Biology subjects

De Coninck, L.

Publications and source records attributed to De Coninck, L..

10 recordsLinked to original sources

bioRxiv2026

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.

microbiology↗

bioRxiv2025

Strong selection of Gammaproteobacteria across Aedes aegypti development suggests diagonal microbiome transmission

BackgroundAedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti, we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing. ResultsWe observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria. Our data suggest that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as "diagonal transmission". Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adults. ConclusionThis study provided new data on the microbiome composition of field-collected Ae. aegypti, contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route.

microbiology↗

bioRxiv2025

Combinations of approved oral nucleoside analogues confer potent suppression of alphaviruses in vitro and in vivo

BackgroundAlphaviruses, including chikungunya virus (CHIKV), pose a significant global health threat, yet specific antiviral therapies remain unavailable. MethodsWe evaluated combinations of three oral directly acting antiviral drugs (sofosbuvir (SOF), molnupiravir (MPV), and favipiravir (FAV)), which are approved for other indications, against CHIKV, Semliki Forest virus (SFV), Sindbis virus (SINV), and Venezuelan Equine Encephalitis virus (VEEV) in vitro and in vivo. We assessed antiviral efficacy in human skin fibroblasts and liver cells, as well as in a mouse model of CHIKV-induced arthritis. FindingsIn human skin fibroblasts, synergistic antiviral effects were observed for combinations of MPV + SOF and FAV + SOF against CHIKV, and for FAV + SOF against SFV. In human liver cells, FAV + MPV conferred additive to synergistic activity against VEEV and SINV, while SOF synergized with FAV against SINV. In mice, MPV improved CHIKV-induced foot swelling and reduced systemic infectious virus titres. Combination treatment with MPV and SOF significantly reduced swelling and infectious virus titres compared to monotherapies of each drug. Sequencing of CHIKV RNA from joint tissue revealed that MPV caused dose- dependent increases in mutations in the CHIKV genome. Upon combination therapy of MPV with SOF, the number of mutations was significantly lower compared to monotherapy with several higher doses of MPV. InterpretationCombining these approved oral nucleoside analogues confers potent suppression of multiple alphaviruses in vitro and in vivo with enhanced control of viral genetic evolution in face of antiviral pressure. These drug combinations may ultimately lead to the development of potent combinations of pan-family alphavirus inhibitors. FundingThis work was supported by a PhD fellowship granted to S.V. by the Research Foundation - Flanders (FWO) (11D5923N). L.D.C. was also supported by Research Foundation - Flanders (FWO) PhD fellowship (11L1325N). Dr. Polyak and Schiffer are partially supported by R01AI121129. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSAlphaviruses such as chikungunya virus (CHIKV), Sindbis virus (SINV), and Venezuelan Equine Encephalitis virus (VEEV) are a major threat for global health. Alphaviruses are responsible for debilitating diseases with major public health implications, yet no antiviral drugs are currently approved for treating these virus infections. Existing treatment options are limited to supportive care and are unlikely to provide protection against future outbreaks of other alphaviruses. Previous studies have shown that oral approved nucleoside analogues such as favipiravir (FAV), molnupiravir (MPV), and sofosbuvir (SOF) have antiviral activity against certain RNA viruses, including alphaviruses. However, systematic in vivo evaluations of these drugs and testing of drug combinations in both in vitro and in vivo settings are limited. Added value of this studyThis study provides a comprehensive evaluation of combinations of FAV, MPV and SOF against multiple alphaviruses in two human cell lines and a CHIKV mouse model. We demonstrate that certain combinations of these drugs confer synergistic antiviral activity, effectively suppressing CHIKV, SFV, SINV, and VEEV replication in vitro. Moreover, in vivo, we show for the first time that MPV treatment results in reduced CHIKV-induced foot swelling and systemic virus replication. Combining MPV with SOF enhances antiviral activity in mice as compared to monotherapy. By sequencing the viral genome, we show that MPV increases the number of mutations in a dose-dependent manner. Combination therapy of MPV and SOF reduces the number of mutations compared to higher doses of MPV. These findings highlight the potential of nucleoside analogue combinations as a promising therapeutic strategy against alphavirus infections. Implications of all the available evidenceThe results of this study suggest that combination therapy with approved nucleoside analogues could provide an effective treatment strategy for alphavirus infections. The observed increased efficacy of drug combinations supports the potential for dose optimization to enhance efficacy while reducing toxicity and development of resistance. Future research should focus on clinical evaluation of these drug combinations, pharmacokinetic studies, and further exploration of their impact on viral evolution. Given the expanding geographical distribution of alphaviruses and the lack of available treatments, these findings provide a foundation for developing pan-alphavirus antiviral therapies that could improve patient outcomes and global outbreak preparedness.

microbiology↗

bioRxiv2024

Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of (RNA) viruses

Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy - hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A whole-genome shotgun sequencing approach was used to detect viral sequences in fifty-five pools of ten blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although, no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families, warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the hematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.

microbiology↗

bioRxiv2023

Metagenomic detection and genetic characterization of human sapovirus among children in Nigeria

Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six near-complete genome sequences and two partial genome sequences. Multiple SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1) and GI (GI.2 and GI.7). Sequence identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were confirmed in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria.

molecular biology↗

bioRxiv2023

Lack of abundant core virome in Culex mosquitoes from a temperate climate region despite a mosquito species-specific virome

In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some studies have indicated a core virome in mosquitoes consisting of mostly ISVs. Employing single mosquito metagenomics, we comprehensively profiled the virome of native and invasive mosquito species in Belgium. This approach allowed for accurate host species determination, prevalence assessment of viruses and Wolbachia, and the identification of novel viruses. Contrary to expectations, no abundant core virome was observed in Culex mosquitoes from Belgium. In that regard, we caution against rigidly defining mosquito core viromes and encourage nuanced interpretations of other studies. Nonetheless, our study identified 45 viruses of which 28 were novel, enriching our understanding of the mosquito virome and ISVs. We showed that the mosquito virome in this study is species-specific and less dependent on the location where mosquitoes from the same species reside. In addition, because Wolbachia has previously been observed to influence arbovirus transmission, we report the prevalence of Wolbachia in Belgian mosquitoes and the detection of several Wolbachia mobile genetic elements. The observed prevalence ranged from 83% to 92% in members from the Culex pipiens complex. ImportanceCulex pipiens mosquitoes are important vectors for arboviruses like West Nile virus and Usutu virus. Culex pipiens virome studies, and virome studies on mosquitoes from the Culex genus in general, are underrepresented in publications about the mosquito virome. To mitigate this, we sequenced the virome of 190 individual Culex and eight individual Aedes japonicus mosquitoes. We report the lack of a core virome in these mosquitoes from Belgium and caution the interpretation of other studies in this light. The discovery of new viruses in this study will aid our comprehension of ISVs and the mosquito virome in general in relation to mosquito physiology and mosquito population dynamics.

microbiology↗

bioRxiv2023

Belgian Culex pipiens pipiens are competent vectors for West Nile virus but not Usutu virus

BackgroundWest Nile virus (WNV) and Usutu virus (USUV) are emerging arboviruses in Europe transmitted by Culex mosquitoes. In Belgium, it is currently unknown which Culex species are competent vectors for WNV or USUV and if these mosquitoes carry Wolbachia, an endosymbiotic bacterium that can block arbovirus transmission. The aims of our study were to measure the vector competence of Belgian Culex mosquitoes to WNV and USUV and determine if a naturally acquired Wolbachia infection can influence virus transmission. Methodology/Principal FindingsWe captured 876 non-engorged female Culex mosquitoes from urban and peri-urban sites in Leuven, Belgium. We provided females with an infectious bloodmeal containing WNV lineage 2, USUV European (EU) lineage 3, or USUV African (AF) lineage 3. Blood-fed females (n=154) were incubated for 14 days at 25{degrees}C after which the body, head, and saliva were collected to measure infection (IR), dissemination (DR), and transmission (TR) rates, respectively. Mosquito species were identified by qRT-PCR or Sanger sequencing, the presence of infectious virus in mosquitoes was confirmed by plaque assays, and viral genome copies were quantified by qRT-PCR. We found that Culex pipiens pipiens were able to transmit WNV (11% IR, 40% DR, 100% TR) but not USUV (EU lineage: 13% IR, 0% DR; AF lineage: 16% IR, 17% DR, 0% TR). In contrast, Culex modestus was able to transmit USUV (AF lineage: 60% IR, 67% DR, 50% TR), but not WNV (0% IR). We found that the presence or absence of Wolbachia was species-dependent and did not associate with virus transmission. Conclusions/SignificanceThis is the first report that Belgian Culex mosquitoes can transmit both WNV and USUV, forewarning the risk of human transmission. More research is needed to understand the potential influence of Wolbachia on arbovirus transmission in Culex modestus mosquitoes. Author SummaryWest Nile virus and Usutu virus can cause seasonal epidemics in humans. They are maintained in a transmission cycle between wild birds and Culex mosquitoes, and humans that are bitten by infected mosquitoes can develop life-threatening neurological disease. Certain Culex species carry the symbiotic bacterium Wolbachia which can block virus transmission in mosquitoes. In Belgium, it is currently unknown which Culex species can transmit West Nile virus and/or Usutu virus, or if they carry Wolbachia bacteria. In our study, we captured wild mosquitoes from Belgium and infected them with West Nile virus or Usutu virus. We found that a common European species (Culex pipiens pipiens, the Northern House mosquito) could transmit West Nile virus, whereas a lesser known species (Culex modestus) could transmit Usutu virus. Wolbachia bacteria could be found in almost all Culex pipiens pipiens, but not in Culex modestus, suggesting that Wolbachia prevalence is species-specific. More research is needed to understand if Wolbachia can block virus transmission in Culex modestus. This is the first report on the ability of Culex mosquitoes to transmit West Nile virus and Usutu virus in Belgium, forewarning the risk of transmission to humans.

