Frontiers in Virology

The ubiquitin-conjugating enzyme UBE2J1 functions in the proteasomal degradation of proteins at the ER. Existing evidence suggests that it plays a role during viral infection, with elevated UBE2J1 levels generally associated with increased infection. This is particularly relevant for some RNA viruses; however, the regulation of UBE2J1 during infection has not been well studied. Here, we used a BHK21 cell model to demonstrate that UBE2J1 overexpression promotes the replication of Vesicular Stomatitis Virus (VSV), as indicated by a significant increase in viral titres. To better understand the underlying molecular processes, cells were co-transfected to express the VSV-G protein and wild-type UBE2J1 protein, and we observed a significant increase in the syncytial fusion area. This effect was not observed when catalytically inactive (C91S) or phospho-deficient (S184A) forms of the protein were used. Interestingly, overexpression of a truncated, non-ER localized form of UBE2J1 ({Delta}TM) led to the largest increase in the syncytial fusion area. This arose as a result of increased syncytia size, and may indicate an enhanced cellular role if soluble forms of UBE2J1 are not anchored to the ER. Additional studies using truncated, mutated and wild-type proteins confirmed that UBE2J1 increases VSV viral replication and is associated with an increase in the number of infection plaques. Considering the emerging evidence for UBE2J1 involvement in viral infection, our finding should help in understanding the role of this protein in viral pathogenesis and cellular processes linked to syncytialization.

Borealpox virus (BRPV; formerly Alaskapox) is an orthopoxvirus that has caused seven reported human infections in Alaska since 2015, including a fatal case in 2023. The natural reservoir of BRPV is unknown, although previous investigations have raised the possibility of wild small mammals transmitting the virus to humans, either through direct contact or via domestic cats and dogs. To understand which species may be involved in the maintenance and/or spillover of BRPV in Alaska, we trapped and sampled wild small mammals (including voles, shrews, and squirrels) in 2021 and 2024 near reported human case locations in Fairbanks and the Kenai Peninsula, respectively. We found evidence of previous exposure to orthopoxviruses in five species (including the House Mouse, Mus musculus) and detected BRPV DNA as well as viable virus in Northern Red-backed Voles (Clethrionomys rutilus). Further, screening of tissues from historical museum specimens revealed BRPV DNA in C. rutilus specimens collected in Denali National Park and Preserve in 1998 and 1999, 17 years before the first reported human case of BRPV. Phylogenomic analysis of all human and animal BRPV isolates strongly supports the hypothesis of local human infections through multiple spillover events. These findings suggest C. rutilus as a possible reservoir species for BRPV and indicate that BRPV has been present in Alaskan wild small-mammal populations for at least 25 years. Our study highlights the potential of museum collections to elucidate the temporal, spatial, and host ranges of emerging pathogens. Further museum- and field-based sampling will clarify the true geographic range of BRPV, which is closely related to Old World orthopoxviruses and may be circulating beyond North America.

Avian influenza virus (AIV) epidemiology is well-documented in temperate regions but remains poorly understood in isolated ecosystems like tropical oceanic islands. On these islands, seabirds nest in dense interspecific colonies where the role of different species as reservoirs and dispersers of AIV may vary greatly. Here, we examine the role of noddies (Anous spp.) as potential reservoirs for low pathogenic AIV and evaluate their potential as sentinel species for highly pathogenic AIV introduction on tropical oceanic islands. We analyzed blood samples from 11 seabird species across eight islands in the southwestern Indian Ocean (2015-2020). Noddies exhibited high, stable seroprevalence (30-45%), comparable to reservoir host species in temperate regions. The detection of two N7-positive noddies, sampled the same year on two distinct islands, provided direct molecular evidence that AIV actively circulates on these island colonies. While most other species showed low exposure, Bridled Terns (Onychoprion anaethetus) had exceptionally high seroprevalence (80%), though their reservoir status requires further investigation due to limited sampling. Given noddies consistent exposure and regional distribution, we recommend prioritizing islands with large noddy populations for AIV surveillance. Continued investigation of viral dynamics within and among islands is now called for to elucidate the ecological drivers of AIV maintenance and transmission.

