PLOS Pathogens: New Articles

Parallel adaptation and admixture drive the evolution of virulence in the grapevine downy mildew pathogen

2026-03-10T14:00:00Z

by Etienne Dvorak, Thomas Dumartinet, Isabelle D. Mazet, Alexandre Chataigner, Manon Paineau, Dario Cantù, Pere Mestre, Marie Foulongne-Oriol, François Delmotte

Plant pathogens can rapidly adapt to host defenses, threatening the durability of resistance in crop varieties. It is thus crucial to identify the genetic determinants of virulence and understand how it arises and spreads in pathogen populations. In Plasmopara viticola, the biotrophic oomycete causing grapevine downy mildew, virulent strains have recently emerged following the deployment of cultivars carrying partial resistance factors. To investigate the genetic bases of adaptation to grapevine resistances, we carried out a QTL mapping study using two P. viticola biparental populations segregating for the ability to overcome two major loci, Rpv10 and Rpv12. We identified the AvrRpv12 locus, in which strains virulent towards Rpv12 exhibited large homozygous deletions encompassing several RXLR effector genes. Population structure analyses further revealed that distinct alleles were selected independently in different winegrowing regions in Europe, highlighting multiple parallel adaptation events in response to resistance deployment. By contrast, the breakdown of Rpv10 was determined by a dominant locus, suggesting an active suppressor mechanism. The virulent haplotype showed extensive structural rearrangements and a divergent effector repertoire. The locus corresponds to an admixed genomic segment likely originating from a recent secondary introduction of P. viticola into Europe. Beyond merely identifying candidate effectors, these results illustrate the range of evolutionary pathways through which pathogen populations adapt to plant resistances.

PDE4B deficiency aids macrophage differentiation and contributes to Cryptococcus neoformans brain infection

2026-03-10T14:00:00Z

by Ying Gong, Ting Wang, Xin Chen, Yuwei Li, Shaofan Ye, Shan Liu, Chunan Sun, Xia Zhang, Chen Yang, Yonglin Yang, Guannan Zhang, Mingshun Zhang

Cryptococcal meningitis is a fatal complication. Macrophages have been proposed to function as candidate “Trojan horse” cells, transferring Cryptococcus neoformans (C. neoformans) into the brain. The mechanisms of Trojan horses in cryptococcal meningitis are largely elusive. In this study, we performed scRNA-Seq on immune cells infiltrating the brain in a murine model of cryptococcal meningitis. Bioinformatics analysis revealed that phosphodiesterase 4B (PDE4B) is a candidate regulator associated with C. neoformans infected-macrophage. C. neoformans increases the total level of PDE4B in macrophages. However, virulent strains with increased production of melanin paradoxically decreased PDE4B expression in macrophages, implying that PDE4B in macrophages may be negatively associated with C. neoformans invasion. PDE4B inhibition increased Arg1, CXCR4 and CCR7 expression in macrophages, a process regulated by the cAMP/PKA signaling pathway. As expected, PDE4B inhibitors promote the ability of C. neoformans infected-macrophages to cross the blood–brain barrier (BBB) in vitro. Similarly, PDE4B inhibitors or PDE4B knockout increase the fungal burden in the brain, which is, at least partially, rescued by macrophage depletion, and adoptive transfer experiments further support macrophage-mediated fungal delivery to the brain. In contrast, PDE4B activation reduces fungal burden in the brain, including when administered after infection onset. Overall, this study revealed that PDE4B functions as an important regulator of macrophage functional programming during infection and supports a macrophage-mediated dissemination mechanism contributing to brain invasion, and is a potential therapeutic target for cryptococcal meningitis.

Candida in the lung: Fact, fiction, friend or foe?

2026-03-10T14:00:00Z

by Philip Mitchelmore, Seána Duggan

Correction: Inactivation of branched-chain amino acid uptake halts Staphylococcus aureus growth and induces bacterial quiescence within macrophages

2026-03-10T14:00:00Z

by Adriana Moldovan, Ronald S. Flannagan, Marcel Rühling, Kathrin Stelzner, Clara Hans, Kerstin Paprotka, Tobias C. Kunz, David E. Heinrichs, Thomas Rudel, Martin J. Fraunholz

Fifty shades of iron: Unorthodox mechanisms of iron acquisition and utilization in blood-stage Plasmodium parasites

2026-03-10T14:00:00Z

by Kade M. Loveridge, Paul A. Sigala

Plasmodium falciparum parasites cause severe human malaria and depend on iron for essential metabolic processes during all phases of their complicated lifecycle, including when growing in human red blood cells (RBCs). Despite decades of study, the major pathways by which malaria parasites access, distribute, and regulate iron during blood-stage infection remain incompletely defined. The parasite genome lacks many canonical transporters, storage proteins, reductases, and regulatory circuits that are essential for maintaining iron homeostasis in model organisms. Emerging evidence suggests that blood-stage parasites employ unconventional strategies to maintain iron homeostasis. In this review, we synthesize current knowledge of how blood-stage P. falciparum manages iron, from initial uptake through cellular distribution to utilization, highlighting the key proteins and pathways that shape parasite iron metabolism. We also identify major unanswered questions that will guide future efforts to understand and therapeutically target this essential aspect of Plasmodium biology.

