Biology subjects

Torres, C.

Publications and source records attributed to Torres, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Modeling human embryonic adrenogenesis in pluripotentstem cell-derived corticomedullar-like assembloids

During embryogenesis, the cortical and medullary compartments of the adrenal gland emerge from two distinct sources: intermediate mesoderm-derived steroidogenic progenitors that comprise the cortex, and migratory neural crest-derived catecholaminergic progenitors that give rise to the medulla. The distinct cellular origins and paracrine signaling environments that foster induction, differentiation, and/or migration of cortical and medullary layers present challenges to recapitulating their co-emergence and incorporation in a human pluripotent stem cell (hPSC) based system. To address this, we developed an approach for modeling the adreno-gonadal primordium (AGP) in compound organoids that are organized along a gradient of NR5A1 expression and which unexpectedly incorporate SOX10-expressing Schwann cell precursors that ultimately generate chromaffin cells. Deconstruction of paracrine signaling within AGP-like organoids (AGPLOs) identified a fibroblast growth factor 9 (FGF9)-driven mechanism that expands bridge cell-like chromaffin progenitors and correlates to paracrine signaling cues encountered by physiological correlates along their migration corridor to the cortex in vivo. Combination of NR5A1-expressing cells with chromaffin cell clusters generated corticomedullar-like assembloids (CMLAs) that generated steroids and catecholamines and were responsive to adrenocorticotropic hormone. This work establishes a platform for modeling the reciprocal signaling relationships that drive adrenal gland development and function in health and disease and provides an approach for generating hPSC-derived adrenal cells/tissues that can be applied therapeutically.

developmental biology↗

bioRxiv2026

A Dominant-Negative HIF-1 Isoform Protects Neuronal Development by Buffering the Response to Hypoxia in C. elegans

Animal cells respond to hypoxic stress through cell-autonomous stabilization of HIF-1, a conserved transcription factor that mediates adaptation to low-oxygen environments. Although HIF-1 is essential for viability under hypoxia, its persistent activation during development causes miswiring defects in the nervous system, raising the question of how developing neurons balance the pro-survival benefits of HIF-1 stabilization against these associated risks. Here we show that C. elegans neurons address this challenge by mobilizing an internal promoter within the hif-1 locus to generate a dominant-negative isoform, HIF-1c, which acts in the nucleus to limit HIF-1/AHA-1 heterodimer formation. This buffering mechanism supports proper neuronal migration, axon guidance, and circuit formation and its loss phenocopies the defects seen when the ubiquitous HIF-1 degradation pathway is disrupted, confirming that HIF-1c serves as a critical layer of protection for the developing nervous system against hypoxic-induced errors. Lastly, we identify the retinoblastoma protein LIN-35 as a modulator of HIF-1 signaling in worms via control of hif-1c expression. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/745244v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@3ad347org.highwire.dtl.DTLVardef@4fd4forg.highwire.dtl.DTLVardef@1928804org.highwire.dtl.DTLVardef@11fd1e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2026

Ephrin Signaling Patterns Sensory Neurons During Tissue Homeostasis in Planarians

Eph and ephrin genes encode receptor-ligand pairs that mediate contact-dependent cell signaling and are essential for nervous system development. However, less is known about the role of Ephrin signaling during adult tissue homeostasis and regeneration. Here, we investigated the role of Ephrin signaling in neural patterning in the planarian Schmidtea mediterranea. We discovered that RNAi against the Eph receptor EphR1 led to striking ectopic expression of the mechanosensory neuron markers pkd1L-2 and hmcn-1-L, without obvious disruption of the overall architecture of the central nervous system. To investigate the basis of this phenotype, we identified additional Eph receptor homologs and four putative ephrin ligands and assessed their function. An RNAi screen revealed that ephrin-1 phenocopies the defects of EphR1 RNAi. Temporal analyses of EphR1 and ephrin-1 inhibition revealed a progressive increase in pkd1L-2+ and hmcn-1-L+ cells, indicating an unappreciated role for Ephrin signaling in regulating neural patterning and cell number during adult tissue homeostasis. Together, these findings provide a framework for dissecting Ephrin-dependent mechanisms in adult tissue maintenance and regeneration.