In an infection, Hepatitis B Virus (HBV) core protein (HBc) normally assembles into icosahedral capsids. Capsid Assembly Modulators (CAMs) are direct acting antivirals that induce HBc mis-assembly and are the subject of active research and development. Two versions of HBc are used in structural studies of CAM-HBc complexes: Cp150 and Cp149-Y132A. Cp150 forms empty icosahedral capsids that are structurally indistinguishable from those found in virions. The Y132A mutation of Cp149 leads to an assembly defective soluble protein that crystalizes as flat hexagonal sheets, where the hexagons resemble icosahedral quasi-sixfold vertices. In this study, we compare structures of CAM-bound Cp150 to CAM-bound Cp149-Y132A. In capsids, the residues forming the CAM site shift to match the structure of bound CAMs, an induced fit. In Cp149-Y132A crystals, CAM sites show little structural adjustment in response to different CAMs binding. In turn, the array of residues that interact with CAMs varies from CAM to CAM in capsid structures but remains nearly constant in Cp149-Y132A crystals. These results illustrate important differences between CAM binding in Cp149-Y132A and Cp150 structures that will contribute to future CAM design.

Deer tick virus (DTV), or lineage II Powassan virus, is an emergent tick-borne encephalitis virus in North America. Survivors frequently sustain neurologic sequelae. Nationally reported cases have been increasing. DTV is thought to be maintained in nature by multiple modes including horizontal transmission (from viremic host to tick), cofeeding transmission (between ticks feeding nearby) and by transovarial transmission (female to progeny). Analysis of the relative importance of each mode has been hindered by low enzootic transmission. In 2021, Marthas Vineyard, Massachusetts experienced an epizootic that allowed us to probe the modes of transmission on the island. We detected virus in 7.8% of questing deer tick nymphs (161 of 2063) and in 0.3% of lone star nymphs (2 of 678). Infected ticks had a highly focal distribution; 56% of infected ticks derived from only 4 of 71 collection sites. Tick mitochondrial genome sequencing demonstrated that infected ticks were not more likely to be siblings than negative ticks and, therefore, were unlikely to have inherited the infection. Whole viral genome sequencing revealed the presence of 3 genotypes, 58% were type1, 0.6% type2, and 13.7% type3. Tick host bloodmeal identification analyses determined that nymphs infected with type1 were significantly associated with having fed on shrews (50 of 94 type1 ticks, odds ratio=2.3, p<0.001). This is consistent with shrews serving as a reservoir. Ticks infected with type3, however, had no host associations, consistent with infection acquired by cofeeding. It may be that local DTV genetic variation is shaped by transmission modes or host associations. ImportanceDeer tick virus (DTV; Powassan lineage II) is a tick-borne encephalitis virus that causes a rare zoonosis in North America. Cases have been increasingly reported within the last decade. Is the recent risk trend due to increased transmission? How this virus is perpetuated in nature is not well understood. We took advantage of a natural epizootic on Marthas Vineyard to probe how the ticks there had become infected. Using a combination of viral whole genome sequencing and bloodmeal remnant identification in ticks, we find that the mode of transmission varied by viral genotype. One genotype is associated with ticks that had fed on shrews, and another did not depend on a specific reservoir host. Host associations may drive genetic diversity of deer tick virus and thus local host population dynamics may influence zoonotic risk.

Understanding the dynamics of HIV epidemics is important to control them effectively. Classical methods that mainly rely on occurrence data are limited by the fact that an unknown part of the epidemic eludes sampling. Since the early 2000s, phylodynamic methods have enabled the estimation of key epidemiological parameters from virus genetic sequence data. These methods have the advantage of being less sensitive to partial sampling and to provide insights about epidemic history that even predates the first samples. In this study, we analysed 2,205 HIV sequences from the French ANRS PRIMO C06 cohort. We identified and were able to reconstruct the temporal dynamics of two large clades that represent the HIV-1 epidemics in the country. Using Bayesian phylodynamic inference models, we found that the first clade, from subtype B, originated in the end of 1970s, grew rapidly during the 80s before decreasing from 2000 to 2015 and stagnating since then. The second clade, from circulating recombinant form CRF02 AG, emerged and spread in the 80s, grew again in the early 2000s, before declining slightly. We also estimated key epidemiological parameters associated with each clade. Finally, using numerical simulations, we investigated prospective scenarios and assessed the possibility to meet the 2030 UNAIDS targets. This is one of the rare studies to analyse the HIV epidemic in France using molecular epidemiology methods. It highlights the value of routine HIV sequence data for studying past epidemic trends or designing public health policies. Author summaryDespite huge progress in prophylaxis and treatment, HIV epidemics remain a major public health issue in most countries. Therefore, understanding, tracking, and predicting epidemic dynamics is essential to design optimal prevention and screening strategies. A strong limitation is that most methods rely on occurrence data and are very sensitive to the unsampled portion of the epidemic (also known as the HIV hidden epidemic). To address this issue, we take advantage of phylodynamics methods that rely on viral sequence data. Thanks to data from the ANRS Primo cohort, we identify two epidemics present in France since the early 1980s that exhibit consistent, but some times different, dynamics. By simulating future scenarios, we demonstrate that the UNAIDS goal to reduce new HIV infections by 90 % from 2010 by 2030 is uncertain, at least for one of the two epidemics we consider. This is one of the first studies to leverage phylodynamic methods to analyse the French HIV epidemic. It also highlights how routinely-generated genomics data can enable detailed analyses that facilitate the design of efficient public health policies.