The adeno-associated virus Rep proteins target PP4:SMEK1 by preventing substrate recruitment

2026-03-10T14:00:00Z

by Bram Vandewinkel, Sophie Torrekens, Zander Claes, Mathieu Bollen, Els Henckaerts

Despite the widespread use of adeno-associated virus (AAV) vectors in gene therapy, their clinical efficacy and large-scale manufacturing remain constrained by an incomplete understanding of the virus-host interactions that govern AAV gene expression and replication. Here, we identify the PP4:SMEK1/2 phosphatase complex as an important regulator of wild-type AAV replication. Binding studies show that the AAV replication proteins engage SMEK1 to negatively influence PP4 activity. Specifically, AAV Rep68 interferes with substrate recruitment to the PP4:SMEK1 complex, resulting in hyperphosphorylation of the PP4 substrates KAP1^S824 and RPA2^S4/8/33, which in turn enhances viral gene expression and replication. We further uncover a direct interaction between KAP1 and SMEK1, mediated by a MAPP short linear motif that binds the SMEK1 EVH1 domain. Additionally, we identify a multifunctional complex comprising PP4:SMEK1 and PP1:NIPP1 that contributes to KAP1^S824 dephosphorylation. These findings reveal a previously unrecognized mechanism by which viruses subvert host phosphatases to promote replication. This mechanistic insight not only advances our understanding of AAV and phosphatase biology but also has the potential to inform strategies for enhancing AAV vector potency.

Conserved non-coding RNA motifs influence the neuropathogenicity of Simbuviruses: Molecular dissection in the Schmallenberg virus model

2026-03-10T14:00:00Z

by Laura Bonil, Laetitia Wiggers, Hélène Dumont, Marco Caporale, Marie-Cécile Nollevaux, Charles Nicaise, Benoît Muylkens, Damien Coupeau

The Simbu serogroup, part of the Peribunyaviridae family, includes arboviruses associated with febrile illnesses in humans and fetal congenital malformations due to viral neurotropism in ruminants. These viruses possess a tripartite, negative-sense RNA genome lacking the poly(A) tail. Notably, the 5’ untranslated region (UTR) of the small (S) genomic segment contains conserved RNA elements, including a stem-loop (SL) structure and a sequence-based motif (GC signal) flanking the messenger RNA (mRNA) termination site. Although their functions remain unclear, their conservation and specific location suggest a potential role in mRNA transcription termination and translation initiation. A reverse genetics system for Schmallenberg virus (SBV) was used to create a viral recombinant library bearing deliberate mutations in both motifs. Replication kinetics, S segment transcription termination, and Nucleocapsid protein (N) abundance of rescued virus mutants were evaluated in mammalian and insect cell culture. Virulence was assessed in an immunocompetent mouse model. Characterization of the mutant viruses indicated that the SL structure is essential for viral production, with the stem length as a key feature; more than three complementary base pairs between the stem arms are necessary for replication. A shorter stem length impaired replicative fitness, N protein abundance and altered the mRNA to genomic RNA ratio. Point mutations in the GC signal disrupted proper mRNA termination, thereby limiting viral N protein synthesis and, thus, virion assembly. In vivo, attenuated viruses resulted in lower viral loads, reduced dissemination in mice brains, and improved survival rates compared to wild-type SBV. The GC signal mutants exhibited strong attenuation while still maintaining active transcription. Overall, these findings indicate that the SL and GC signal serve as cis-regulatory elements and are indirect determinants of SBV virulence, regulating viral replication and influencing neuropathogenesis.

CD28-deficient mice are vulnerable to mouse papillomavirus MmuPV1 infection of the skin and mucosae

2026-03-10T14:00:00Z

by Sarah Brendle, Jingwei Li, Song Lu, Todd D. Schell, Michael Kozak, Vonn Walter, Debra Shearer, Joshua Place, Karla Balogh, Jean-Laurent Casanova, Neil Christensen, Adam D. Burgener, Thomas T. Murooka, Yusheng Zhu, Vivien Béziat, Jiafen Hu

CD28 is a co-stimulatory molecule expressed on the surface of T cells. To date, three individuals with germline CD28 deficiency have been reported to develop recalcitrant, HPV-driven warts: one exhibited persistent lesions, another experienced disease resolution, and the third developed a chronic “tree-man” phenotype. In mice, we confirmed that CD28-knockout (CD28ko) animals on the C57BL/6 (B6) background are susceptible to cutaneous infection with mouse papillomavirus (MmuPV1); however, their skin warts regressed spontaneously approximately five weeks post-infection. Furthermore, we demonstrate that CD28ko mice are vulnerable to MmuPV1 infection at HPV-relevant mucosal sites, including the most HPV prevalent sites: anogenital tract and oral cavity. Virions recovered from vaginal lavage were infectious but could be neutralized by the neutralizing monoclonal antibody MPV.A4. Viral clearance at mucosal sites was delayed in CD28ko mice, persisting for up to six weeks in the lower genital tract. Blocking the CD28 ligands CD80 and CD86 in B6 mice reproduced the CD28ko phenotype following MmuPV1 infection and markedly reduced CD28 expression, implicating the CD28-CD80/CD86 axis in delayed viral clearance. Infected CD28ko mice showed a reduction in both CD4⁺ and CD8⁺ T cell population in the spleen compared to infected B6 mice, but an increase in CD11c⁺/F4-80⁺ cells, particularly the plasmacytoid dendritic cell (pDCs, SiglecH⁺) subset. Additionally, CD28ko mice exhibited delayed recruitment of activated CD4⁺ T cells to infected tissues. Accumulation of MmuPV1 E6/90–99-specific, tetramer-positive CD8⁺ cytotoxic T lymphocytes (CTLs) was slower in CD28ko than in B6 mice; these CTLs remained FoxP3 negative but displayed reduced efficacy in both in vitro killing and antiviral cytokine assays. Adoptive transfer of CTLs from either B6 or CD28ko mice into MmuPV1-infected Rag1ko mice induced viral clearance at mucosal (oral) sites, whereas B6-derived CTLs achieved more complete regression of cutaneous (tail) lesions. Collectively, these findings indicate that CD28 deficiency delays but does not prevent the clearance of papillomavirus infections at both cutaneous and mucosal sites in mice.

