Archives Of Virology[JOURNAL]
Sun
200 papers
Identification of a novel toti-like virus symbiotic with Giardia duodenalis.
Shichinohe S, Izumiyama S, Takaki Y … +4 more , Hirai M, Urayama SI, Nunoura T, Kazama M
Arch Virol · 2026 Mar · PMID 41874807 · Publisher ↗
Giardiasis is a parasitic intestinal infection of both animals and humans, caused by the enteric protozoan Giardia duodenalis (syn. G. lamblia and G. intestinalis). To date, symbiont RNA viruses of G. duodenalis: Giardia...
Giardiasis is a parasitic intestinal infection of both animals and humans, caused by the enteric protozoan Giardia duodenalis (syn. G. lamblia and G. intestinalis). To date, symbiont RNA viruses of G. duodenalis: Giardia lamblia virus (GLV) and Giardia duodenalis RNA virus-2 (GdRV-2) have been reported. Here, we report the complete genome sequence of a novel virus identified in a human isolate of G. duodenalis using fragmented and primer-ligated double-stranded RNA sequencing. This virus, designated the Non-GLV Giardia duodenalis ISE strain (Noggi) virus, is genetically distinct from GLV and GdRV-2 and likely represents the third symbiont virus in Giardia parasites.
A plant gallotannin pentagalloyl d-glucose elicits antiviral activity against influenza A and B viruses through multi-targeting mechanisms.
Kim S, Kim JW, Ayoobi A … +5 more , Lee S, Jeon S, Yoon SW, Choi HW, Jang YH
Arch Virol · 2026 Mar · PMID 41874776 · Publisher ↗
Influenza virus infection remains a major threat to human health. Considerable antigenic diversity and variability of influenza viruses underpin the need for the development of novel antiviral agents against the viruses....
Influenza virus infection remains a major threat to human health. Considerable antigenic diversity and variability of influenza viruses underpin the need for the development of novel antiviral agents against the viruses. In this study, we examined the antiviral activity of pentagalloyl D-glucose (PGG), a plant gallotannin, against influenza A and B viruses. PGG showed strong virucidal activity against influenza A and B viruses at noncytotoxic concentrations. Time-of-addition experiments revealed that PGG exerted potent antiviral activity irrespective of the timing of treatment (pre-infection, during infection, or post-infection). Of note, PGG was shown to have potent inhibitory activity against both influenza A and B viral neuraminidases (NA) than oseltamivir phosphate (OP), the prodrug of the most widely used antiviral drug against the viral infections. Significantly higher binding affinity of PGG to influenza NA protein than OP was substantiated by surface plasmon surface analysis. PGG also suppressed the viral gene expression in virus-infected cells when PGG was added to cells before and after viral infection, suggesting that the antiviral activity of PGG was shown both outside and inside the cells. Comparative analyses of antiviral activity between PGG and OP demonstrated that PGG has multi-target antiviral mechanisms involving virucidal activity, HA inhibition, NA inhibition, and replication inhibition in cells. Our data demonstrate the promising potential of PGG to be an attractive antiviral agent against influenza A and B virus infections.
Structural and electrostatic determinants of RNA recognition by the CSFV Erns glycoprotein.
Ganesh KR, Patil SS, Harish J … +3 more , Suresh KP, Hiremath J, Nayakvadi S
Arch Virol · 2026 Mar · PMID 41874769 · Publisher ↗
Classical swine fever virus (CSFV) employs the envelope glycoprotein Erns as a secreted viral ribonuclease that suppresses host innate immune recognition by degrading extracellular RNA. Despite extensive functional chara...