Zoos may serve as sentinel sites for zoonotic vector-borne diseases. West Nile virus (WNV) and Usutu virus (USUV) are closely related orthoflaviviruses transmitted between Culex mosquitoes and a bird reservoir. Both viruses can also infect mammals, including humans, where they may cause symptoms and, more rarely, hospitalization and death. However, serological cross-reactivity between WNV and USUV complicates their differential diagnosis. Here, we aimed to reconstruct the dynamics of emergence of WNV in a zoo located in a newly affected area in Europe, using ELISA and Virus Neutralization Test (VNT) serological analysis of 1707 animal sera collected between 2015 and 2024. Combining this data in a model accounting for cross-reactivity with USUV, we estimated yearly forces of infection (FOI) by both viruses, and thus found that WNV likely circulated in the area one year prior to the first cases reported to the passive surveillance system. Our results also showed that, in the zoo, mammals and reptiles had a lower risk of infection than birds (relative risk of 0.14 [0.05; 0.28]), and that the exposure of birds to water (aquatic lifestyle or proximity to stagnant water) affected the risk. Finally, we estimated diagnosis parameters, including the sensitivity of the VNT (80.4% [76.5%; 84.3%]), the expected VNT titer value, and the level of serological cross-reactivity between viruses during the VNT. To conclude, our modelling framework allowed to disentangle the co-circulation of two closely related viruses, a crucial point in ensuring the reliable sentinel surveillance of these vector-borne zoonotic pathogens.

Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents a major threat to the global swine industry. The epidemiological dynamics of PRRSV-2 are characterized by the recurrent annual emergence of dozens of variants. Long-distance spread of PRRSV-2 is largely driven by animal shipments. Spatiotemporal dynamics of PRRSV-2 in the USA have been explored; however, how fast variants spread to new regions after their emergence remains unclear, and this information could improve preparedness. To address this, we analyzed 14,835 sequences, retrieved from the Morrison Swine Health Monitoring Project (MSHMP), representing 156 variants sampled from 2015 to 2024, covering the five major swine-producing regions in the USA: the Upper Midwest (UM), Lower Midwest (LM), Atlantic Seaboard (AS), Northeast (NE), and Great Plains (GP). Time to spread was assessed using the time-to-dispersal event analysis and waiting time analyses. Genetic diversity was measured using Hill numbers. The UM had the highest variant richness (n=123), followed by the LM (n=47), AS (n=35), NE (n=45), and GP (n=38). Of the 62 variants that initially emerged in the UM, 17 later spread to other regions. The UM also received the highest number of variant introductions (n=24), followed by LM (n=14), NE (n=14), AS (n=4), and GP (n=7), highlighting regional differences in connectivity and risk. Our results suggest faster dispersal corridors among interior regions (e.g., GP to UM and LM to UM, [~]1.2-2.0 years) and slower for coast to interior pathways (AS to interior, [~]2-3 years). These findings may help anticipate the risk of PRRSV-2 variant introduction and provide more accurate dispersal time estimates, which are useful for improving epidemiological models and disease preparedness.

