A5031871746- Genomics and Phylogenetic Studies
- Viral Infections and Vectors
- Bacteriophages and microbial interactions
- Animal Virus Infections Studies
- Vector-borne infectious diseases
- SARS-CoV-2 and COVID-19 Research
- Plant Virus Research Studies
- Mosquito-borne diseases and control
- Vector-Borne Animal Diseases
- COVID-19 Clinical Research Studies
- RNA and protein synthesis mechanisms
- Viral Infections and Outbreaks Research
- Genetic diversity and population structure
- Viral gastroenteritis research and epidemiology
- Viral Infections and Immunology Research
- Groundwater flow and contamination studies
- Insect symbiosis and bacterial influences
- Microbial Community Ecology and Physiology
- Bioinformatics and Genomic Networks
- Heat and Mass Transfer in Porous Media
- Microbial infections and disease research
- Influenza Virus Research Studies
- Soil and Unsaturated Flow
- Photosynthetic Processes and Mechanisms
- Kawasaki Disease and Coronary Complications
Institut Pasteur
2019-2024
Université Paris Cité
2022-2024
Centre National de la Recherche Scientifique
2013-2021
Department of Virology
2020-2021
Inserm
2019-2020
Biology of Infection
2019-2020
Université Gustave Eiffel
2020
Génomique Bioinformatique et Applications
2019
Laboratoire de Biométrie et Biologie Evolutive
2013-2017
Université Claude Bernard Lyon 1
2013-2017
Efficient algorithms and programs for the analysis of ever-growing amount biological sequence data are strongly needed in genomics era. The pace at which new methodologies generated calls use pre-existing, optimized—yet extensible—code, typically distributed as libraries or packages. This motivated Bio++ project, aiming developing a set C++ analysis, phylogenetics, population genetics, molecular evolution. main attractiveness is extensibility reusability its components through...
Background Children’s role in SARS-CoV-2 epidemiology remains unclear. We investigated an initially unnoticed outbreak linked to schools northern France, beginning as early mid-January 2020. Aims This retrospective observational study documents the extent of transmission, affected high school (n = 664 participants) and primary 1,340 participants), context unsuspected circulation limited control measures. Methods Between 30 March April 2020, all staff, well pupils their parents relatives were...
Abstract The animal reservoir of SARS-CoV-2 is unknown despite reports various SARS-CoV-2-related viruses in Asian Rhinolophus bats, including the closest virus from R. affinis, RaTG13. Several studies have suggested involvement pangolin coronaviruses emergence. presents a mosaic genome, to which different progenitors contribute. spike sequence determines binding affinity and accessibility its receptor-binding domain (RBD) cellular angiotensin-converting enzyme 2 (ACE2) receptor responsible...
Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily in various tick genera originating China, geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification Jingmen-related mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge host range,...
Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because their inherent inability to be predictable, conversely emergences known that could targeted routine surveillance programs. zoonotic infections either originate from increasing contacts between wildlife and populations, or geographical expansion hematophagous arthropods act as vectors, this latter being more capable impact large-scale populations. While characterizing viral...
<ns4:p>We present RVDB-prot, a database corresponding to the protein equivalent of nucleic acid reference virus RVDB. Protein databases can be helpful perform more sensitive sequence comparisons. Similarly its homologous public repository, RVDB-prot aims provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) profiles for distant searching.</ns4:p>
Metagenomic next-generation sequencing (mNGS) allows untargeted identification of a broad range pathogens, including rare or novel microorganisms. Despite the recognition mNGS as valuable diagnostic tool for infections, most relevant indications this innovative strategy remain poorly defined. We aimed to assess determinants positivity and clinical utility mNGS.
<ns4:p>We present RVDB-prot, a database corresponding to the protein equivalent of nucleic acid reference virus RVDB. Protein databases can be helpful perform more sensitive sequence comparisons. Similarly its homologous public repository, RVDB-prot aims provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) profiles for distant searching.</ns4:p>
BackgroundChildren have a low rate of COVID-19 and secondary severe multisystem inflammatory syndrome (MIS) but present high prevalence symptomatic seasonal coronavirus infections.AimWe tested if prior infections by coronaviruses (HCoV) NL63, HKU1, 229E or OC43 as assessed serology, provide cross-protective immunity against SARS-CoV-2 infection.MethodsWe set cross-sectional observational multicentric study in pauci- asymptomatic children hospitalised Paris during the first wave for reasons...