developmental biology↗

bioRxiv2026

Rapid expansion overcomes inbreeding in cross-hemisphere colonization of Barn Swallows

Switching migratory behavior appears to promote speciation in birds through colonization of their wintering grounds for breeding. However, colonization episodes often fail, especially when they lead to inbreeding depression associated with small population sizes. We studied the dynamics of a new and thriving breeding population of migratory Barn Swallows (Hirundo rustica erythrogaster) that began nesting on their traditional wintering grounds in South America in the 1980s and evolved an "inverse" migration and breeding cycle. We show that in four decades, behavioral flexibility and standing genetic variation have facilitated the establishment of a breeding population that has grown exponentially in abundance and breeding range size. By breeding under bridges and culverts, Barn Swallows exploited ecological opportunities that outweighed the costs of inbreeding and began an independent evolutionary trajectory from their North American relatives.

evolutionary biology↗

bioRxiv2026

Identification of highly immunogenic endogenous dsRNAs from cellular MDA5 filaments

ADAR1 converts adenosine to inosine in endogenous double-stranded RNAs (dsRNAs) to prevent excessive MDA5-driven interferon-stimulated gene expression. The source of endogenous immunogenic dsRNAs remains enigmatic because only a small fraction of ADAR1 substrates activate MDA5, and cellular MDA5 filaments have not been isolated. Here, we couple affinity purification of cellular MDA5 filaments with RNA sequencing to define immunogenic endogenous dsRNAs. Greater than 84% of dsRNAs suppressed by combined DDX3X RNA helicase and ADAR1 base-editing activities were present in MDA5 filaments, compared to less than 1% of dsRNA substrates acted on by ADAR1 alone. Dual substrate dsRNAs consisted of inverted repeats embedded in 3-UTRs with high base-pair complementarity and longer intervening sequences between repeats, with a minor contribution coming from intermolecular dsRNAs formed by sense and antisense transcripts. Moreover, the majority of dual substrate immunogenic dsRNAs were hyperedited in DDX3X mutant cancers. This reveals the identity of endogenous immunogenic dsRNAs and quality control mechanisms underlying their suppression.

cell biology↗

bioRxiv2026

An RNA-centric interactomics screen identifies novel proviral and antiviral genome binding interactors for tick-borne encephalitis virus

The tick-borne encephalitis virus (TBEV), which belongs to the Orthoflavivirus genus, is a medically significant arbovirus in Europe and Asia. Despite distinct pathobiological outcomes, arboviruses have evolved specific strategies to co-opt cellular factors for replication and immune evasion, that involve both viral proteins and viral RNA. The RNA genome of TBEV, as both the substrate for genome replication and translation and a designated target for innate antiviral immunity, is a nexus for interactions with the proteome of host cells. Nonetheless, the molecular bases of these interactions and their implications for the replicative cycle of TBEV remain poorly understood. To create an inventory of such interactions and gain understanding of their functional import, we have resolved the set of cellular proteins bound to TBEV RNA in infected human cells using an agnostic RNA-centric approach. Functional annotation of the resulting core interactome of 215 human host factors showed that viral RNA is deeply embedded in multiple cellular pathways, including those related to RNA and protein metabolism, cytoskeletal scaffolding, vesicle trafficking and innate antiviral immunity. For selected human interactors, we addressed their impact on TBEV infection in gene knockdown experiments, thereby identifying multiple restriction and dependency factors. These included sensors and effectors of innate immune pathways, as well as epitranscriptomic modifiers. Among the former, the dynamin-like GTPase MX2 protein, an interferon-stimulated gene with antiviral activity against multiple viruses including mosquito-borne orthoflaviviruses, displayed unexpected proviral activity against TBEV and a second tick-borne orthoflavivirus. Among the latter, WDR4, the non-catalytic component of the METTL1-WDR4 methyltransferase complex, emerged as a restriction factor with broad-spectrum activity against arboviruses belonging to multiple families of positive-strand RNA viruses. In conclusion, this first description of the RNA interactome of a tick-borne orthoflavivirus illuminates the molecular interactions that underpin TBEV infection of human cells, which taken together reflect both the common ancestry of tick- and mosquito-borne orthoflaviviruses and their considerable evolutionary divergence.