The 2024 dengue epidemic in Brazil-the largest arboviral emergency in the country's history-exposed critical gaps in the reliability of molecular diagnostics across its national public health laboratory network. Quality control (QC) of RT-qPCR assays performed by geographically dispersed Central Public Health Laboratories (LACENs) is essential to ensure the accuracy of epidemiological surveillance and clinical management. We conducted a multicenter QC evaluation of 3,192 complete RT-qPCR runs (19,152 datapoints) for dengue virus serotypes 1-4 (DENV1-4), Zika virus (ZIKV), and Chikungunya virus (CHIKV) across 15 LACENs over one epidemic year. An automated R-based bioinformatic pipeline applied hierarchical clustering (AGNES and DIANA), principal component analysis (PCA), linear and quadratic discriminant analysis (LDA/QDA), Shewhart and XmR control charts, process capability analysis, ANOVA, Baker's gamma permutation testing, and PVClust bootstrap clustering to positive-control cycle threshold (CT) value datasets. Median CT values for DENV4 positive controls ranged from 26.3 to 30.5 across laboratories, representing an approximately 16-fold difference in measured RNA quantity. PCA explained 54.1%-100% of total variance on PC1 across viral targets. Baker's gamma permutation tests confirmed significant concordance between AGNES and DIANA hierarchies across all six viral targets. LDA achieved 37.7% and QDA 49.1% cross-validated accuracy in laboratory-of-origin classification. PVClust bootstrap clustering identified DENV2+DENV4 (approximately unbiased probability, AU = 90) as the most analytically coherent serotype pair. ANOVA confirmed significant operator effects on ZIKV CT values (F = 8.799, df = 23), with regression coefficients for specific operators reaching beta; = +4.01 cycles-equivalent to an approximately 16-fold inferred difference in RNA quantity. Extreme outlier CT values signaled data integrity failures requiring immediate corrective action. The integrated multivariate QC framework substantially outperformed univariate Westgard-rule monitoring. Operator-specific CT deviations of up to four cycles carry direct consequences for clinical classification of borderline specimens. The automated R-based pipeline is operationally feasible in low-resource public health networks and provides a replicable model for arboviral diagnostic QC governance during epidemic emergencies.

The North American deermouse Peromyscus leucopus is reservoir for several zoonotic agents, including bacterial, protozoan, and viral. It is remarkable for indiscernible or limited fitness consequences of these infections, a trait known as infection tolerance. But experimental infections have largely been of pathogens that P. leucopus naturally harbors. We asked whether infection tolerance extended to an agent, like SARS-CoV-2 virus, it had presumably not encountered before. Following protocols for experiments with mice and hamsters, we infected 8 female and 8 male P. leucopus of heterogeneous stock and compared responses of these animals on days 3 or 6 to those of 14 controls inoculated with virus-free medium. Serologic and virologic confirmation of infection was obtained for all exposed deermice. Moderate inflammation in lungs was histologically evident in infected animals, but no histological changes were noted in brains, even when viral RNA was present. Fourteen (88%) animals displayed no or only mild sickness; two had more severe illness. Genome-wide RNA-seq revealed an interferon-stimulated response on day 3 superceded mainly by a cell-mediated response by day 6. In brains transcription of the interferon-stimulated genes Isg15 and Mx2 positively correlated with viral RNA levels. The findings confirmed susceptibility of this species of Peromyscus to SARS-CoV-2 virus. For most infected outbred animals the immune response was swift and effective in controlling the pathogen and without evidence of excessive inflammation. Whatever is the basis for P. leucopus trait of infection tolerance, it extended to at least one pathogen that for it would be novel. ImportancePeromyscus leucopus is North American rodent that is reservoir for several agents of human disease, while exhibiting minimal illness, a phenotype termed infection tolerance. Whether this trait is pathogen-specific or represents a broader strategy has remained uncertain. By experimentally infecting P. leucopus with SARS-CoV-2 virus, which it is unlikely to have encountered, we investigated whether infection tolerance extends to a novel virus. Despite disseminated infection and lung pathology, most animals showed only mild or no disease. Expression analyses revealed early interferon-stimulated responses followed by cell-mediated responses with only limited production of inflammatory mediators interferon-gamma and nitric oxide synthase 2. Compared with results with a mouse model of infection, deermice displayed higher baseline expression of antiviral genes and quicker resolution of interferon responses. These findings suggest that infection tolerance is a strategy that limits immunopathology generally while resisting microbes, which has implications for understanding reservoir competence and host resilience.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved since its emergence in the human population in 2019. As of 1st August 2025, more than 1,700 Omicron subvariants have been designated by the Pango nomenclature system. The Pango nomenclature system designates a new lineage based on genetic and epidemiological information of SARS-CoV-2 strains. However, there is a possibility that strains that have similar genetic backgrounds and the same phenotype are given different Pango lineage names. In this paper, we propose a new algorithm, called FindPart-w, which can identify groups of viral lineages that share the same relative effective reproduction numbers. We introduced a new lineage replacement model, called the constrained RelRe model, which constrains groups of lineages to have the same relative effective reproduction numbers. The FindPart-w algorithm searches the equality constraints that minimise the Akaike Information Criterion of constrained RelRe models. Using hypothetical observation count data created by simulation, we found that the FindPart-w algorithm can identify groups of lineages having the same relative effective reproduction number in a practical computational time. Applying FindPart-w to actual real-world data of time-stamped lineage counts from the United States, we found that the Pango lineage nomenclature system may have given different lineage names to SARS-CoV-2 strains even if they have the same relative effective reproduction number and similar genetic backgrounds. In conclusion, this study showed that viruses that had the same relative effective reproduction number were identifiable from temporal count data of viral sequences. These findings will contribute to the future development of lineage designation systems that consider both genetic backgrounds and transmissibilities of lineages.