Classical swine fever virus (CSFV) employs the envelope glycoprotein Erns as a secreted viral ribonuclease that suppresses host innate immune recognition by degrading extracellular RNA. Despite extensive functional characterization, the structural determinants governing RNA recognition remain poorly defined because no high-resolution experimental structure is available. This study provides an integrative structural analysis of CSFV Erns combining evolutionary conservation mapping, electrostatic surface characterization, RNA docking, and intrinsic dynamics analysis to identify a conserved RNA-recognition interface. This approach reveals a structurally defined electropositive groove adjacent to the catalytic site that likely guides RNA substrate engagement during immune evasion. Structural modeling and validation indicate that the predicted Erns structure adopts a canonical RNase T2 fold with a highly conserved catalytic core. Conservation mapping across diverse CSFV isolates reveals strong evolutionary constraints extending beyond catalytic residues to adjacent surface-exposed regions. Electrostatic analysis identifies a conserved electropositive groove proximal to the RNase active site, consistent with a defined RNA-recognition surface. Docking consistently positions double-stranded RNA within this groove, while elastic network-based correlated motion analysis reveals coordinated collective movements associated with the predicted binding region. Interface profiling further identifies stabilizing hydrogen bonds and hydrophobic contacts at the Erns–RNA interface. Together, these complementary structure-based findings provide predictive mechanistic insight into Erns-mediated RNA recognition and immune evasion and establish a structural framework for future experimental validation of CSFV pathogenesis and for guiding biochemical and structural.
Plant viruses and the microbiome: a complex network shaping plant health and disease resistance.
Tamang A, Chaudhary S, Pandey SS … +1 more , Hallan V
Arch Virol · 2026 Mar · PMID 41874766 · Publisher ↗
Plant viruses and microbiomes are pivotal to plant health, growth, and their ability to withstand environmental challenges. However, the extent to which viruses engage in direct or indirect crosstalk with plant-associate...
Plant viruses and microbiomes are pivotal to plant health, growth, and their ability to withstand environmental challenges. However, the extent to which viruses engage in direct or indirect crosstalk with plant-associated microbial communities remains largely unexplored. Traditionally, plant viruses are considered as harmful agents that disrupt normal plant functions, but new research indicates they may also engage in complex interactions with the plant's microbiome. On the other hand, the plant microbiome, comprising a diverse assembly of bacteria, fungi, and other microbes, can influence the plant's responses to viral infections, potentially altering the course of the disease. Thus, we emphasize the intricate interplay between plant viruses and microbiomes, particularly how viruses might "communicate" with microbial communities to alter the host environment or bypass immune defenses. The mechanisms driving these interactions, such as virus-induced shifts in plant metabolism, signaling pathways, and immune responses that indirectly affect microbiome composition are also discussed. The beneficial effect of plant-associated microbial communities against viral infections and the strategy of microbiome-based approaches for managing viral diseases are also focused. By moving beyond the traditional view of pathogen-host interactions, this review will highlight the importance of considering the three-way relationship among plants, viruses, and microbiomes to advance our understanding of plant health and foster innovative solutions for sustainable agriculture.
A victorivirus infecting Colletotrichum falcatum: genomic characterization and evolutionary analysis.
Henrique MO, Gallan DZ, Schrank A … +4 more , Dias RO, Coutts RHA, Kotta-Loizou I, Silva-Filho MC
Arch Virol · 2026 Mar · PMID 41874762 · Full text
Colletotrichum falcatum is a major fungal pathogen responsible for severe disease in sugarcane. Here, we report the complete genomic characterization of a novel mycovirus infecting C. falcatum, designated Colletotrichum...
Colletotrichum falcatum is a major fungal pathogen responsible for severe disease in sugarcane. Here, we report the complete genomic characterization of a novel mycovirus infecting C. falcatum, designated Colletotrichum falcatum victorivirus 1 (CfVV1). The CfVV1 genome is 4,906 base pairs (bp) long and comprises two open reading frames encoding a capsid protein (CP) and an RNA-dependent RNA polymerase (RdRP), overlapping at an AUGA motif. The predicted proteins share ca. 70% and 68% identity with those of Colletotrichum cliviicola victorivirus 1 and Colletotrichum nativitas totivirus 1, respectively. Phylogenetic analysis based on concatenated RdRP and CP amino acid sequences places CfVV1 within the genus Victorivirus of the recently established family Pseudototiviridae. Transmission electron microscopy confirmed the presence of isometric virus-like particles ca. 40 nm in diameter, consistent with the typical morphology of victoriviruses. To our knowledge, this is the first report of a complete victorivirus genome infecting C. falcatum.