molecular biology↗

bioRxiv2026

MDA5 multimerization on LINE RNA drives pathogenic extracellular immune complexes in autoimmunity

Autoantibodies are hallmarks of many autoimmune diseases, but their potential pathogenic roles, particularly for those targeting intracellular proteins, remain unclear. Anti-MDA5-positive dermatomyositis (anti-MDA5 DM) is characterized by autoantibodies against the intracellular protein MDA51,2, a conserved innate immune receptor that recognizes viral dsRNA by forming filaments3. Here, using four patient-derived monoclonal autoantibodies (mAbs), we reconstitute and define the molecular architecture, biogenesis, and immunological activity of pathogenic MDA5 immune complexes. Our cryo-EM analysis revealed that these mAbs bind dsRNA-scaffolded MDA5 filaments in at least two distinct binding modes, each exhibiting striking epitope convergence using germline-encoded residues. Extracellular immune complexes formed between mAbs and filamentous, but not monomeric, MDA5 potently activate multiple innate immune pathways, with the magnitude of activation determined by antibody binding mode and immune complex stoichiometry. Antibody bivalency further crosslinks MDA5 filaments into higher-order aggregates with heightened immunostimulatory activity, demonstrating an active role of autoantibodies in shaping immune complex architecture. Analysis of patient plasma reveals elevated levels of extracellular MDA5 filaments and identifies LINE retroelement-derived dsRNA as a structural scaffold. Notably, MDA5 immune complexes induce endogenous LINE dsRNA expression, likely promoting additional MDA5 filament formation and extracellular release through inflammatory cell death. These data thus support a self-amplifying inflammatory cycle as a pathogenic mechanism for anti-MDA5 DM. Collectively, our study defines a broadly applicable architectural principle, in which higher-order organization and binding modes of autoantibodies--beyond antibody affinity or nucleic acid presence alone--govern innate immune activation.

biochemistry↗

bioRxiv2025

The N-terminal region of malaria vaccine candidate Plasmodium falciparum asparagine-rich merozoite antigen is immunodominant and targeted by polyreactive antibodies

The development of malaria blood-stage vaccines has been hampered by sequence variation in many Plasmodium falciparum proteins involved in erythrocyte invasion. In the past few years, asparagine-rich merozoite antigen (PfARMA) has emerged as a potential vaccine candidate due to its low amino acid sequence diversity and the association between anti-PfARMA antibody levels and protection to malaria. Here, we used samples from P. falciparum-exposed individuals to study naturally acquired B cell and antibody responses to PfARMA. B cell responses to PfARMA were dominated by IgM+ B cells that recognized the N-terminal intrinsically disordered region 1 (IDR1) of PfARMA. A human monoclonal antibody (hmAb) to IDR1 was non-neutralizing, while a second hmAb binding to the folded domain showed weak neutralizing activity. Both PfARMA-specific plasma IgM and IgG responses predominately targeted IDR1 and their levels increased with P. falciparum exposure. However, in contrast to previous reports, these antibody responses did not correlate with protection in age and exposure-matched children. Interestingly, approximately 30% of unexposed individuals had IgG that also targeted IDR1 and was polyreactive, binding to regions with high asparagine content. Finally, we determined that PfARMA is located in or near PfEBA-175+ micronemes. These data suggest that while IgG to the folded domain of PfARMA may inhibit parasite growth, antibody responses to PfARMA are primarily directed to IDR1 and may not directly contribute to protection against malaria.