Small ruminants (sheep and goats) are one of the few mammals in which an exogenous retrovirus (XRV) and closely related endogenous retroviral elements (ERV) coexist within the same host genome. The betaretroviruses Jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV) cause pulmonary and nasal adenocarcinomas, respectively, and share extensive sequence similarity with their endogenous counterparts. Consequently, molecular surveillance must rely on assays that can unequivocally distinguish true exogenous infection from ERV-derived templates; failure to do so compromises diagnosis, phylogenetic inference, and epidemiological conclusions. We retrieved all complete JSRV, ENTV-1/2, and related ERV genomes deposited in public repositories and performed a comprehensive alignment. Only a limited number of genomic segments were capable of distinguishing exogenous from endogenous sequences. We refer to these as discriminating regions (DRs). Phylogenies built using DRs revealed that several entries annotated as XRV are, in fact, ERV-derived or chimeric artefacts generated by short-amplicon reconstruction. A systematic literature review of over 100 articles identified 286 distinct primers and probes used for the XRV amplification. In-silico mapping of each oligonucleotide onto the full alignment showed that only 28 % reliably differentiate XRV from ERV. We experimentally validated the predictive power of this approach for 17 primer/probe sets, confirming that non-discriminating assays produce false-positive signals from endogenous templates. The misannotation of ERV sequences as exogenous viruses has resulting in the population of databases with dubious entries, fostering erroneous hypotheses such as vector-borne transmission of JSRV and ENTV. To address this issue, we propose a concise set of criteria for assay design, validation, and database annotation emphasizing DR targeting, specificity testing against endogenous templates, and transparent reporting. Although this framework was developed for small ruminants, it is readily applicable to any host-virus system in which exogenous viruses coexist with endogenous viral elements. This will strengthen viral surveillance, phylogenetics, and the One Health initiatives.

BackgroundHeartland virus (HRTV) is an emerging tick-borne virus capable of causing severe illness and death. The burden of disease is likely underestimated due to limited seroprevalence studies, lack of commercially available diagnostic tests, and an overlapping clinical syndrome with more commonly diagnosed bacterial diseases such as spotted fever group rickettsiosis or ehrlichiosis. MethodsActive surveillance for Heartland virus disease was conducted at a large academic center from March to September 2024. Enrolled subjects included those who had testing sent for Ehrlichia polymerase chain reaction (PCR) along with fever and 2 of the 3 criteria: leukopenia, thrombocytopenia, and/or elevated liver function tests. Specimens with detectable RNA underwent whole genome sequencing and analysis. FindingsOver 800 specimens were received with 53 individuals meeting enrollment criteria. Among these 53, two (3.8%) had detectable HRTV RNA in whole blood during the time of Ehrlichia PCR testing. The two cases had disparate clinical manifestations: one with mild disease which was identified in an outpatient setting, while a second case required intensive care unit-level support. Heartland virus genome sequences from the two cases were more similar to viruses from other states than they were to one another. InterpretationDespite only two prior reported cases of Heartland virus disease in North Carolina, we identified two individuals with acute HRTV viremia. Further surveillance for HRTV disease is necessary to understand the burden of disease and to facilitate further studies of virus pathogenesis and host responses. FundingFunding for the study was provided by a Creativity Hub Award to Dr. Boyce from the UNC Office of the Vice Chancellor for Research. Dr. Zychowskis effort was supported by the T32 NIAD grant AI070114.