Characterization and genomic analysis of vB_CoeS_P1, a novel marine bacteriophage, and definition of the new family Estoviridae.
P K S, Ammini P, Sriram PRA
Arch Virol · 2026 Mar · PMID 41874675 · Publisher ↗
A novel bacteriophage vB_CoeS_P1, isolated in the surface waters of the Cochin estuary of Kerala, India, was identified as phage known to infect Vibro spp_SR1_COC. Transmission electron microscopy analysis revealed that...
A novel bacteriophage vB_CoeS_P1, isolated in the surface waters of the Cochin estuary of Kerala, India, was identified as phage known to infect Vibro spp_SR1_COC. Transmission electron microscopy analysis revealed that the phage had a myovirus morphotype with an icosahedral head and a long contractile tail. Characterization experiments showed that the phage was stable across a temperature range of 4 °C to 60 °C, a pH of 4 to 12, and a salinity range of 0.5% to 16%. One-step growth curve analysis revealed a burst size of 40 PFU/Cell and a latent period of 20 min. The phage contains a double-stranded DNA with 136,927 bp and 34.93% GC content. The NCBI BLASTn analysis reveals that vB_CoeS_P1 exhibits very low sequence similarity (1% query coverage and 77.82% identity) with Vb_VpaM_R16F (OP793884.1). It has 265 predicted ORFs, among them 57 have putative functions with no tRNA, antibiotic encoding genes, and resistance encoding genes. Three putative auxiliary metabolic genes were identified, encoding pyrophosphohydrolase enzyme (ORF 75), PhoH-like phosphate starvation-inducible (ORF 34), and Endonuclease V N-glycosylase UV repair enzyme (ORF 248). Phylogenetic analysis of conversed genes revealed that vB_CoeS_P1 is clustered with Vb_VpaM_R16F but diverged into a distinct clade. Further, whole genome proteomic tree analysis, comparative genome analysis using average nucleotide identity (ANI), and network analysis confirmed that vB_CoeS_P1 contains a unique genetic and evolutionary architecture. These findings support the proposal of a new bacteriophage family Estoviridae, within the Caudoviricetes class.
Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.
Stevens KA, de Souza JO, Li H … +3 more , Ouro-Djobo A, Alabi OJ, Al Rwahnih M
Arch Virol · 2026 Mar · PMID 41860726 · Full text
We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an A...
We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.
Liquid-liquid phase separation in the viral replication cycle: new paradigms and therapeutic opportunities.
Sanjida F, Hossain MI, Akash SR … +1 more , Ali MS
Arch Virol · 2026 Mar · PMID 41860722 · Publisher ↗
Liquid–liquid phase separation (LLPS) has emerged as a central principle for organizing biomolecular condensates in eukaryotic cells, providing new perspectives on how viruses spatially and temporally coordinate infectio...
Liquid–liquid phase separation (LLPS) has emerged as a central principle for organizing biomolecular condensates in eukaryotic cells, providing new perspectives on how viruses spatially and temporally coordinate infection. Accumulating evidence indicates that LLPS contributes to multiple stages of viral life cycles in diverse RNA and DNA viruses, including the formation of replication compartments, sites of genome packaging, and structures involved in immune modulation. In this review, we synthesize current data on how viral and host factors co-assemble into biomolecular condensates, highlight shared biophysical features and virus-specific strategies, and discuss whether these structures are causally required for efficient replication versus correlative markers of infection. We emphasize mechanistic insights into condensate composition, material state transitions, and functional consequences for viral replication, latency, and pathogenesis, as well as key experimental strengths and limitations underlying LLPS assignments. Finally, we summarize emerging therapeutic approaches that target viral condensates or their regulatory pathways, while underscoring that most LLPS-directed antiviral strategies remain at an early preclinical stage and face substantial challenges in specificity, toxicity, and delivery. A deeper mechanistic and quantitative understanding of viral LLPS will be essential to determine when condensates represent viable antiviral targets and how they can be modulated without disrupting critical host functions.