immunology↗

bioRxiv2025

Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria

BackgroundUnregulated antibiotic use in poultry farming drives the emergence of multidrug-resistant (MDR) bacteria, which can spread to humans through the food chain and environment, posing serious public health risks. Whole-genome sequencing (WGS), combined with antimicrobial susceptibility testing (AST), enables detailed characterization of resistance mechanisms and supports antimicrobial stewardship. This study investigated the phenotypic and genotypic antimicrobial resistance (AMR), plasmid content, and virulence factors of an MDR Escherichia coli strain isolated from chicken droppings in Enugu State, Nigeria. ResultsDisk diffusion AST showed resistance to six of seven antibiotics tested (cefotaxime, ampicillin, erythromycin, gentamicin, ciprofloxacin, and doxycycline). Broth microdilution confirmed elevated minimum inhibitory concentrations across multiple classes, indicating an MDR phenotype. Hybrid WGS (Illumina and Nanopore) produced a 5.33 Mb genome comprising one chromosome and four plasmid-associated contigs. Chromosomal antimicrobial resistance genes (ARGs), including aac(6)-Ib-cr, blaCTX-M-15, and blaOXA-1, conferred resistance to aminoglycosides, fluoroquinolones, cephalosporins, and penicillins. Additional resistance determinants included efflux pumps, transport-associated genes, regulatory elements, and membrane modification genes. Plasmid-borne ARGs conferring resistance to aminoglycosides, trimethoprim, macrolides, sulfonamides, penicillins, and tetracyclines were also identified. The presence of Col156 and IncF-type plasmids indicates strong potential for horizontal gene transfer. Virulence profiling revealed numerous chromosomally encoded factors related to adhesion, iron acquisition, and toxin production. These included the pap gene cluster encoding P fimbriae; adhesion-associated genes (yagW/ecpD, ykgK/ecpR); multiple iron acquisition systems (enterobactin, yersiniabactin, aerobactin, and heme uptake); and sat, which encodes an autotransporter toxin. Additionally, the plasmid-borne gene senB encodes an enterotoxin that induces intestinal fluid secretion and contributes to diarrheal disease. Multilocus sequence typing identified the strain as ST131, a globally disseminated high-risk lineage. ConclusionsThis study provides a comprehensive genomic characterization of an MDR E. coli strain from poultry, revealing multiple chromosomal and plasmid-borne ARGs, and a diverse virulence gene repertoire. The detection of ST131 in poultry waste highlights a complex public health issue involving zoonotic transmission, veterinary impact, and environmental spread of AMR. These findings underscore the need for prudent antibiotic use, continuous monitoring, and integrated genomic surveillance across agricultural and environmental sectors, alongside improved antimicrobial stewardship and strengthened farm biosecurity measures.

microbiology↗

bioRxiv2025

Light and sex modify Snord116 genotype effects on metabolism, behavior, and imprinted gene networks following circadian entrainment

Mammals utilize imprinted and X-linked epigenetic mechanisms in development, metabolism, and behavior. Imprinted genes, including Prader-Willi syndrome Snord116 noncoding RNAs, are implicated in the regulation of sleep and circadian rhythms through poorly understood mechanisms. Utilizing mouse models of Snord116 deficiency and overexpression, we performed an integrated, sex-stratified analysis of free running behaviors, indirect calorimetry, and cortical transcriptomes following entrainment to a 22 hour light:dark T-cycle. We observed significant interactions of sex, entrainment, and Snord116 genotype in period length at baseline and after-effects of post-entrainment. Snord116 deletions effect on respiratory exchange ratio was light sensitive, with sex and entrainment effects dominant under total darkness. Snord116 genotype impacted both rhythmic and non-rhythmic cortical gene networks that integrated sex, light, and entrainment effects with genotype-phenotype correlations. A co-expressed gene network enriched for imprinted, Snord116-target, and Xist-proximal long noncoding RNAs was identified as a light-sensitive regulatory hub of sexual dimorphic responses to a dynamic environment.