Gelatinase regulates the egress of intracellular replicating populations during Enterococcus faecalis infection

2026-03-10T14:00:00Z

by Frederick Reinhart Tanoto, Jia Hui Liew, Claudia J. Stocks, Deepti Rawat, Kelvin Kian Long Chong, Kevin Pethe, Haris Antypas, Kimberly A. Kline

Enterococcus faecalis is a common opportunistic pathogen, frequently isolated from chronic wounds, yet the mechanisms underlying its virulence and persistence in this niche remain incompletely understood. We previously showed that a subpopulation of E. faecalis can survive intracellularly for several days during murine wound infection and can replicate within macrophages, revealing an unexpected intracellular phase for this traditionally extracellular bacterium. Here, we identify the secreted metalloprotease gelatinase (GelE) and its regulator, the Fsr quorum sensing system, as key modulators of E. faecalis intracellular survival and replication. Mechanistically, Fsr quorum sensing is induced during intracellular replication, promoting GelE-dependent host cell lysis and bacterial egress. In the absence of active GelE, E. faecalis accumulates as large intracellular clusters, a phenotype observed consistently across GelE deficient wound isolates. In a mouse wound model, GelE deficient E. faecalis similarly exhibited higher intracellular numbers within wound infection-associated host cells. Together, our study uncovers GelE as a central effector that orchestrates the transition between intracellular and extracellular lifestyles of E. faecalis, providing a possible explanation for its persistence in chronic wound infection.

Mutualism in disguise: A mosquito parasite with mixed transmission mode displays mutualistic traits promoting oogenesis

2026-03-09T14:00:00Z

by Maxime Girard, Mathieu Laÿs, Edwige Martin, Laurent Vallon, An-nah Chanfi, Mélanie Bretton, Aurélien Vigneron, Séverine Balmand, Patricia Luis, Anne-Emmanuelle Hay, Claire Valiente Moro, Guillaume Minard

Mutualistic traits are frequently associated with vertically transmitted symbionts, in part because repeated interactions can align host and symbiont fitness. However, how such traits emerge in symbionts combining vertical and horizontal transmission remains unclear. Here we show that Ascogregarina taiwanensis, previously described as a weak horizontally transmitted parasite of the Asian tiger mosquito (Aedes albopictus), also displays mutualistic traits that enhance mosquito reproduction. Infected females show improved embryogenesis and an extended egg-laying period, while most pseudo-vertically transmit oocysts to their progeny at oviposition sites. This interaction ultimately produces larger larvae that are more frequently infected by As. taiwanensis. Dual transcriptomic analyses further reveal that early oogenesis in infected females involves increased nitrogen metabolism in both partners, enhanced detoxification of blood waste, and activation of egg development pathways. These changes improve assimilation of blood proteins essential for egg production. Together, our results illustrate how physiological coupling during reproduction, combined with mother-biased transmission, can generate mutualistic traits within an interaction that also retains parasitic features, blurring the boundary between parasitism and mutualism.

RND-mediated efflux couples antimicrobial resistance and hypervirulence in contemporary Vibrio cholerae

2026-03-09T14:00:00Z

by Yuding Weng, X. Renee Bina, Mia E. Van Allen, James E. Bina

The prevailing view in bacterial pathogenesis is that antimicrobial resistance and virulence are constrained by evolutionary trade-offs, with resistance mechanisms imposing fitness costs that attenuate pathogenic potential. Herein we document that contemporary Vibrio cholerae clinical isolates from the ongoing seventh pandemic have circumvented this paradigm by coupling multidrug resistance with hypervirulence. We examined five geographically diverse Wave 3 isolates collected between 2017 and 2019 and compared them to early pandemic strains. These contemporary isolates exhibited both broad-spectrum antimicrobial resistance and markedly enhanced colonization capacity in the infant mouse model. Phylogenetic analysis of 67 O1 El Tor genomes spanning 1960–2019 confirmed that the isolates cluster within a representative Wave 3 sublineage. We identified the VexB RND efflux pump as a mediator of this coupled phenotype. Elevated vexB expression in the contemporary isolates conferred resistance to multiple antibiotic classes, while vexB inactivation simultaneously impaired resistance and colonization. This dual function was not observed in early pandemic strains, consistent with a recent evolutionary adaptation. VexB-mediated hypervirulence occurred through multiple pathways independent of cholera toxin and toxin-coregulated pilus production levels. VexB deletion impaired bacterial adherence to intestinal epithelial cells, impaired motility, and increased susceptibility to membrane-active antimicrobials. In contrast, laboratory evolution under antibiotic pressure alone generated resistant but avirulent strains, demonstrating that complex selective forces in nature enabled the co-optimization of resistance and virulence. These findings establish VexB as a molecular link between antimicrobial resistance and hypervirulence in pandemic V. cholerae, highlighting efflux pumps as dual-function therapeutic targets whose inhibition could both restore antibiotic activity and attenuate disease.