Viral subversion of neddylation: dual roles in replication efficiency and evasion of antiviral immunity.
Mo X, Yu B, Tang X
Arch Virol · 2026 Mar · PMID 41854790 · Publisher ↗
Neddylation, a conserved ubiquitin-like modification, critically regulates viral pathogenesis and host immunity. This review synthesizes recent advances demonstrating how viruses exploit host neddylation to enhance repli...
Neddylation, a conserved ubiquitin-like modification, critically regulates viral pathogenesis and host immunity. This review synthesizes recent advances demonstrating how viruses exploit host neddylation to enhance replication—either by direct neddylation of viral proteins or by subverting cullin-RING ligases (CRLs) to degrade antiviral restriction factors. Conversely, neddylation bolsters innate immunity by activating Interferon Regulatory Factor 7 (IRF7) nuclear translocation, potentiating cylic GMP-AMP synthase -Stimulator of Interferon Genes ༈cGAS-STING༉ signaling, and regulating inflammasome-dependent cytokine responses. The NEDD8 activating enzyme E1 subunit 1(NAE1) inhibitor MLN4924 exhibits broad antiviral activity against herpesviruses, influenza, Human Immunodeficiency Virus, and coronaviruses. Understanding neddylation’s dual roles - as a proviral facilitator and immune modulator - provides novel insights for antiviral strategies.
Deciphering cassava brown streak virus infection in cassava through VPg mediated host protein interactions.
Kakkunnath SM, Bouvaine S, Kavil SP … +1 more , Maruthi MN
Arch Virol · 2026 Mar · PMID 41851384 · Full text
Cassava brown streak disease (CBSD) poses a major threat to cassava production in Africa. Identifying cassava proteins that interact with cassava brown streak virus (CBSV), the major causal virus, can help elucidate the...
Cassava brown streak disease (CBSD) poses a major threat to cassava production in Africa. Identifying cassava proteins that interact with cassava brown streak virus (CBSV), the major causal virus, can help elucidate the mechanisms of infection and resistance. Here we constructed a cassava cDNA library and screened for proteins interacting with CBSV viral genome-linked protein (VPg) using yeast two-hybrid assays, identifying 36 interactors. Four candidates were validated in Nicotiana benthamiana via bimolecular fluorescence complementation. Functional categories included chloroplast proteins, ribosomal components, chaperones, metabolic enzymes, and defence-related proteins. In prior RNA-seq datasets from CBSV or UCBSV-inoculated cassava, comprising the susceptible variety Albert and the resistant variety Namikonga, 16 VPg-interacting genes were identified among the differentially expressed genes (|log₂FC| > 1), with 2 detected in Albert and 15 in Namikonga. These results indicate that VPg-interacting host proteins are involved in CBSV infection dynamics and also explaining the differential responses of resistant and susceptible cassava varieties, thus offering potential new molecular targets for CBSD management.
Immune responses in chicken mucosal lymphoid tissues following oral and eye drop vaccination and revaccination with live modified vaccine of infectious laryngotracheitis virus (ILTV).
Tran TT, Andronicos NM, Ketheesan N … +2 more , Walkden-Brown SW, Gerber PF
Arch Virol · 2026 Mar · PMID 41848937 · Full text
Mass vaccination with attenuated infectious laryngotracheitis virus (ILTV) via drinking water is commonly used in commercial chicken farms, although the effectiveness of oral (OR) vaccination is lower than eye drop (ED)....