animal behavior and cognition↗

bioRxiv2025

Minimal impact of ivermectin on immune response and transcriptional profiles in naïve adults with mild COVID-19

Ivermectin (IVM), an antiparasitic drug, was repurposed to treat COVID-19 based on its in vitro antiviral effects. However, it was abandoned after multiple clinical trials reported a lack of efficacy. Immunomodulatory effects have been proposed but remain unclear, yet they may be relevant given IVM use for other infections. We assessed the IVM immunomodulatory effect in 24 participants from a clinical trial evaluating its potential to reduce COVID-19 transmission in mild cases within 48 hours of symptoms onset. The IVM-treated patients showed non-significant lower viral loads, and a significantly shorter duration of hyposmia/anosmia. We measured IgG, IgA, and IgM against five SARS-CoV-2 antigens, and 30 cytokines by Luminex, alongside whole blood RNA sequencing, pan-leukocyte immunophenotyping, and SARS-CoV-2-specific T cell analysis by flow cytometry from day 1 to day 28 post-treatment. All antibody responses increased from day 4, while 13 cytokines significantly decreased over time (adjusted p<0.05). IVM-treated patients had only significantly higher anti-nucleocapsid IgG levels at day 4 (adjusted p=0.041) and 7 (adjusted p=0.045) compared to placebo. SARS-CoV-2-specific CD4+ and CD8+ T cells increased over time, with significantly higher effector memory CD4+ T cells at day 7 compared to day 1 (p=0.027) and the only difference between groups was lower frequencies of spike-specific naive CD4+ T cells at day 7 in IVM-treated participants (0.006% vs 0.036% p=0.02). Transcriptomic data showed downregulation of innate and antiviral blood transcriptional modules (BTMs) over time, with an increase in adaptive immune related BTMs. While no differential gene expression was detected, the IVM-treated had upregulated innate and downregulated T cell and cell cycle BTMs compared to placebo. Overall, our comprehensive longitudinal analysis of early immune responses in mild COVID-19 revealed no robust immunological effects of IVM, consistent with clinical trials results and suggesting a lack of efficacy of IVM in COVID-19 treatment. AUTHOR SUMMARYIvermectin (IVM), an antiparasitic drug, was tested in clinical trials as a potential treatment for COVID-19 due to its in vitro antiviral properties and hypothetical immunomodulatory effects. In this study, we explored the immunomodulatory effects of IVM in a clinical trial involving 24 mild COVID-19 patients who received IVM within 48 hours of symptoms onset. The IVM group showed a trend towards lower viral loads post-treatment, and a significantly shorter duration of hyposmia/anosmia. We comprehensively analyzed immune responses by measuring antibody levels, cytokine profiles, immune cell subsets and whole blood gene expression over 28 days. The IVM group only had increased levels of IgG against the SARS-CoV-2 nucleocapsid compared to the control group. IVM did not affect the kinetics of SARS-CoV-2 T cells, despite a slight decrease in naive CD4+ T cells. Additionally, gene expression analysis showed a decrease in innate and antiviral responses and an increase of adaptive responses over time that were slightly stronger in the placebo compared to the IVM group. In conclusion, despite some differences in IVM treated participants, our detailed analyses do not support significant immunomodulatory effects that could benefit disease progression.

immunology↗

bioRxiv2024

Flexible behavioral adjustment to frustrative nonreward in anticipatory behavior, but not in consummatory behavior, requires the dorsal hippocampus