Correction: Extracellular vesicles from diverse fungal pathogens induce species-specific and endocytosis-dependent immunomodulation

2026-03-09T14:00:00Z

by Geneva N. Kwaku, Kirstine Nolling Jensen, Patricia Simaku, Daniel J. Floyd, Joseph W. Saelens, Christopher M. Reardon, Rebecca A. Ward, Kyle J. Basham, Olivia W. Hepworth, Tammy D. Vyas, Daniel Zamith-Miranda, Joshua D. Nosanchuk, Jatin M. Vyas, Hannah Brown Harding

Decoding the Pine Wood Nematode’s survival mystery: Gene family expansion drives adaptation revealed by dual-omics

2026-03-06T14:00:00Z

by Hudie Shao, Jing Chen, Wenxin Hu, Yuxin Zou, Hengliang Liu, Yanjun Zhang, Fengyuan Wei, Quan Li, Kai Guo, Pan Zhang, Jiafu Hu

The pine wood nematode (PWN) Bursaphelenchus xylophilus is a highly destructive invasive pest that has spread from North America to Eurasia, demonstrating remarkable adaptability across environments. However, the molecular mechanisms underlying environmental adaptation of B. xylophilus remain poorly understood. In this study, we integrated genomic and transcriptomic analyses of B. xylophilus and its native sibling species B. mucronatus, which is native in China. Functional validation of key genes was conducted using RNA interference, BAX, and inoculation assays. Our research focused on three rapidly expanding gene families in B. xylophilus, including the BolA-like superfamily, diacylglycerol acyltransferase (DGAT), and papain-like cysteine peptidase (PLCP). Key genes were functionally validated to elucidate their roles in environmental adaptability. The BolA-like genes were identified as critical stress-response elements, enabling B. xylophilus to survive under harsh conditions. The DGAT genes are essential for lipid biosynthesis and play pivotal roles in resisting starvation and cold. Regarding pathogenicity, the PLCP gene family has been identified as a critical virulence determinant facilitating B. xylophilus infection on host pine trees. These expanded gene families collectively enhance stress tolerance and virulence in B. xylophilus. The findings of this study not only reveal the genetic basis of PWN’s invasive success, but also provide a foundation for managing climate-driven disease spread.

Repurposing metformin as a dual-function agent to combat E. coli-induced mastitis: Mechanistic insights into biofilm dispersion and AMPK/SIRT1-mediated NF-κB inhibition

2026-03-06T14:00:00Z

by Tianle Xu, Wendi Cao, Shuangyuan Fan, Run Liu, Hao Zhu, Xubin Lu, Zhipeng Zhang, Xiaojiao He, Kai Zhang, Jie Huang, Nana Ma, Guangjun Chang, Zhangping Yang

Escherichia coli-induced bovine mastitis represents a major challenge in dairy production due to the prevalence of multidrug-resistant strains. This study repurposes metformin as a dual-function agent that simultaneously targets bacterial virulence and host inflammation. Epidemiological surveillance identified phylogroup B1 as the most prevalent (52.5%) and resistant E. coli lineage. Against a representative B1 strain, metformin potently inhibited and dispersed bacterial biofilms, and synergized with conventional β-lactam antibiotics. Bacterial transcriptomics revealed metformin downregulated genes critical for membrane integrity and metabolism. In parallel, metformin attenuated the inflammatory response in bovine mammary epithelial cells and in murine and ovine mastitis models. In vivo, it significantly reduced bacterial colonization in mammary tissue and suppressed key pro-inflammatory cytokines. Mechanistically, metformin activated the AMPK/SIRT1 axis, leading to deacetylation of NF-κB p65. In the ruminant model, this culminated in epigenetic regulation, with increased chromatin compaction at promoters of inflammatory genes, and a significant inverse correlation (r = -0.77) between NF-κB binding and chromatin accessibility. Collectively, metformin combats resistant E. coli mastitis through a dual mechanism: disrupting biofilm-dependent bacterial persistence and reprogramming host immunometabolism via AMPK/SIRT1-mediated epigenetic regulation. These findings provide a compelling non-antibiotic strategy for overcoming antimicrobial resistance.