Mass vaccination with attenuated infectious laryngotracheitis virus (ILTV) via drinking water is commonly used in commercial chicken farms, although the effectiveness of oral (OR) vaccination is lower than eye drop (ED). The gene expression of a select set of immune markers associated with inflammatory responses (TLR4, TLR7, TLR2-2, IL6, CCL4, CCR5, IFNγ, IL2, IL17C), immune synapse (CD80), T helper cell polarisation (IL4) and effector cell receptors (CD4, CD8α and CD14), following OR and ED primary vaccination and revaccination using the same or alternate route [ED/ED (primary/revaccination), OR/OR, ED/OR and OR/ED] with ILTV SA2 strain in chickens were evaluated. Both ED and OR primary vaccinations were associated with increased gene expression of inflammation-associated markers in the conjunctiva and trachea, with a statistical interaction between application route and profile of immune responses. Revaccination via the alternative route elicited upregulation of more immune markers in the conjunctiva and trachea compared to other methods, while most immune markers were downregulated in the ED/ED group, and close to baseline in the OR/OR group. In conclusion, the immune responses in the conjunctiva and trachea following the ED and OR primary vaccination with ILTV vaccine were tissue-specific, showing increased gene expression of markers related to the inflammatory response. Revaccination using the alternative route elicited upregulation of markers associated with inflammatory responses CCR5 and TLR7 in the conjunctiva and/or trachea. Challenge studies are necessary to confirm the role of these immune responses in protecting vaccinated birds from ILTV.
Enhancing the immunogenicity of a recombinant PEDV subunit vaccine: the role of lipoprotein signal peptide.
Afzal H, Umar M, Hoa NT … +2 more , Ke GM, Cheng LT
Arch Virol · 2026 Mar · PMID 41848923 · Publisher ↗
The spike (S) protein of Porcine Epidemic Diarrhea Virus (PEDV) is a major structural glycoprotein responsible for viral attachment and entry, making it a critical target for the development of subunit vaccines. Within t...
The spike (S) protein of Porcine Epidemic Diarrhea Virus (PEDV) is a major structural glycoprotein responsible for viral attachment and entry, making it a critical target for the development of subunit vaccines. Within the S1 domain, a well-characterized region spanning residues 499–799, commonly referred to as the core neutralizing epitope (COE) the equivalent of the CO-26 K domain, contains multiple predicted B-cell, T-cell, and virus-neutralizing epitopes, making it highly immunogenic. This study investigates whether the incorporation of a bacterial lipoprotein signal peptide into the COE domain can enhance its antigenicity and protective efficacy by inducing lipidation-mediated activation of Toll-like receptor 2 (TLR2). A truncated COE construct was engineered either with a signal peptide (SP-COE) or without one (COE), and evaluated through a combination of in-silico, in vitro, and in vivo analyses. In silico epitope prediction tools identified strong B-cell and T-cell epitope coverage within COE. Molecular docking revealed favorable interactions with immune receptors, and structural modeling demonstrated the construct’s stability. In vitro, HEK-Blue hTLR2 reporter cells revealed that SP-COE elicited significantly higher NF-κB activation compared to COE, confirming effective TLR2 engagement. In vivo, mice immunized with SP-COE displayed significantly elevated total IgG and virus-neutralizing antibody titers, enhanced cytokine responses (e.g., IFN-γ, IL-4), and a stronger CD4⁺ T-cell response relative to the COE group. These findings demonstrate that incorporating a lipoprotein signal peptide improves the immunogenicity and protective potential of the PEDV COE antigen, highlighting its utility as an intrinsic adjuvant in subunit vaccine design.
PEDV infection induces ferroptosis in Vero cells via an ACSL4-mediated lipid peroxidation pathway.
Weng Q, Li Y, Wei Y … +5 more , Wang S, Hu T, Pei Z, Wang K, Hu G
Arch Virol · 2026 Mar · PMID 41848908 · Publisher ↗
Porcine epidemic diarrhea virus (PEDV) is a highly contagious viral pathogen causing severe economic losses in the swine industry. However, the underlying mechanisms by which PEDV induces host cell death are largely unkn...
