding of the evolutionary histories of important virus families and test the "prisoner-of-war" hypothesis, that virus evolution over long evolutionary time-scales is directed by host adaptation, ultimately leading to the restriction of rates of viral evolution by the rate of evolution of their hosts. I expect this doctoral project to lead to four high impact manuscripts and will substantially improve our understanding of the drivers of evolutionary divergence and adaptation of RNA viruses.

Researcher(s)

• Promoter: Gryseels Sophie
• Fellow: Dharmadhikari Tanmay

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

OMEgA studies emerging zoonotic diseases in Afrotropical mammals by investigating the ecology of the infections and the evolutionary aspects of the diversity of the pathogens and their associated natural hosts. Our two main objectives are to (i) unravel how the phylogeography, evolutionary history and ecology of hosts can provide insights about the diversity, origin and distribution of these zoonotic pathogens; (ii) discern which ecological mechanisms and environmental changes (climate, landscape, biodiversity loss, …) may facilitate host switching of pathogens or maintain host specificity, even in the absence of a strong molecular barrier. To address these questions, we will use Next-generation sequencing (NGS) methods to screen specimens and tissues from museum collections as well as freshly collected material for the presence of pathogens, to verify the hosts' taxonomy, the phylogenetic and ecological relationships among host species, and the distribution ranges of genetically discrete host populations. The resulting information on the hosts' taxonomy, biology, the transmission ecology of reliably identified pathogens inferred from their presence, diversity, host specificity and evolution will allow us to answer the profiles' main objectives. These findings will not only increase our fundamental knowledge on parasites/pathogen diversity, but also address important One Health aspects as they will shed new light on the conditions that result in zoonotic pathogens switching hosts from wildlife humans. Crucially, our results will contribute towards a better understanding of the relative contributions of anthropogenic global changes (climate change, erosion of tropical forests, changing landscape and human activity patterns) to the emergence of novel zoonotic pathogens, some of which pose potential global health risks.

Researcher(s)

• Promoter: Leirs Herwig
• Fellow: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

In recent years there has been growing attention for scientific research on zoonotic and wildlife-borne pathogens, further accelerated by the current pandemic of the zoonotic virus SARS-CoV-2. Owing to a continuing series of successful third-party research grants, our Evolutionary Ecology research group has significantly expanded its research on zoonotic and wildlife pathogens, with a growing group of PhD students, postdocs and even ZAP working on these topics. At the same time, there are increasing expectations for biosafety measurements when processing tissue samples of wild animals, which should be processed under at least biosafety level 2. For these reasons, we currently lack sufficient infrastructure to process samples of our extensive and growing mammal specimen collection simultaneously for the various ongoing projects and under the required biosafety conditions; significantly hindering progress on our wildlife-pathogen research. We therefore request a bundle of equipment that together will increase the safety of our work procedures and significantly augment the throughput of wildlife samples we can process for detection and characterization of pathogens. The requested bundle is meant to expand our currently available infrastructure, and contains equipment to further outfit a newly renovated lab room dedicated for processing potentially infectious and/or contamination-prone samples (a biosafety cabinet, refrigerated centrifuge, thermoshaker), for storing newly collected samples and RNA extracts (an -80°C ultrafreezer), and to perform pathogen whole genome sequencing (a PCR cabinet, a Nanodrop). The resulting state-of-the art lab facilities will allow for successful continuation of the current 10+ infectious disease projects and will leverage the expanding Evolutionary Ecology group's leading expertise in zoonotic and wildlife pathogen research.

Researcher(s)

• Promoter: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Arthropod borne viruses (arboviruses) rely on hematophagous arthropods as a vector for the transmission to a vertebrate host, either an animal or human. During enzootic transmission periods, arboviruses survive in sylvatic cycles using a variety of vertebrate species of which many are currently not identified. This project aims to gain more insight in the ecology and life cycle of these viruses and their vertebrate hosts. I will focus the research on the African continent, since several zoonotic viruses originated in West-, Central- and East Africa. I will mainly target small animal wildlife, such as rodents and bats, with the intention to determine their contribution to the persistence and spread of arboviruses. I hypothesize that these small, but high density and turnover rate, species are an important reservoir that supports sylvatic cycles during epizootic periods. These species often live in proximity to humans, creating spillover opportunities. To examine the hypotheses, I will screen wildlife samples across Africa and perform genetic analyses on the arboviral RNA and antibodies . Additionally, host species, distribution ranges, phylogeographical relations and transmission models will be determined and created. The results will contribute to a better understanding of arbovirus occurrence and spread in wildlife, leading to a better prediction, control, prevention of arbovirus epidemics in humans.

Researcher(s)

• Promoter: Gryseels Sophie
• Fellow: De Kesel Wim

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Most research on the eco-epidemiology of bat-borne viruses is conducted on "one host–one virus" systems. Here, we propose to characterize patterns in the structure of the bat virome at the community level to go beyond the one host-one pathogen paradigm. This project aims to investigate the exchange of viruses between different species and families of bats, and livestock in East Africa by analyzing the structure and dynamic of viral communities in Tanzanian bat communities using a comparative metagenomic approach. We aim at examining the role of host community composition, roost type, and phylogeny in shaping viral diversity as well as identifying patterns in the structure of bat virome. We will also investigate the role of seasonal bat reproduction as a driver of viral community structure and further assess whether certain bat species and/or periods may be at higher risk for pathogen transmission. Besides, the exploration of potential silent circulation of bat-borne viruses in livestock will help to assess if spillovers of bat-borne viruses to other hosts are stochastic events or if the frequency of these events is underestimated. Together, these results will provide important elements for understanding patterns of viral diversity in bat communities and are expected to alter the general view of bat-borne disease ecology.

Researcher(s)

• Promoter: Leirs Herwig
• Co-promoter: Gryseels Sophie
• Fellow: Joffrin Léa

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

The evolutionary interactions of host-pathogen systems are a very interesting topic of fundamental biology, but also contribute to a better understanding of the ecology and epidemiology of infections. I will focus my research on Mopeia virus (MOPV), which is closely related to the dangerous human pathogen Lassa virus (LASV) and has the same rodent host, Mastomys natalensis. MOPV is not pathogenic to humans though, making research on this virus in natural populations of M. natalensis much more feasible. I am aiming to identify the basis of the MOPV-M. natalensis interaction, by performing infection experiments in a laboratory population of M. natalensis and by genotyping different strains of MOPV. After this, I will analyse the variability of these loci in host and virus genome in natural populations through time and space.

Researcher(s)

• Promoter: Leirs Herwig
• Co-promoter: Gouy de Bellocq Joëlle
• Fellow: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

The evolutionary interactions of host-pathogen systems are a very interesting topic of fundamental biology, but also contribute to a better understanding of the ecology and epidemiology of infections. I will focus my research on Mopeia virus (MOPV), which is closely related to the dangerous human pathogen Lassa virus (LASV) and has the same rodent host, Mastomys natalensis. MOPV is not pathogenic to humans though, making research on this virus in natural populations of M. natalensis much more feasible. I am aiming to identify the basis of the MOPV-M. natalensis interaction, by performing infection experiments in a laboratory population of M. natalensis and by genotyping different strains of MOPV. After this, I will analyse the variability of these loci in host and virus genome in natural populations through time and space.

Researcher(s)

• Promoter: Leirs Herwig
• Co-promoter: Gouy de Bellocq Joëlle
• Fellow: Gryseels Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project