Defective interfering particles (DIPs) derived from the influenza A virus (IAV) are a promising antiviral agent due to their strong antiviral efficacy demonstrated in various animal models. OP7 is an unconventional IAV DIP with multiple point mutations in the viral RNA (vRNA) of genome segment 7, as opposed to the large internal genomic deletions typically found in conventional IAV DIPs. Further, OP7 showed an even higher interfering efficacy than conventional DIPs. However, the inhibitory effect of OP7 on standard virus (STV) replication has primarily been investigated in Madin-Darby Canine Kidney (MDCK) cells, which lack a functional myxovirus resistance (Mx)-mediated antiviral activity against IAV. In this study, we examined the antiviral activity and mechanism of antiviral action of OP7 in an interferon (IFN)-competent human lung carcinoma cell line (Calu-3) in vitro. We performed STV and OP7 co-infection experiments using a variety of infection conditions and measured the time-resolved dynamics in viral titer, vRNA, protein level, and host cell gene expression. We observed that OP7 co-infection results in enhanced type I IFN responses and markedly reduced infectious virus release, even at low doses. Additionally, we found that at a high STV multiplicity of infection (MOI), the replication interference of OP7, suppressing the replication of STV vRNA, appears to be the dominant mechanism of its antiviral action. At a low MOI, however, IFN induction seems to be more important. Furthermore, we examined the efficacious co-infection time window for potential prophylactic and therapeutic antiviral treatment. We observed an antiviral effect exerted by OP7 infection for up to seven days before STV infection and up to 24 hours after STV infection. Together, these findings demonstrate that OP7 is a potent antiviral DIP. Therefore, this work supports the further development of OP7 as a therapeutic and prophylactic antiviral agent.

This novel study detected persistent low level infections of Elephant Endotheliotropic Herpesviruses (EEHV), that can cause highly pathogenic Elephant Hemorrhagic Disease (EHD) in Loxodonta and Elephas, and co-infection of presumed less pathogenic Elephant Gammaherpesviruses (EGHV), in skin nodule biopsies, saliva and tissues collected from 43 wild L. africana (savannah elephant) in Botswana, Kenya, South Africa and Zimbabwe; in saliva from 25 wild L. cyclotis (forest elephant) in Gabon; and in saliva collected over seven years from 7 wild-born L.africana at Six Flags Safari Park, USA; and in saliva, blood and tissues from an additional 200 L. africana in USA zoos. DNA from these samples was extracted in our USA laboratories and amplified by conventional polymerase chain reaction using three-round nested primer sets designed specifically to screen for known EEHV and EGHV genes loci and to discover new species and subtypes. Sanger sequencing of purified DNA from nearly all samples yielded unambiguous positive genetic matches to previously known Loxodonta-associated EEHV2, EEHV3A, EEHV3B, EEHV6, EEHV7A, and EGHV1B, EGHV2, EGHV3B, EGHV4B, EGHV5B and discovered novel types EEHV3C-H and EEHV7B and the prototype EGHV1B. Many of the primer sets used could also have detected known Elephas-associated EEHV1A, EEHV1B, EEHV4, and EEHV5 if present in these samples, but they did not. Our extensive library of EEHV and EGHV sequences from wild and zoo Loxodonta, (as well as from 100 zoo Elephas maximus not discussed in this review), is a significant contribution to the elephant virology community, particularly for comparing subtypes types of EEHV found in pathogenic cases of EHD in zoos as well as determining and comparing species and subtypes of EEHV present in existing zoo herds, and in individual elephants being transported between zoos, and for importation of wild elephants into existing zoo herds.