Response to comment on: Is “pre-sepsis” the new sepsis? A narrative review

2026-03-06T14:00:00Z

by Rémy Gerard, Antoine Dewitte, Fridolin Gross, Thomas Pradeu, Maël Lemoine, Julien Goret, Maria Mamani-Matsuda

Comment on: Is “pre-sepsis” the new sepsis? A narrative review

2026-03-06T14:00:00Z

by Andres Giglio, Maria Aranda, Eric Macias, Marcio Borges

The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures

2026-03-06T14:00:00Z

by Franck Dumetz, Kaylee J. Watson, Melissa Perry, Robin E. Bromley, Anushka R. Shome, Julie C. Dunning Hotopp, Iqbal Hamza, David Serre

Leishmania spp. regulate gene expression post-transcriptionally, yet untranslated regions (UTRs) that can affect mRNA stability and translation remain poorly delineated. We generated a de novo assembled genome for Leishmania donovani strain 1S2D (Ld1S) using PacBio HiFi and characterized the transcriptomes of promastigotes and axenic amastigotes with Oxford Nanopore direct RNA sequencing. The genome assembly consists of 65 scaffolds totaling ~33.3 Mb. Structural comparisons to LdBPK282A1 revealed numerous rearrangements, including genes reshuffled among polycistronic transcription units and validated by RNA sequencing of polycistronic reads. Promastigote and amastigote RNA sequencing produced 469,010 and 46,729 monocistronic reads containing a spliced-leader and a polyA tail sequences, defining 8,479 transcripts and supporting 7,415 of the 7,969 annotated protein-coding genes, as well as 604 putative long non-coding RNAs. We annotated UTRs for 4,921 genes and observed that putative RNA G-quadruplexes were markedly enriched in these regions. We also noted that 31.9% and 11.5% of genes were expressed into multiple isoforms in promastigotes and amastigotes, respectively. Collectively, these data provide a genome-wide annotation of L. donovani genes and their UTRs and reveal widespread and stage-specific UTR length polymorphisms and, overall, points to an important role of 3’ UTRs in post-transcriptional regulation in L. donovani.

Regulatory diversity in Bacillus thuringiensis cry genes reveals flexible evolutionary strategies for in vivo toxin expression

2026-03-04T14:00:00Z

by Isabel Gómez, Blanca I. Garcia-Gómez, Nathaly A. do Nascimento, Oscar Infante, Pablo Emiliano Cantón, Sabino Pacheco, Angel E. Peláez-Aguilar, Jorge Sanchez, Mario Soberón, Alejandra Bravo

Bacillus thuringiensis (Bt) is a highly effective insect pathogen, largely due to the expression of diverse insecticidal proteins upon sporulation. Among them, the three-domain Cry protein family represent the largest family, targeting a wide range of insect species and nematodes. While it is proposed that they have evolved from a common ancestral gene, the comparative analysis of their upstream regulatory regions revealed significant variability. To investigate this divergence, we employed Multiple Expectation maximization for Motif Elicitation (MEME) and Find Individual Motif Occurrences (FIMO) motive discovery tools, to identify conserved regulatory elements, including canonical -10 and -35 promoter motifs and Shine-Dalgarno (SD) sequences. Our analyses clearly revealed that upstream regulatory sequences are not conserved across the entire cry family. However, we identify subsets of genes with similar insect specificity which shared conserved motif architectures in their upstream regulatory sequences, suggesting a correlation between regulatory evolution and host range. Conversely, some proteins targeting the same insect order (e.g., Cry1 and Cry9Ca or Cry3 and Cry8) showed to be regulated by entirely different upstream sequences, indicating that Bt has evolved multiple regulatory strategies to achieve similar expression patterns. To test relevance of the upstream sequences, we cloned cry1Ab and cry4Ba genes under the control of heterologous upstream regions: P1P2 from lepidopteran-specific cry1Aa gene, and P4 from dipteran-specific cry4Ba gene. These constructions were expressed in non-toxic Cry^- acrystalliferous Bt-backgrounds with distinct host specialization: Bt subsp thuringiensis 407 strain (lepidopteran adapted) and Bt subsp israelensis 4Q7 strain (dipteran adapted). Gene expression was assessed in vitro and in vivo after oral infection of lepidopteran and dipteran larvae with purified spores. Our findings indicate that Cry protein expression is influenced by both, the promoter identity, and Bt strain background, underscoring the evolutionary and functional significance of upstream regulatory sequences in the diversification and ecological success of Bt.

Correction: Fusaric acid-mediated S-glutathionylation of MaAKT1 channel confers the virulence of Foc TR4 to banana

2026-03-04T14:00:00Z

by The PLOS Pathogens Staff

Histone demethylase JMJD1A protects mice from enteric bacterial infection by upregulating CCL8 expression to recruit macrophages and CD4⁺ T cells

2026-03-04T14:00:00Z

by Guifang Lin, Lichun Yang, Shuyan Jiang, Yong Zhang, Ping Luo, Weihua Li, Jianming Xu, Gongpeng Xiong, Chundong Yu, Wenbo Chen