microbiology↗

bioRxiv2022

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on gut virome

Viruses are the most abundant components of the microbiome in human beings with a significant impact on health and disease. However, the impact of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analyzed. On the other hand, several studies suggested that not all antiretrovirals for treating HIV infection exert similar effects on the gut bacteriome, being the integrase strand transfers inhibitors (INSTIs) --first-choice treatment of naive HIV-infected patients nowadays-- those associated with a healthier gut. Thus, the aim of this study was to evaluate the effects of HIV infection and INSTIs in first line of treatment on gut virome composition. To accomplish this objective, 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and gut virome composition was analysed using shotgun sequencing. The results showed that bacteriophages are the most abundant and diverse viruses in the gut independent from the HIV-status and the use of treatment. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment (p<0.01 naive vs. control Richness index and p<0.05 naive vs. control Fishers alpha index). {beta}-diversity of phages revealed that samples from HIV-infected samples clustered separately from those belonging to the control group (padj<0.01 naive vs. control and padj<0.05 INSTIs vs. control). However, it is worth mentioning that samples coming from INSTIs-treated patients were more grouped than those from naive patients. Differential abundant analysis of phages showed an increase of Caudoviricetes class in the naive group compared to control the group (padj<0.05) and a decrease of Malgrandaviricetes class in the INSTIs-treated group compared to the control group (padj<0.001). Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection (p<0.05 vs. control) or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages (p<0.05 vs. control). To sum up, our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis not only at bacterial but also at viral level, which opens several opportunities for new studies focused on microbiota-based therapies. Author summaryThe impact of human immunodeficiency virus (HIV) infection and the effects of integrase strand transfer inhibitors (INSTIs)-based treatments --first-choice treatment of naive HIV-infected patients nowadays-- on gut virome are unknown. In this study, we have confirmed that phages are the most abundant viral component of the human gut virome. Besides, we have described for the first time that INSTIs-based treatments are able to partially restore gut dysbiosis induced by HIV infection not only at bacteria but also at viral level. This fact opens new opportunities for future studies and approaches focused on microbiota-based therapies in the context of HIV infection and treatment.

microbiology↗

bioRxiv2022

First report of kdr L1014F and ace-1 G119S insecticide resistance in Belgian Culex mosquitoes

The emergence of West Nile virus and Usutu virus in Europe poses a significant risk to public health. In the absence of efficient antiviral therapy or vaccine candidates, the only strategy to control these arboviruses is to target the Culex (Diptera: Culicidae) mosquito vector. However, the selection pressure caused by exposure to insecticides for vector control or agricultural pest control can lead to insecticide resistance, thereby reducing the efficacy of insecticide-based vector control interventions. In Culex mosquitoes, two of the most common amino acid substitutions associated with insecticide resistance are the kdr L1014F in voltage gated sodium channels and G119S in acetylcholinesterase. In this study, Culex pipiens biotype pipiens, Culex torrentium, and Culex modestus were sampled from 2019 to 2021 in three distinct environmental habitats (urban, peri-urban, and agricultural) in and around the city of Leuven, Belgium. Individual mosquitoes were screened for two mutations resulting in L1014F and G119S amino acid substitutions. Both mutations were observed in Culex pipiens and Culex modestus but not in Culex torrentium mosquitoes across the four collection sites. Furthermore, multi-resistance or cross-resistance in Culex pipiens could be a threat in these areas, as both mutations were observed at low frequencies. These results provide the first report of kdr L1014F and ace-1 G119S resistance in Culex pipiens and Culex modestus mosquitoes from Belgium, highlighting the importance of mosquito surveillance to design effective arbovirus outbreak control strategies.

molecular biology↗

bioRxiv2020

Establishment of Culex modestus in Belgium and a glance into the virome of Belgian mosquito species

Culex modestus mosquitoes are known transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including only one larva confirmed in Belgium in 2018. Mosquitoes were collected in the city of Leuven and surroundings in the summer of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit 1 (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species: Cx. pipiens (24.3%), Cx. modestus (48.6%), Cx. torrentium (0.9%), Culiseta annulata (0.9%), Culiseta morsitans (0.9%), Ae. sticticus (14.0%), Ae. cinereus (9.3%) and Anopheles plumbeus (0.9%), suggesting the presence of an established Cx. modestus population in Belgium. Collection of Cx. modestus mosquitoes at the same locations in 2020, confirmed the establishment in the region. Haplotype network analysis of the COI sequences for Cx. modestus showed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The Belgian Cx. modestus population was most closely related to populations from the UK and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (near-) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses. In conclusion, we here report the presence of Cx. modestus in the surroundings of Leuven, Belgium. As this species is known to be a vector of several arboviruses, the implementation of vector surveillance programs monitoring this species is recommended. ImportanceCulex modestus is a mosquito species that plays a role as a bridge vector, being able to transmit pathogens between birds, as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent, until the finding of one larva in 2018 and subsequent evidence of a large population in 2019-2020 described here. We collected mosquitoes in the summer of 2019 and 2020 in the city of Leuven and surroundings. The mosquito species was identified by morphological and molecular methods, demonstrating the presence of Cx. modestus in this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harboured by Belgian mosquitoes. As Cx. modestus is able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs monitoring this species.

microbiology↗