Porcine epidemic diarrhea virus (PEDV) is a highly contagious viral pathogen causing severe economic losses in the swine industry. However, the underlying mechanisms by which PEDV induces host cell death are largely unknown, leading to an initial stage of drug development against PEDV. In this study, we investigated the role of ferroptosis, a non-apoptotic form of programmed cell death, in PEDV-infected cells. The experiments were divided into four groups: a control group, a PEDV group, an Erastin positive control group, and a Liprostatin negative control group. Levels of GSH, ROS, Fe3+, and cell viability were evaluated using ELISA test kits. Fluorescence microscopy was employed to assess Fe2+ aggregation, while flow cytometry was utilized to measure lipid peroxide levels. The mRNA transcript levels of key genes involved in the ferroptosis pathway -ACSL4, GPX4, ALOX15, and LPCAT3 - were determined by quantitative reverse transcription PCR. Compared to the control group, the PEDV group exhibited a significant decrease in GSH levels and a gradual reduction in Fe3+ levels. Furthermore, the PEDV group showed a substantial increase in ROS release and a corresponding decrease in cell viability relative to the control group. The expression levels of ACSL4, ALOX15 and LPCAT3 mRNA were significantly elevated in the PEDV group. Additionally, the protein expression levels of ACSL4, ALOX15 and LPCAT3 also increased progressively. In conclusion, our findings suggest that PEDV can induce iron prolapse in Vero cells via the ACSL4-mediated lipid peroxidation pathway, which furthers our knowledge of PEDV and provides a theoretical basis for drug development.
Specific features of the infection caused by SARS-CoV-2 variants in Vero cell culture.
Chepurnov A, Miroshnichenko S, Ivanov M … +10 more , Solomatina M, Kazachinskaia E, Kazachkova E, Kononova Y, Voevoda M, Shelemba A, Mishchenko O, Surovyatkin A, Gulyaeva M, Shestopalov A
Arch Virol · 2026 Mar · PMID 41848776 · Publisher ↗
Variants of SARS-CoV-2 differ in pathogenicity. Vero E6 cells are used to isolate, propagate, and study many viruses, including SARS-CoV-2. The aim of this work is to evaluate morphological differences during infection,...
Variants of SARS-CoV-2 differ in pathogenicity. Vero E6 cells are used to isolate, propagate, and study many viruses, including SARS-CoV-2. The aim of this work is to evaluate morphological differences during infection, and their relationships with the dynamics of viral titer. The cytopathic effect of the SARS-CoV-2 Wuhan-like variant was found to mainly follow an apoptotic pattern in 83 ± 6.1% of the cells. Infection resulted in near complete destruction of the cell monolayer. The maximum titer of the Wuhan variant reached 6.2 ± 0.2 log10 TCID50/ml on 4 d.p.i. At an inoculation dose of 3.5 log10 TCID50/ml. During infection with the delta variant (infection dose 4 = log10 TCID50/ml), up to 30% of cells remained alive, and cell death was accompanied by the formation of necrotic foci involving 41 ± 7.8% cells, and apoptosis of 30 ± 9.4% cells, with maximum titer reaching 5 ± 0.3 log10 TCID50/ml on day 5. In case of Omicron infection (infection dose = 3 log10 TCID50/ml), 90% cells survived, and for the rest 10% of cells the infection followed the classical pattern of apoptosis. At 5 d.p.i., the monolayer remained well preserved, but the morphology of all cells was changed suggested a wide infection of Vero cell culture with the Omicron variant. The maximum titer was 4.2 ± 0.3 log10 TCID50 on day 5. The higher doses were preferable for virus replication with Wuhan-like and Omicron viruses infection. For delta variant lower dose showed more effectivity as necrotic pattern of cell death was observed.