Jumonji domain-containing 1A (JMJD1A, also known as KDM3A) is a histone demethylase that specifically demethylates H3K9me1/2 to enhance gene expression. The roles of JMJD1A in many physiological and pathological processes have been revealed. However, it is unclear whether JMJD1A is involved in host defense against enteric pathogen infection. In this study, we found that enteric infection with C. rodentium induced JMJD1A expression in colonic epithelial cells at the transcriptional level partly mediated by IRF1. After C. rodentium infection, JMJD1A^-/- mice exhibited increased mortality, colonic injury, and C. rodentium load and systemic spread, suggesting that JMJD1A protects host against C. rodentium infection by enhancing C. rodentium clearance. JMJD1A^-/- mice exhibited an impaired colonic recruitment of macrophages and CD4⁺ T cells as well as a reduced production of C. rodentium-specific IgG, leading to impaired clearance of C. rodentium. Reduced induction of a chemoattractant CCL8 in the colon of JMJD1A^-/- mouse was responsible for reduced recruitment of macrophages and CD4⁺ T cells to the colon after C. rodentium infection. Mechanistically, JMJD1A cooperated with STAT1 and demethylated H3K9me2 on IRF1 promoter to promote the expression of IRF1, which can enhance CCL8 expression. Furthermore, JMJD1A cooperated with IRF1 and demethylated H3K9me2 on CCL8 promoter to induce CCL8 expression. Collectively, our study suggests that JMJD1A contributes to host defense against enteric bacteria, at least in part, by promoting CCL8 expression to enhance the recruitment of macrophages and CD4⁺ T cells.

Panzootic H5 influenza viruses acquired resistance to human head interface antibodies

2026-03-04T14:00:00Z

by Aaron L. Graber, Holly C. Simmons, Kevin R. McCarthy

Antibodies to the influenza hemagglutinin protein (HA) confer the strongest protection against infection. Immunity elicited by endemic, seasonal, human viruses is correlated with diminished disease severity and death caused by antigenically novel viruses. Antibodies to the HA head interface are broadly protective and abundant in human serologic and memory repertoires. Notably, few head interface antibodies from H5 naive donors are reported to bind H5 HAs. We find head interface antibodies engage a wide range of H5 isolates but fail to engage most isolates from the goose Guangdong (GsGd) lineage. We identify a single substitution, P221S, largely dictates antibody binding. Phylogenetic analysis indicates that P221S arose in a Chinese avian reservoir by the year 2000. Descendants of these viruses have caused the current global panzootic and have achieved sustained mammal-mammal transmission in farmed and wild mammals. Our findings demonstrate that viral evolution in non-mammalian species can, by chance, produce viruses that resist broadly protective human antibody responses.

Structures of nucleotide-bound Redondovirus Rep protein link conformation and function

2026-03-04T14:00:00Z

by Saira Montermoso, Kushol Gupta, Ruth Anne Pumroy, Vera Moiseenkova-Bell, Frederic D. Bushman, Gregory D. Van Duyne

Circular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3’ end for polymerase extension, provide an NTP-dependent helicase activity for DNA unwinding, and join nicked ends to form circular viral genomes. Here, we present the first structures of a Rep protein from the Redondoviridae family, a newly discovered family of human-associated CRESS-DNA viruses that replicates within the oral protozoan Entamoeba gingivalis. Using cryo-EM, we characterized the hexameric structures of a Redondovirus Rep helicase bound with ATPγS, representing the initial ATP-bound state, and with ADP, reflecting the protein state after hydrolysis. The ADP state, but not the ATP state of Rep shows a staircase arrangement of DNA-binding loops that plays a central role in current models for SF3 helicase function. Additionally, we determined a head-to-tail dodecameric structure of ATPγS-bound Rep, in which both the helicase and endonuclease domains are ordered. Conservation of residues involved in stabilizing the dodecamer suggest that this assembly may be functionally relevant for many CRESS-DNA viruses. The positioning of endonuclease domains in the Rep hexamer, combined with our biophysical analyses of Rep oligomerization, provide new insights into Rep function during viral replication.

Type VI secretion system degeneration accelerates intestinal epithelial cell death in Escherichia coli O157:H7

2026-03-03T14:00:00Z

by Zhibin Sun, Chao Dong, Pengcheng Zhou, Quanquan Guan, Zhongli Cui, Yankai Xia, Yu-Feng Yao

The type VI secretion system (T6SS) is a specific protein secretion apparatus that contributes to bacterial virulence. Enterohemorrhagic Escherichia coli O157:H7 (EHEC) harbors multiple prophages and can cause severe human diseases worldwide. Here, we compared the EHEC T6SS main gene cluster with its ancestral strain E. coli O55:H7 (aEPEC) and predicted 26 mutation loci in protein-coding regions. Sequence analysis of these mutation loci indicated a degenerative trend in T6SS function in EHEC. Notably, a 28-bp tandem repeat insertion in the T6SS core gene tssM significantly compromised T6SS secretion activity. Inactivation of the T6SS significantly enhanced EHEC cytotoxicity and accelerates epithelial cell death. Mechanistically, inactivation of T6SS promotes EHEC Stx2-converting prophage (Φstx2) expression, and deletion of Φstx2 weakens the T6SS-deficient strain’s cytotoxicity. Analysis of EHEC evolutionary path revealed that tssM mutation may occur after Φstx2 integration, and this mutation is widely distributed in E. coli bearing Φstx2 (E. coli_Φstx2), suggesting T6SS degeneration may be closely associated with Φstx2 integration in E. coli_Φstx2. Crucially, degenerative T6SS could render Φstx2 more sensitive to activation, and in turn activates EHEC major virulence factors such as Shiga toxin and type III secretion system. Taken together, our findings suggest that the ancestral aEPEC strain acquired Φstx2 and underwent T6SS degeneration, ultimately evolving into a highly cytotoxic EHEC lineage.

