Biology subjects

Debat, H.

Publications and source records attributed to Debat, H..

14 recordsLinked to original sources

bioRxiv2026

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

Members of the Orthoflavivirus genus in the family Flaviviridae are primarily vector-transmitted RNA viruses infecting humans, other mammals and birds, including major pathogens such as tick borne encephalitis, West Nile, Zika and dengue viruses. Vector-borne flaviviruses are assigned to the Euflavivirus subgenus of orthoflaviviruses, with more divergent largely unclassified insect-specific flaviviruses, including cell fusing agent virus assigned to the second subgenus, Fusivirus. The currently classified 57 orthoflavivirus species have traditionally been assigned descriptively on the basis of their genome and antigenic relatedness, ecology and host and vector tropisms, although many more orthoflavi-like viruses remain unassigned. To investigate whether species might be demarcated using a fixed genetic divergence threshold, we examined distributions of pairwise distances in NS5 and E genes (which encode the RNA-dependent RNA polymerase and envelope protein, respectively) of classified orthoflaviviruses. Demarcation thresholds of 0.1 in the two regions would be most parsimonious with current euflavivirus classification. Exceptions include species in the tick-borne encephalitis virus complex with divergences below the threshold, and dengue virus types currently assigned to a single species that are substantially above. Application of the proposed thresholds would provide the means to establish 25 new euflavivirus and 33 new fusivirus species and reconcile several anomalies and inconsistencies in the current species taxonomy. The use of a species demarcation threshold brings consistency with the classification of viruses in other families. A robust and evolutionarily consistent framework furthermore enables taxonomic assignments of the numerous currently unassigned orthoflaviviruses that lack the phenotypic descriptions required for the current species definition.

microbiology↗

bioRxiv2026

Shedding light on the virome of Caliothrips phaseoli, an emergent pest in peanut

The bean thrips, Caliothrips phaseoli, is an emergent pest affecting peanut production. Thus, gaining a deeper understanding of the naturally occurring viral populations associated with this insect is of major importance, as such knowledge could support the design of novel pest management strategies that are both ecologically responsible and sustainable over the long term. In this study, we performed the first RNA high-throughput sequencing (HTS) analysis of C. phaseoli to unravel its virome, discovering a wide number of novel RNA viruses. Our HTS analysis revealed the presence of 31 viral segments, corresponding to 18 viruses, including double-stranded RNA viruses as well as positive- and negative-sense single-stranded RNA viruses. All these are novel viruses and cover multiple viral lineages belonging to diverse families. Overall, these results indicates that C. phaseoli hides a complex virome. The findings presented here provide an important framework for subsequent studies aimed at understanding the ecological significance, evolutionary patterns, and possible use of these viruses as components of biologically based management programs for this emerging peanut pest.

microbiology↗

bioRxiv2026

Data mining sheds light on a novel family of plant-associated negative-sense RNA viruses linked to lispiviruses

Large-scale mining of public transcriptomic datasets can reveal viral diversity that remains invisible to conventional virus-surveillance approaches, while increasingly powerful structure-prediction methods provide a complementary route to characterizing highly divergent viral proteins. Here, we combine sequence detection, phylogenetic analysis, structural prediction, and host-association analyses to investigate the cryptic diversity and biology of a new clade of plant-associated lispi-like viruses. Analyses of RNA-sequencing datasets identified and enabled assembly of 87 lispi-like virus genomes associated with 75 plant hosts, expanding the known diversity of this new group by approximately 40-fold. The viruses share a conserved four-cistron genome organization, 3'-N-P2-P3-L-5'. Structural analyses provide functional insights into the four conserved proteins. P1 (N) adopts a canonical negative-strand RNA virus nucleocapsid architecture with conserved RNA-interacting residues and a predicted RNA-packaging configuration. P2 is exceptionally divergent; although a subset of structures resembles the ITPase/HAM1 fold. P3 forms a conserved trimeric coiled-coil architecture reminiscent of a viral fusion-protein stalk, but lacks the family-wide sequence features expected of a canonical membrane glycoprotein. P4 contains a structurally resolved Mononegavirales-type RNA-dependent-RNA-polymerase (RdRp) core with invariant catalytic motifs, including the characteristic GDN signature, whereas its accessory regions are substantially more divergent. Phylogenetic insights form a distinct monophyletic lineage sister to the predominantly invertebrate-associated Lispiviridae, supporting their recognition as a new proposed family Masuviridae, comprising 15 tentative genera. Genus-level clustering is accompanied by marked differences in host association, ranging from strong specialization to broader host ranges. Retrospective screening of public sequencing libraries further identified lispi-like virus sequences in 1,536 libraries representing 134 plant species, 11 plant families and 182 geographic locations, highlighting a substantial and geographically widespread cryptic virome. Together, these results establish Masuviridae as a deeply divergent lineage of plant-associated negative-sense RNA viruses and illustrate how the integration of sequence, structural, and large-scale transcriptomic analyses can move viral dark matter from detection towards evolutionary and functional characterization.