The hippocampus (HC) is recognized for its pivotal role in memory-related plasticity and facilitating adaptive behavioral responses to reward shifts. However, the nature of its involvement in the response to reward downshifts remains to be determined. To bridge this knowledge gap, we explored the HCs function through a series of experiments in various tasks involving reward downshifts and using several neural manipulations in rats. In Experiment 1, complete excitotoxic lesions of the HC impaired choice performance in an 8-maze task after reducing the quantity of sugar pellet rewards. In Experiment 2, whereas chemogenetic inhibition of the dorsal HC left consummatory responses unaffected after a sucrose downshift, it significantly disrupted anticipatory behavior following a food-pellet reward reduction. Experiments 3-5 used peripheral lipopolysaccharide (LPS) treatment and found an increase in cytokine levels in the dorsal HC (dHC, Experiment 3), impaired anticipatory choice (Experiment 4), but no effect on consummatory behavior in two reward-downshift tasks. In Experiment 6, after a sucrose downshift, we found no evidence of increased activation in either the dorsal or ventral HC, as measured by c-Fos expression. These findings highlight the HCs pivotal role in adaptively modulating anticipatory behavior in response to frustrative nonreward, while having no effect on adjustments of consummatory behavior. Spatial orientation, memory update, choice of reward signals of different value, and anticipatory vs. consummatory adjustments to reward downshift are discussed as potential mechanisms that could elucidate the specific effects observed from HC manipulations.

neuroscience↗

bioRxiv2024

Rating Pome Fruit Quality Traits Using Deep Learning and Image Processing

Quality assessment of pome fruits (i.e. apples and pears) is used not only crucial for determining the optimal harvest time, but also the progression of fruit-quality attributes during storage. Therefore, it is typical to repeatedly evaluate fruits during the course of a postharvest experiment. This evaluation often includes careful visual assessments of fruit for apparent defects and physiological symptoms. A general best practice for quality assessment is to rate fruit using the same individual rater or group of individuals raters to reduce bias. However, such consistency across labs, facilities, and experiments is often not feasible or attainable. Moreover, while these visual assessments are critical empirical data, they are often coarse-grained and lack consistent objective criteria. Granny, is a tool designed for rating fruit using machine-learning and image-processing to address rater bias and improve resolution. Additionally, Granny supports backwards compatibility by providing ratings compatible with long-established standards and references, promoting research program continuity. Current Granny ratings include starch content assessment, rating levels of peel defects, and peel color analyses. Integrative analyses enhanced by Grannys improved resolution and reduced bias, such as linking fruit outcomes to global scale-omics data, environmental changes, and other quantitative fruit quality metrics like soluble solids content and flesh firmness, will further enrich our understanding of fruit quality dynamics. Lastly, Granny is open-source and freely available.

plant biology↗

bioRxiv2023

Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection

HIV-1 infection requires passage of the viral core through the nuclear pore of the cell, a process that depends on functions of the viral capsid 1,2. Recent studies have shown that HIV- 1 cores enter the nucleus prior to capsid disassembly 3-5. Interactions with the nuclear pore complex are necessary but not sufficient for nuclear entry, and the mechanism by which the viral core traverses the comparably sized nuclear pore is unknown. Here we show that the HIV-1 core is highly elastic and that this property is linked to nuclear entry and infectivity. Using atomic force microscopy-based approaches, we found that purified wild type cores rapidly returned to their normal conical morphology following a severe compression. Results from independently performed molecular dynamic simulations of the mature HIV-1 capsid also revealed its elastic property. Analysis of four HIV-1 capsid mutants that exhibit impaired nuclear entry revealed that the mutant viral cores are brittle. Suppressors of the mutants restored elasticity and rescued infectivity and nuclear entry. Elasticity was also reduced by treatment of cores with the capsid-targeting compound PF74 and the antiviral drug lenacapavir. Our results indicate that capsid elasticity is a fundamental property of the HIV-1 core that enables its passage through the nuclear pore complex, thereby facilitating infection. These results provide new insights into the mechanisms of HIV-1 nuclear entry and the antiviral mechanisms of HIV-1 capsid inhibitors.