Plant viruses interfere with host signaling pathways, but it remains unclear how calcium (Ca2+) signaling, reactive oxygen species (ROS), and changes in the plasma membrane interact during viral infection. Here, we investigated how plantago asiatica mosaic virus (PlAMV) modulates host Ca2+ and ROS-associated signaling in Arabidopsis thaliana. Using live-cell imaging and the R-GECO1.2 Ca2+ sensor, we observed a rapid increase in cytoplasmic Ca2+ before the virus was detected, indicating that Ca2+ release occurs early in infection. Genetic analysis showed that GLR, CPK3, and CNGC, core components of Ca2+ signaling, limit PlAMV spread between cells, while the usual pattern-triggered immunity (PTI) co-receptors were not needed. This means that Ca2+-based antiviral restriction operates independently of PTI. With the plasma membrane-tethered and cytosolic HyPer7 biosensor, we found that ROS levels were lower inside infection foci in the inoculated leaves, but higher in nearby cells, respectively. The NADPH oxidases RBOHD and RBOHF, which produce ROS, slowed down the local viral propagation. The PM sphingolipid biosynthetic enzyme MOCA1 altered ROS patterns and reduced the viruss spread. Epistasis analysis revealed a functional interaction between RBOHD and MOCA1, suggesting that ROS signaling and plasma membrane sphingolipid homeostasis are interconnected in antiviral defense. Overall, our findings suggest that PlAMV triggers Ca2+ influx and ROS signaling at the plasma membrane, which induces sphingolipid reorganization and helps restrict the propagation of the virus. This study shows how Ca2+, ROS, and membrane sphingolipid signaling work together in plant antiviral immunity and points to possible ways to improve resistance to viruses.

RNA helicases encoded by positive-strand RNA viruses are essential for genome replication, yet the specific biological functions and mechanochemical basis underlying these functions remain poorly defined. Progress has been limited by the difficulty of resolving individual catalytic steps under single-turnover conditions, which are often experimentally inaccessible for viral enzymes. Alphaviruses replicate within membrane-bound spherules that may alter local metabolite concentrations, raising the possibility that the enzymatic properties of alphaviral proteins differ from those of viruses with greater cytosolic exposure. Here, we present a kinetic and binding analysis of full-length non-structural protein 2 (nsP2) from Chikungunya virus, a multifunctional superfamily 1B NTPase and RNA helicase. Purified nsP2 binds nucleoside triphosphates with high affinity, exhibiting equilibrium dissociation constants in the single digit micromolar range. This property enabled single-turnover, pre-steady-state, and isotope-trapping experiments that are rarely feasible for viral helicases. These analyses identified two sequential conformational-change steps required for nucleotide hydrolysis. Molecular dynamics simulations suggest tightening of the RecA1 and RecA2 domains upon ATP binding followed by compaction of the enzyme mediated by interactions between the 1B subdomain and RecA2 domain. Product inhibition patterns support random release of ADP and inorganic phosphate, with relative binding affinities indicating that ADP dissociates first. The reaction is irreversible. Although nsP2 binds RNA tightly, strand separation under single-turnover conditions is too slow to represent ATP-driven unwinding, instead likely reflecting formation of an unwinding-competent nsP2-RNA complex. Together, these findings establish a quantitative framework for nsP2 function and provide a roadmap for mechanistic studies of alphaviral helicases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/723793v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@13899a1org.highwire.dtl.DTLVardef@ee1aadorg.highwire.dtl.DTLVardef@1991e1org.highwire.dtl.DTLVardef@b877f6_HPS_FORMAT_FIGEXP M_FIG C_FIG

Thogotoviruses are a group of tick-borne, six-segmented, negative-sense single-stranded RNA viruses. These viruses encode an RNA-dependent RNA polymerase that recognizes promoter sequences located at the genomic termini to initiate RNA synthesis. The 5' and 3' ends of the genome bind to the polymerase and function as a promoter. Outside the catalytic center, they base-pair with each other to form a double-stranded RNA structure. This structure is referred to as the distal duplex and plays an important role in RNA synthesis. In this study, we investigated how the RNA sequence of the distal duplex influences polymerase activity using minigenome systems of two thogotoviruses, Oz virus (OZV) and Dhori virus (DHOV). Each virus exhibits distinct activities among its six segments. In OZV, one determinant of these differences is the base pair at positions 5'12 and 3'11 within the distal duplex, where promoter activity varies depending on whether the base pair is G:C or A:U. In contrast, the DHOV polymerase is not affected by this difference. These results indicate that, even within the genus Thogotovirus, viruses differ in whether they possess a mechanism that modulates promoter activity based on subtle sequence differences within the distal duplex. Furthermore, phylogenetic analysis and comparison of promoter sequences suggest that thogotoviruses can be divided into groups that do or do not regulate intersegment promoter activity via the base pair at positions 5'12 and 3'11. HighlightsO_LIMinigenome systems of Oz virus and Dhori virus reveal segment-specific differences in promoter activity C_LIO_LIThe distal duplex sequence modulates RNA synthesis in a virus-dependent manner C_LIO_LIThe base pair at positions 5'12/3'11 determines promoter activity in Oz virus but not in Dhori virus C_LIO_LIThogotoviruses can be divided into groups that do or do not regulate promoter activity via distal duplex sequence variation at positions 5'12/3'11 C_LI