microbiology↗

bioRxiv2026

An ancestral mitochondrial DNA insertion disrupts RNAi and enables persistence of a novel mycovirus in Cryptococcus neoformans

RNA interference (RNAi) is a widely conserved genome-defense mechanism that protects eukaryotes against viruses and transposable elements. We previously showed that RNAi loss can lead to hypermutation and antifungal drug resistance in the human fungal pathogen Cryptococcus neoformans, illuminating the potential clinical relevance of this pathway. In this study, we identified another function of RNAi in C. neoformans: mycovirus restriction. By screening known RNAi-deficient C. neoformans isolates, we identified a novel dsRNA mycovirus of the Orthototiviridae family, which we named CnTV1. We subsequently detected CnTV1 in three additional RNAi-deficient isolates. All CnTV1-positive isolates shared an ancestral nuclear mitochondrial DNA segment (NUMT) insertion that disrupts the gene encoding Argonaute (Ago1). Restoration of RNAi in sexually produced zygotes efficiently eliminated CnTV1. RNAi rescue by CRISPR-Cas9-mediated allele exchange eliminated CnTV1 during vegetative growth, further demonstrating RNAi is sufficient for mycoviral control. Loss of the RNA helicase Ski2 or the exoribonuclease Xrn1 increased CnTV1 abundance, revealing RNAi-independent restriction of the virus. Restoration of RNAi cleared the virus even in the absence of Ski2 or Xrn1, indicating a dominant role for RNAi in antiviral defense. To investigate the biological implications of CnTV1 infection, we developed a cytoplasmic-mixing approach and generated isogenic strain pairs in an RNAi-deficient background that differ only in viral infection status. Leveraging these strains, we show that CnTV1 infection leads to coordinated, low-magnitude transcriptomic changes and that strains lacking the mycovirus were moderately less virulent in a murine infection model. Our findings reveal that RNAi serves as a dominant antiviral defense system in C. neoformans and suggest that naturally occurring RNAi deficiency may be more prevalent than previously appreciated. This work highlights mycovirus persistence as an important consequence of RNAi loss in this WHO-designated critical priority fungal pathogen.

genetics↗

bioRxiv2026

Exploring the virome of Gyropsylla spegazziniana, a major yerba mate pest

The yerba mate psyllid (Gyropsylla spegazziniana) poses a significant threat to yerba mate crops, causing extensive economic losses. While some ecological aspects as well as control strategies have been studied, its associated viral diversity remains unexplored. Here, by generating the first RNA high-throughput analysis (HTS) of this pest, we explored the G. spegazziniana virome, revealing novel and diverse RNA viruses. We characterized five new viral members belonging to distinct families, with evolutionary cues of beny-like viruses (Benyviridae), picorna-like viruses (Picornaviridae), and sobemo-like viruses (Solemoviridae); which were tentatively named Gyropsylla spegazziniana beny-like virus 1 (GSBlV1), Gyropsylla spegazziniana picorna-like virus 1 (GSPlV1), and Gyropsylla spegazziniana sobemo-like virus 1-3 (GSSlV1-3), respectively. Phylogenetic analysis of the bi-segmented and highly divergent sobemo-like viruses showed a distinctive evolutionary trajectory of its encoding proteins at the periphery of recently reported invertebrate Sobelivirales. The beny-like virus belonged to a cluster of insect-associated beny-like viruse; while the picorna-like virus clustered together with psyllid-associated picorna-like viruses. These results highlight the existence of a complex virome within G. spegazziniana and establish the basis for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses in the G. spegazziniana -yerba mate eco-systems.

microbiology↗

bioRxiv2023

A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) encodes a divergent class 1b XRN1-resistant RNA element.