biophysics↗

bioRxiv2023

Identification of a new human polyomavirus in distinct populations and tissues

ObjectivesThis work aimed to characterize a novel human polyomavirus (HPyV) with cutaneous tropism. MethodsSwabs of healthy skin (forehead) of 75 immunocompetent individuals from Argentina were screened for HPyV through sequence amplification techniques. Publicly available metagenomic datasets were also analyzed. ResultsA previously unknown polyomavirus sequence was detected in two skin swab samples. A nearly identical sequence was detected in public datasets representing metagenomic surveys of human skin and feces. Further analyses showed that the new polyomavirus diverges from its nearest relative, human polyomavirus 6 (HPyV6), by 17.3-17.7% (in nucleotides for the large T antigen), which meets criteria for a new species designation in the genus Deltapolyomavirus. The screening also revealed more distant HPyV6 relatives in macaque genital and chimpanzee fecal datasets. Since polyomaviruses are generally thought to cospeciate with mammalian hosts, the high degree of similarity to HPyV6 suggests the new polyomavirus species is human-tropic. ConclusionsA novel polyomavirus was identified and characterized from samples of distinct populations and tissues. We suggest the common name human polyomavirus 16 (HPyV16).

microbiology↗

bioRxiv2022

The population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection

Enterococcus faecalis is a commensal pathogenic bacterium commonly found in the human gastrointestinal tract and a cause of opportunistic infections typically associated with multidrug resistance. The E. faecalis genetic changes associated with pathogenicity and extraintestinal infection, particularly through gut-to-bloodstream translocation, are poorly understood. Here, we investigate the E. faecalis genetic signatures associated with intestinal colonisation and extraintestinal infection and infection of hospitalised and non-hospitalised individuals using heritability estimation and a genome-wide association study (GWAS). We analysed 750 whole-genome sequences of faecal and bloodstream E. faecalis isolates from hospitalised patients and non-hospitalised individuals, respectively, predominantly in Europe. We found that E. faecalis infection of individuals depending on their hospitalisation status and extraintestinal infection are heritable traits and that [~]24% and [~]34% of their variation is explained by the considered genetic effects, respectively. Further, a GWAS using linear mixed models did not pinpoint any clear enrichment of individual genetic changes in isolates from different isolation sites and individuals with varying hospitalisation statuses, suggesting that these traits are highly polygenic. Altogether, our findings indicate that E. faecalis infection and extraintestinal infection are influenced by variation in genetic, host, and environmental factors, and ultimately the opportunistic pathogenic lifestyle of this versatile host generalist bacterium.

microbiology↗

bioRxiv2022

An unwanted association: the threat to papaya crops by a novel potexvirus in northwest Argentina

An emerging virus isolated from papaya (Carica papaya) crops in northwestern (NW) Argentina was sequenced and characterized using next-generation sequencing. The resulting genome is 6,667-nt long and encodes five open reading frames in an arrangement typical of other potexviruses. This virus appears to be a novel member within the genus Potexvirus. Blast analysis of RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes showed the highest amino acid sequence identity (67% and 71%, respectively) with pitaya virus X. Based on nucleotide sequence similarity and phylogenetic analysis, the name papaya virus X is proposed for this newly characterized potexvirus that was mechanically transmitted to papaya plants causing chlorotic patches and severe mosaic symptoms. RT-PCR based detection of papaya virus X (PapVX) revealed that it is widely present in papaya crops from NW Argentina. The prevalence of PapVX, which seems to be restricted to the NW region of Argentina, and the fact that it has only been detected in this region could be associated with a recent emergence or adaptation of this virus to papaya in NW Argentina.

microbiology↗

bioRxiv2022

An outbreak of SARS-CoV-2 in big hairy armadillos (Chaetophractus villosus) associated with Gamma variant in Argentina three months after being undetectable in humans

The present pandemic produced by SARS-CoV-2 and its variants represents an example of the one health concept in which humans and animals are components of the same epidemiologic chain. Animal reservoirs of these viruses are thus the focus of surveillance programs to monitor their circulation and evolution in potentially new hosts and reservoirs. In this work, we report the detection of SARS-CoV-2 Gamma variant infection in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina. In addition to the finding of a new wildlife species susceptible to SARS-CoV-2 infection, the identification of the Gamma variant three months after its last detection in humans is a noteworthy result, raising the question of potential unidentified viral reservoirs.

microbiology↗