The CD97-PPM1G axis dampens antiviral immunity by dephosphorylating IRF7 in type I interferon pathway

2026-03-03T14:00:00Z

by Huasong Chang, Wenjing Qi, Rukun Yang, Peili Hou, Ran Kang, Xiaoyu Liu, Yingying Li, Hongmei Wang, Hongbin He

The activation of type I interferon (IFN-I) signaling is crucial for defending host cells against viral infections. A comprehensive IFN-I response necessitates the activation of several cellular factors, among them Interferon Regulator Factor 7 (IRF7). Nonetheless, the mechanisms governing IRF7 inactivation in response to viral infection remain largely unknown. Here, we illustrate that Cluster of differentiation 97 (CD97), a G protein-coupled receptor, interacts with PPM1G via intracellular Arg-819 and Arg-822 residues. PPM1G then recruits and dephosphorylates IRF7, leading to its inhibition. CD97-mediated inactivation of IRF7 impedes its translocation into the nucleus and subsequent activation of IFN-I, ultimately promoting the viral replication. Moreover, mice lacking CD97 display heightened resistance to viral infection. The compound sanguinarine (SANG) hinders viral replication by dampening CD97 expression. This study provides a basis for CD97 as a potential antiviral target and SANG as a candidate antiviral small molecule drug.

Duration of immunity following infection with moderately virulent ASFV

2026-03-03T14:00:00Z

by Virginia Friedrichs, Paul Deutschmann, Kerstin Wernike, Tessa Carrau, Martin Beer, Sandra Blome, Alexander Schäfer

African swine fever virus (ASFV) poses a significant threat to pork production and wild pig populations worldwide. The study assessed the long-term fate and immunity of animals recovering from a moderately virulent ASFV infection, following the principles of a duration of immunity study for live vaccines. Pigs inoculated with the moderately virulent ASFV strain Estonia14 largely developed mild clinical signs and only transient viremia. Six months after the initial inoculation and once fully recovered, all the animals were challenged with highly virulent ASFV Armenia08. Only one of the previously exposed pigs exhibited mild clinical signs, while all control animals showed typical signs of acute, lethal ASF. Moreover, only a subset of pigs inoculated with the ASF strain Estonia14 displayed temporary detectability of ASFV genomes following challenge infection. Virus isolation corroborated these findings, with low levels of infectious virus in organs of previously inoculated pigs (28 days post challenge). Furthermore, monitoring of ASFV-specific IgM and IgG kinetics enabled the analysis of humoral responses. IgG levels were sustained over the study period and increased slightly upon challenge infection. Lastly, plasma analysis revealed elevated complement factor C3a levels post inoculation and challenge in the recovered pigs, directly correlating with challenge virus presence. In contrast, both C3a and C5a levels were increased in the control group. It could be shown that complement system activation was mediated by the lectin pathway, possibly by interaction of mannose-binding lectins and ASFV particles. This study suggests that protective immunity following recovery can last at least six months. No cases of persistent or chronic disease were observed in convalescent pigs. These findings have implications for both vaccine development and assessment, as well as for disease control strategies including surveillance actions.

Will animal reservoirs give us the next SARS-CoV-2 variant?

2026-03-03T14:00:00Z

by Davey Smith

Acoziborole resistance associated mutations in Trypanosoma brucei CPSF3

2026-03-03T14:00:00Z

by Melanie Ridgway, Markéta Novotná, Cesar Mendoza-Martinez, Michele Tinti, Simone Altmann, Graeme Sloan, David Horn

Acoziborole is a safe, single dose, oral therapy, for treatment of both early and late-stage sleeping sickness, a deadly disease caused by African trypanosomes. Other benzoxaboroles show efficacy against other trypanosomatids, apicomplexans, fungi, bacteria, and viruses. Acoziborole targets the trypanosome pre-mRNA processing endonuclease, cleavage and polyadenylation specificity factor 3 (CPSF3), and triggers CPSF3 degradation, but it remains unclear whether additional mechanisms contribute to efficacy. We used oligo targeting for site saturation mutagenesis of the native CPSF3 gene. Among >1,500 edits around the putative drug binding site, only Asn²³²His edits conferred moderate resistance to acoziborole. Using a combinatorial oligo targeting method we edited multiple sites simultaneously, including sites that differ in human CPSF3, and found that an Asn²³²His, Tyr³⁸³Phe, Asn⁴⁴⁸Gln triple-mutant strain was > 40-fold resistant to acoziborole. We used gene tagging to show that all three edits were on the same allele, and to show that triple-mutant CPSF3 was highly resistant to rapid acoziborole and proteasome-dependent degradation. Computational modelling revealed how the combinatorial mutations can disrupt acoziborole – CPSF3 interactions by introducing steric clash and by disrupting hydrophobic and water-mediated interactions. We conclude that acoziborole safety and efficacy can be explained by selective affinity for, and rapid turnover of, trypanosome CPSF3.