Flavivirids are small, enveloped, positive-sense RNA viruses from the Flaviviridae family with genomes between [~]9-13kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. To date, however, no flavivirus-like or flavivirid has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the United Kingdom, utilising high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid [~]11.2kb in length. The virus encodes a single open reading frame of 3456 amino acids and 5 and 3 untranslated regions (UTRs) of 227 and 666nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, 95.64-97.39% pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of putative secondary structures in the 3'-UTR of RaTV indicated a potential exoribonuclease-resistant RNA (xrRNA) structure identified in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro XRN1 digestion assay showing that RaTV likely forms a divergent but functionally homologous XRN1-resistant xrRNA.

microbiology↗

bioRxiv2022

Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina

Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations, are still scarce, especially from South America. The aim of this work was to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta and Tucuman, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in NWA, revealed that the substitution rate of lineage N.5 (7.9 x 10-4 substitutions per site per year, s/s/y) was a [~]40% faster than that of lineage B.1.499 (5.9 x 10-4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.

bioinformatics↗

bioRxiv2022

A glimpse into the DNA virome of the unique "living fossil" Welwitschia mirabilis

Here, we report the identification and characterization of four novel DNA viruses associated with Welwitschia mirabilis. Complete circular virus-like sequences with affinity to Caulimoviridae members and geminiviruses were detected and characterized from Welwitschia mirabilis genomic data. The two newly Caulimoviridae-like viruses have been tentatively named as Welwitschia mirabilis virus 1 and 2 (WMV1-WMV2); whereas the two identified geminiviruses were named as Welwitschia mirabilis associated geminivirus A and B (WMaGVA-WMaGVB). Phylogenetic analysis suggests that WMV1-2 belong to a proposed genus of Caulimoviridae-infecting gymnosperms. WMaGVA-B are phylogenetically related with both mastreviruses and capulaviruses and likely represent a distinct evolutionary lineage within geminiviruses.

microbiology↗

bioRxiv2021

Exploring the tymovirids landscape through metatranscriptomics data

Tymovirales is an order of viruses with positive-sense, single-stranded RNA genomes that mostly infect plants, but also fungi and insects. The number of tymovirid sequences has been growing in the last few years with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 31 novel tymovirid genomes associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through a homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirids sequences as query. Identification, assembly and curation of raw SRA reads resulted in 29 viral genome sequences with full-length coding regions, and two partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known tymovirids. Phylogenetic analysis showed that six of the novel viruses were related to alphaflexiviruses, seventeen to betaflexiviruses, two to deltaflexiviruses and six to tymoviruses. These findings resulted in the most complete phylogeny of tymovirids to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and diversity of tymovirids genomes and demonstrates that analyzing SRA public data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.

microbiology↗

bioRxiv2021

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

microbiology↗

bioRxiv2020

A New World begomovirus infecting Grapevine

Cotton (Gossypium spp.) is a globally significant cash crop cultivated for its versatile fiber, widely used in the textile industry. Cotton, as other crops, is vulnerable to infectious pathogens. Several of them, including viruses, are a major threat to cotton production. Geminiviruses (family Geminiviridae) are insect transmitted, small non-enveloped viruses, with circular single-stranded DNA genomes, which are encapsidated in quasi-icosahedral geminated virions. Here we present evidence of a novel begomovirus (genus Begomovirus) infecting cotton from Argentina. Two circular ssDNA virus sequences were assembled from high-throughput sequencing data from Gossyipium hirsutum cotton samples showing mosaic symptoms from Argentina. Structural and functional annotation indicated that the virus sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, a tentative prototype member of a novel species which we propose the name "Cotton mosaic virus" (CoMV).

microbiology↗

bioRxiv2019

Identification of a Nidovirales Orf1a N7-guanine cap methyltransferase signature-sequence as a genetic marker of large RNA genome Tobaniviridae