Varicella Zoster Virus (VZV) is a dsDNA virus that infects dermal cells and causes characteristic cutaneous lesions. The virus undergoes neurotropism and later causes secondary cycles of infection. In the host nucleus, Promyelocytic Leukaemia Nuclear Bodies (PML-NBs) spontaneously form around the VZV genome to repress viral gene expression. VZV encodes for a ubiquitin E3 ligase ORF61 to disperse PML-NBs and alleviate repression. ORF61 functions as a ubiquitin E3 ligase with a conserved RING domain at the N-terminal end. It carries three SUMO-interacting motifs (SIMs) that mediate interactions with SUMOylated proteins within PML bodies. The mechanism by which ORF61 disperses PML-NBs is poorly understood. To understand how ORF61 interacts with SUMOylated proteins, we investigated its interaction with SUMO and studied its SUMO-Targeted Ubiquitin Ligase (STUbL) activity. Our studies reveal that ORF61 co-opts the E2D family for ubiquitination activity. A specific network of interactions between the E2 enzyme, ORF61, and Ub facilitates polyubiquitination. ORF61 can synthesize branched polyubiquitin chains of K11, K48, and K63 linkages. The C-terminal SIM in ORF61 is a high-affinity binder of SUMO chains. Utilizing the SIM, ORF61 targets specific lysines on SUMO chains for ubiquitination. These studies provide crucial insights into the functional mechanism of viral STUbL ORF61.

Fjord systems are susceptible to anthropogenic pressures, including discharges from wastewater treatment plants (WWTPs), which introduce micropollutants into coastal waters. We investigated the impact of micropollutants on bacteria and fungi within a fjord system adjacent to a significant petrochemical industry hub on the Swedish west coast. We characterised microbial assemblages along a land-to-sea transect, encompassing freshwater streams receiving agricultural and urban runoff, as well as the direct effluent from a WWTP. Our findings revealed elevated concentrations and a diverse array of micropollutants in the WWTP effluent and the stream running through the urban/industrial zone, highlighting these areas as major sources of pollution to the fjord. Bacterial and fungal communities inhabiting the WWTP effluent and the receiving marine waters near the marine outflow exhibited distinct structural compositions, indicating a selective pressure exerted in part by the micropollutant load. While freshwater sites generally displayed higher overall microbial diversity compared to marine sites, the WWTP effluent showed reduced diversity in both bacterial and fungal communities, likely due to the impact of micropollutants. Interestingly, marine sites far from the WWTP discharges exhibited a recovery in bacterial diversity, suggesting a potential response or adaptation. In contrast, fungal diversity remained comparable to that observed in other marine locations. Multivariate analyses identified physicochemical parameters and nutrients, alongside with summed fungicides and antibiotic stress as key factors driving the community dissimilarities across the fjord. Significant disruptions in potential bacterial metabolism and fungal ecological functions were evident at the WWTP discharge point, underscoring the ecological consequences of wastewater pollution. HighlightsO_LIWWTP discharge is the primary source of complex micropollutants in the fjord. C_LIO_LIAntibiotics and fungicides significantly shape bacterial and fungal communities. C_LIO_LIWastewater impacts reduce microbial diversity and disrupt functional potential. C_LIO_LIMarine sites show microbial recovery and enrichment away from discharge points. C_LIO_LIeDNA and toxic unit modeling link chemical stress to microbiome restructuring. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/711609v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1751e5forg.highwire.dtl.DTLVardef@1d0d78org.highwire.dtl.DTLVardef@15f446aorg.highwire.dtl.DTLVardef@184bb0a_HPS_FORMAT_FIGEXP M_FIG C_FIG