Biology subjects

Vandenabeele, L.

Publications and source records attributed to Vandenabeele, L..

6 recordsLinked to original sources

bioRxiv2026

Small aberrant viral genomes induce the innate immune response to arenaviruses

Arenaviruses are a family of negative-sense RNA viruses mainly found in rodents in which they cause chronic asymptomatic infections. Some arenaviruses, however, can occasionally infect humans and cause pathogenic viral haemorrhagic fevers. These viral haemorrhagic fevers are associated with a massively dysregulated immune response characterized by excessive release of pro-inflammatory cytokines resulting in hyperinflammatory immunopathology. Here, we systematically characterize the immune response of human cells to a wide panel of mammalian arenaviruses and identify a clear distinction between New World viruses, which uniformly induce a robust interferon response, and Old World viruses, which do not induce any significant host response. This innate immune response is primarily driven by RIG-I-mediated RNA sensing and might be aided by differences in viral interferon antagonist expression patterns. Furthermore, we identified differences in quantity and type of non-standard viral genomes produced in unpassaged Old World and New World virus infections. Finally, we demonstrate that small non-standard viral RNA expression by New World viruses are key drivers of the innate immune response and might help explain how the host response can shape viral disease phenotypes and inform triage of patients.

microbiology↗

bioRxiv2026

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys)

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as sexual swindling. However, the rapid and substantial diversification of this genus, combined with its capacity for hybridisation and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each sub-genera. By combining phylogenetic network inference with introgression analyses based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.

evolutionary biology↗

bioRxiv2025

Hantavirus stability and inactivation

Hantaviruses are zoonotic viruses that can cause highly pathogenic disease, including hantavirus cardiopulmonary syndrome (HCPS) and haemorrhagic fever with renal syndrome (HFRS), in humans with case-fatality rates of up to 50%. However, our understanding of the basic viral life cycle and the underlying causes of viral pathogenesis remains sparse, in large part due to a lack of molecular biology tools for hantaviruses and the need to work in high-containment laboratory facilities with these viruses. Here, we investigated the kinetics of infectious Tula virus (TULV) particle production in Vero E6 cells and subsequent stability in cell culture media. In addition, we evaluated the stability of infectious virus particles in response to different physical and environmental stresses, including heat, freezing, dehydration and UV exposure, answering key questions about the environmental transmission potential of hantaviruses. Interestingly, we observed a remarkable stability of TULV when stored at room temperature or colder, as well as after dehydration, which suggests that hantaviruses could remain infectious for a sustained period of time after being secreted by their host species. Subsequently, we determined the ability of commonly used virus inactivation methods, including RNA and protein extraction buffers, to inactivate TULV both in a cell-free and cell-associated context and found that TULV was efficiently inactivated by all these methods similar to other enveloped RNA viruses. Finally, we successfully validated the complete inactivation using these inactivation methods using the highly pathogenic HCPS-causing New World Andes virus (ANDV) and the HFRS-causing Old World Hantaan virus (HTNV). These results provide valuable information about safe and effective inactivation methods of viral samples and about the environmental risk potential of hantaviruses. Author summaryHantaviruses are ubiquitous rodent viruses and contain some of the most lethal known zoonotic viruses, including Andes virus (ANDV) and Hantaan virus (HTNV), with no FDA-or EMA-approved antiviral treatment or prevention options available. However, studying the molecular biology and pathogenesis of these viruses is significantly impeded by the need for biosafety level (BSL) 3 (or higher) containment facilities for most hantaviruses and a general lack of molecular biology tools. Our study provides a comprehensive analysis of the stability of infectious hantavirus particles in response to different physical and chemical stresses. We demonstrate that a diverse range of hantaviruses are effectively and quickly inactivated by commonly used generic viral inactivation methods. However, we also provide evidence for an inherent stability under environmental conditions that could enable prolonged transmission potential of hantaviruses, even after secretion from their host species. These data are essential information to design safe inactivation methods of infectious hantavirus material and offers insights into the environmental risks of hantavirus infections with implications for laboratory safety and public health measures.

microbiology↗

bioRxiv2024

Generation of antigen-specific paired heavy-light chain antibody sequences using large language models

The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize existing antibodies and generate antibody sequences in a target-agnostic manner. In this work, we present MAGE (Monoclonal Antibody GEnerator), a sequence-based Protein Language Model (PLM) fine-tuned for the task of generating paired human variable heavy and light chain antibody sequences against targets of interest. We show that MAGE can generate novel and diverse antibody sequences with experimentally validated binding specificity against SARS-CoV-2, an emerging avian influenza H5N1, and respiratory syncytial virus A (RSV-A). MAGE represents a first-in-class model capable of designing human antibodies against multiple targets with no starting template.

bioinformatics↗

bioRxiv2024

Contrasting patterns of differentiation among three taxa of the rapidly diversifying orchid genus Ophrys sect. Insectifera (Orchidaceae) where their range overlap

In rapidly diversifying groups, taxa defined on the basis of typological criteria can be difficult to support with genetic data. The diversity observed in the insect-mimicking orchid genus Ophrys perfectly illustrates this situation; among 400 described species only 9-10 lineages are detectable by genetic markers such as nrITS. The three taxa described in the Ophrys insectifera group: O. insectifera, O. subinsectifera and O. aymoninii, can be clearly distinguished by their flowers, which have evolved different phenotypes as a result of adaptation to specific pollinator insect species from three different families. However, genetic differentiation between these three taxa has never been really supported by population genetic data and their taxonomic status is still debated. Using population genomic approaches, we found a clustering consistent with the existence of three genetic entities where the geographic distributions of the three taxa overlap. Two of these clusters correspond to France populations of the widespread O. insectifera and the micro-endemic O. aymoninii. However, the last cluster grouped together all the Iberian individuals, suggesting that individuals phenotypically identified as either O. insectifera or O. subinsectifera are genetically weakly differentiated there. Populations of the two pairs of taxa thus may have experienced different patterns of inter-specific gene flow.

evolutionary biology↗

bioRxiv2024

Neutralisation sensitivity of the SARS-CoV-2 BA.2.87.1 variant

Against the backdrop of the rapid global takeover and dominance of BA.1/BA.2 and subsequently BA.2.86 lineages, the emergence of a highly divergent SARS-CoV-2 variant warrants characterization and close monitoring. Recently, another such BA.2 descendent, designated BA.2.87.1, was detected in South Africa. Here, we show using spike-pseudotyped viruses that BA.2.87.1 is less resistant to neutralisation by prevailing antibody responses in Sweden than other currently circulating variants such as JN.1. Further we show that a monovalent XBB.1.5-adapted booster enhanced neutralising antibody titers to BA.2.87.1 by almost 4-fold. While BA.2.87.1 may not outcompete other currently-circulating lineages, the repeated emergence and transmission of highly diverged variants suggests that another large antigenic shift, similar to the replacement by Omicron, may be likely in the future.

immunology↗