Fatal human H3N8 influenza virus has a moderate pandemic risk

2026-03-03T14:00:00Z

by Valerie Le Sage, Michelle N. Vu, Maria A. Maltepes, Shengyang Wang, Brooke A. Snow, Grace A. Merrbach, Alexandra J. Benton, Kylie E. Zirckel, Sarah E. Petnuch, Carly N. Marble, Lora H. Rigatti, James C. Paulson, Elizabeth M. Drapeau, Anita K. McElroy, Scott E. Hensley, Louise H. Moncla, Seema S. Lakdawala

In China, low pathogenic avian influenza (LPAI) H3N8 virus is widespread among chickens and has recently caused three zoonotic infections, with the last one in 2023 being fatal. Here we evaluated the relative pandemic risk of this 2023 zoonotic H3N8 influenza virus, utilizing our previously published decision tree. Serological analysis indicated that a large proportion of the human population does not have any cross-neutralizing antibodies against this H3N8 strain. LPAI H3N8 displayed a dual affinity for α2–3 and α2–6 sialic acids and replicated efficiently in human bronchial epithelial cells. Furthermore, we observed H3N8 transmission via direct contact but not aerosols to ferrets with pre-existing H3N2 immunity. Although pre-existing H3N2 immunity resulted in a shortened disease course in ferrets, it did not reduce disease severity or replication in the respiratory tract. This study suggests that this zoonotic H3N8 strain has moderate pandemic potential and emphasizes the continued need for avian influenza surveillance.

Proximity labelling identifies proteins associated with HSV-2 pUL21 at early and late times after infection

2026-03-02T14:00:00Z

by Safara M. Holder, Maike Bossert, Renée L. Finnen, Bruce W. Banfield

pUL21 is a conserved and multifunctional alphaherpesvirus tegument protein that is critical for both early and late stages in the herpes simplex virus type 2 (HSV-2) replication cycle; however, how pUL21 participates in these activities is poorly understood. To help elucidate the role of pUL21 in these various activities, we used a proximity-dependent biotin identification (BioID) approach by constructing an HSV-2 strain encoding pUL21 fused to the non-specific biotin ligase, miniTurbo (pUL21mT). Cells infected with this strain were treated with exogenous biotin at early and late times post-infection and biotinylated proteins were affinity-purified and identified by mass spectrometry. This approach enabled the identification of many viral and cellular proteins in proximity to pUL21mT at late times after infection, including those involved in cell adhesion and junction organization, as well as components of the spliceosome and the nuclear envelope. We also utilized this system to identify proteins in proximity to tegument-delivered pUL21mT immediately following viral entry, thereby providing a comprehensive profile of pUL21 proximal interactors at both early and late stages of infection. These proximal interactions were further validated by pUL21 affinity purification experiments, which confirmed that many viral and cellular proteins identified by BioID associate with pUL21. These findings provide insights into the role of HSV-2 pUL21 during infection and highlight BioID as a powerful tool for investigating virus-host interactions at multiple stages of infection.

TRIM29 knockout pigs exhibit enhanced broad-spectrum disease resilience by amplifying type I interferon antiviral defenses

2026-03-02T14:00:00Z

by Xiaohui Yang, Haiwen Zhong, Jie Cheng, Huijie Jiang, Jiayong Tan, Cuizhen Wang, Changxu Song, Gengyuan Cai, Huaqiang Yang, Zhenfang Wu

While production traits have seen accelerated genetic improvement through advanced breeding technologies, disease resilience phenotypes continue to pose significant challenges in livestock breeding system. Current gene editing technologies provide an effective and biosafe strategy to enhance livestock disease resilience through precise manipulation of host antiviral genes. In this study, we successfully generated disease-resilient pigs exhibiting broad-spectrum antiviral activity against multiple viruses, with no observed adverse effects on pig health. The E3 ubiquitin ligase TRIM29 functions as a negative regulator of type I interferon (IFN) signaling, thus representing a potential antiviral target. Knockdown of TRIM29 in PK15 cells significantly enhanced antiviral immunity against pseudorabies virus (PRV) and vesicular stomatitis virus (VSV) by augmenting type I IFN production. Translationally, we generated Trim29 knockout (KO) mice and confirmed their enhanced antiviral ability to both PRV and VSV infections. Subsequently, we produced TRIM29-KO pigs via gene editing coupled with somatic cell nuclear transfer. Compared to wild-type controls, the TRIM29-KO pigs exhibited significantly enhanced resilience to PRV infection, which was associated with elevated type I IFN levels in vivo. Furthermore, alveolar macrophages derived from TRIM29-KO pigs showed reduced susceptibility to infection with PRV, VSV, and transmissible gastroenteritis virus (TGEV), highlighting their potential broad-spectrum antiviral activity against multiple viral pathogens.

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Will animal reservoirs give us the next SARS-CoV-2 variant?

Acoziborole resistance associated mutations in Trypanosoma brucei CPSF3

Fatal human H3N8 influenza virus has a moderate pandemic risk

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TRIM29 knockout pigs exhibit enhanced broad-spectrum disease resilience by amplifying type I interferon antiviral defenses

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