Members of the Nidovirales order have (+)RNA genomes amongst the largest in size in the RNA virus world. Expression of their genes is promoted through reading of genomic RNA and mRNA transcripts by the ribosome of the infected cell. The 5-end of these RNAs is supposedly protected by an RNA-cap structure (m7GpppNm) whose most synthesis steps remain elusive. In Eukaryotes, the RNA-cap structure is methylated by RNA methyltransferases (MTases) at the RNA-cap N7-guanine position as well as the 2-O methyl position of the first transcribed nucleotide. In Coronaviridae, two separate enzymes (nsp14 and nsp16) perform the N7-guanine and the 2-OH methylation, respectively. One salient feature of the Nidovirales N7-guanine MTase nsp14 is that it is the only example of non-Rossman fold viral MTase known so far. Conversely, all other Nidovirales nsp16-like MTases have a canonical Rossman fold. Many Nidovirales members lack either any RNA MTase signature sequence (e.g., Arteriviridae), or lack a N7-guanine MTase signature sequence (e.g., Tobaniviridae, Euroniviridae, Roniviridae, Medioniviridae). Both nsp14-and nsp16-like enzyme genes are usually located in Orf1b encoding for the replication machinery. Here, we report the discovery of a putative Rossman fold RNA MTase in the Orf1a of ten Tobaniviridae members. Multiple sequence alignments and structural analyses identify this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.

bioinformatics↗

bioRxiv2019

Redefining the medicago sativa alphapartitivirus genome sequences

In alfalfa samples analyzed by hightroughput sequencing, four de novo assembled contigs encoding gene products showing identities to alphapartitiviruses proteins were found based on BlastX analysis. The predicted amino acid (aa) sequences of two contigs presented 99-100% identity to the RNA-dependent RNA polymerase (RdRp) and the capsid protein (CP) of the recently reported medicago sativa alphapartitivirus 1 (MsAPV1). In addition, the remaining two contigs shared only 56% (CP) and 70% (RdRp) pairwise aa identity with the proteins of MsAPV1, suggesting that these samples presented also a novel Alphapartitivirus species. Further analyses based on complete genome segments termini and the presence/absence of alphapartitivirus RNA in several samples and public alfalfa RNA datasets corroborated the identification of two different alphapartitivirus members. Our results also likely indicate that the reported MsAPV1 genome was previously reconstructed with genome segments of two different alphapartitiviruses. Overall, we not only revisited the MsAPV1 genome sequence but also report a new tentative alphapartitivirus species, which we propose the name medicago sativa alphapartitivirus 2. In addition, the RT-PCR detection of both MsAPV1 and MsAPV2 in several alfalfa cultivars suggests a broad distribution of both viruses.

microbiology↗

bioRxiv2018

Transcriptome analysis of mycorrhizal and non-mycorrhizal soybean plantlets upon infection with Fusarium virguliforme, one causal agent of sudden death syndrome

Soilborne pathogens represent a threat to agriculture causing important yield losses. The \"Sudden Death Syndrome\" (SDS), a severe disease in soybean is caused by a complex of Fusarium species. This pathosystem has been widely investigated and several strategies were proposed to manage SDS. Although a decrease in symptoms and in the level of root tissue infection particularly by F. virguliforme was observed in presence of arbuscular mycorrhizal fungi (AMF), biological control based on AMF has received less attention. Here we report the results, under strict in vitro culture experimental conditions, a transcriptional analysis in mycorrhizal versus non-mycorrhizal soybean plantlets upon infection by F. virguliforme. An important transcriptional reprogramming was detected following infection by the pathogen. Results revealed 1768 and 967 differentially expressed genes in the AMF-colonized (+AMF+Fv) and non-colonized (-AMF+Fv) plants, respectively. Major transcriptional changes, corresponded to defence response related genes belonging to secondary metabolism, stress and signalling categories. The +AMF+Fv treatment showed the largest number of upregulated genes related to defence, as those encoding for disease resistance proteins, WRKY transcription factors, auxins, receptors kinases, and proteases. Only few genes had primed expression in +AMF+Fv treatment, as those coding for a thaumatin-like protein (TLP) and a pleiotropic drug resistance (PDR) protein. Moreover, +AMF+Fv showed a significant number of downregulated genes related to cell wall modification and peroxidases than - AMF+Fv treatment. This detailed insight increases our knowledge on the transcriptional changes and the potential metabolic pathways involved in the enhanced resistance/tolerance of mycorrhizal plants upon infection with F. virguliforme.

plant biology↗