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for health humans livestock. The composition viral communities ticks their interactions with pathogens, is poorly understood, particularly Eastern Europe, an area that represents a major hub animal-arthropod vectors exchanges (e.g., via bird migrations). aim this study was to describe virome Dermacentor sp., Rhipicephalus sp. Haemaphysalis collected from relatively little...
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and such expected to drive adaptation new ecological niches. However, among the many genes acquired through HGT along diversification history genomes, only fraction may have actively contributed sustained adaptation. We used phylogenetic approach accounting for (or groups genes) estimate genomes Agrobacterium biovar 1, diverse group soil plant-dwelling bacterial species. identified clade-specific blocks...
We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, comprehensive, curated regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, scoring the Lowest Common Ancestor (LCA) from translated reads contigs. runs local computer. The outcome is displayed through user-friendly dynamic graphical interface. Based two representative mNGS datasets...
Ticks transmit a wide variety of pathogens including bacteria, parasites and viruses. Over the last decade, numerous novel viruses have been described in arthropods, ticks, their characterization has provided new insights into RNA virus diversity evolution. However, little is known about ability to infect vertebrates. As very few studies present ticks from Caribbean, we implemented an RNA-sequencing approach on Amblyomma variegatum Rhipicephalus microplus collected cattle Guadeloupe...
Abstract Background Children have a lower rate of COVID-19, potentially related to cross-protective immunity conferred by seasonal coronaviruses (HCoVs). We tested if prior infections with impacted SARS-CoV-2 and Multisystem Inflammatory Syndrome (MIS). Methods This cross-sectional observational study in Paris hospitals enrolled 739 pauci or asymptomatic children (HOS group) plus 36 suspected MIS (MIS group). Prevalence, antigen specificity neutralizing capability antibodies were tested....
Human encephalitis represents a medical challenge from diagnostic and therapeutic point of view. We investigated the cause 2 fatal cases unknown origin in immunocompromised patients.Untargeted metatranscriptomics was applied on brain tissue patients to search for pathogens (viruses, bacteria, fungi, or protozoans) without prior hypothesis.Umbre arbovirus, an orthobunyavirus never previously identified humans, found patients. In situ hybridization reverse transcriptase-quantitative polymerase...
Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit the low pathogen load compared to high background host nucleic acids. To overcome this issue, several solutions exist, such as applying very depth sequencing, or performing relative enrichment viral genomes associated with capsids. At end, quantity total acids often below concentrations recommended by manufacturers library kits, which necessitates random amplify Using...
Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% recognized EIDs. To assess new alternatives for arthropod-borne viral surveillance, detection viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at Llobregat River Delta (Catalonia, Spain). Next...
Ticks are involved in the transmission of various pathogens and several tick-borne diseases cause significant problems for health humans livestock. The members Quaranjavirus genus mainly associated with argas ticks but recent studies demonstrated presence novel quaranjaviruses-like ixodid ticks. In 2020, 169 Rhipicephalus sanguineus were collected Southern Romania from small ruminants analyzed by high-throughput transcriptome sequencing. Among viral families that infect Romanian ticks, we...
Tick-borne diseases are responsible for many vector-borne within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics detect virome, including viruses, associated with Ixodes ricinus collected from Romania and France. A bunyavirus-like virus related Bronnoya was identified first time these regions. It presents high level amino-acid conservation Bronnoya-related I. ticks...
Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from high probability of extinction dioecious species because less efficient dispersal and the costs sexual selection, which are expected to harm species' survival on long term. These handicaps should decrease effective population size (Ne) species, turn reduce efficacy selection. Moreover, selection specifically affect some genes, will evolve under positive The relative...
Abstract Background Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many expanding their geographical range due to changing socioeconomic climate factors. The Danube Delta, one Europe’s largest wetlands, is an ecosystem that, despite its ecological importance, remains understudied concerning the risk introducing new tick-borne viruses. This region serves as a critical habitat for migratory birds, which can...