Correction: Lineage replacement of coxsackievirus A10 in Vietnam associated with increased detection and altered disease severity grading of hand, foot, and mouth disease.
Nguyen AT, Ta HTT, Dao ATH … +6 more , Vu HM, Ngu ND, Tran DN, Shimizu H, Nishimura Y, Hoa-Tran TN
Arch Virol · 2026 Mar · PMID 41843231 · Publisher ↗
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Microalga-virus-virophage coculture reveals co-infection of multi-virophages with a giant virus.
Chu T, Wang Q, Hu C … +4 more , Yu J, Chen L, Yu Y, Wang Y
Arch Virol · 2026 Mar · PMID 41843187 · Publisher ↗
Virophages parasitize the replication of co-infecting giant viruses within eukaryotic cells, forming tripartite cell-virus-virophage (CVv) systems. Tripartite interactions are well-documented in protozoa, yet comparable...
Virophages parasitize the replication of co-infecting giant viruses within eukaryotic cells, forming tripartite cell-virus-virophage (CVv) systems. Tripartite interactions are well-documented in protozoa, yet comparable systems in algae remain largely unexplored at the experimental level. Here, we report an experimentally validated CVv system involving the green, single-celled microalga Chlorella sp. DSL01, Dishui Lake large algal virus 1 (DSLLAV1), and multiple Dishui Lake virophages (DSLVs). Inoculation of Chlorella sp. DSL01 at low MOI established laboratory co-cultures in which time-series PCR detected DSLLAV1 early but not after Day 10, whereas all tested virophages persisted. Metagenomic profiling of the terminal supernatant (end-point sample) indicated a virophage-dominated assemblage with DSLV3 most represented. Droplet digital PCR at discrete time points (Days 5, 10, and 15) then provided absolute counts for DSLLAV1 and DSLV1/3/7, corroborating an early DSLLAV1 peak followed by collapse and/or a delayed rise of multiple virophages coincident with host growth recovery. Nested PCR on the algal pellet detected virophages DSLV1/3/7 but not DSLLAV1. Together, these results demonstrate that Chlorella sp. DSL01 supports co-infection by DSLLAV1 and multiple virophages, establishing an experimentally validated algal CVv system and revealing multi-virophage participation in freshwater algal virus-virophage-host dynamics.
Comprehensive high-throughput sequence-based detection and RT-LAMP confirmation of RNA viruses associated with dragon fruit (Selenicereus spp.) in India.
Madhu GS, Venkataravanappa V, Muttappagol M … +2 more , Reddy CNL, Hiremath S
Arch Virol · 2026 Mar · PMID 41831119 · Publisher ↗
Dragon fruit (Selenicereus spp.) is an emerging high-value tropical fruit crop grown extensively in India. However, very limited information is available on viruses associated with its cultivation. Hence, we conducted vi...
Dragon fruit (Selenicereus spp.) is an emerging high-value tropical fruit crop grown extensively in India. However, very limited information is available on viruses associated with its cultivation. Hence, we conducted virome profiling of dragon fruit cladodes collected from major growing regions of southern and western India using high-throughput sequencing (HTS), followed by validation through RT-PCR and RT-loop-mediated isothermal amplification. The survey conducted across Karnataka, Maharashtra, and Andhra Pradesh revealed moderate to high disease incidence (15–45%), with symptoms including mosaic, mottling, chlorotic streaks, and necrotic lesions. The meta-transcriptome analysis of the RNA isolated from infected cladodes revealed the presence of seven viruses; tobacco streak virus (TSV), groundnut bud necrosis virus (GBNV), pitaya virus X (PiVX), cactus virus X (CVX), cucumber mosaic virus (CMV), tomato mosaic virus (ToMV), and tomato brown rugose fruit virus (ToBRFV). However, the complete/near-complete genome sequences were successfully reconstructed for TSV, GBNV, PiVX, and CVX. Relative abundance analysis indicated GBNV as the dominant virus, followed by CVX, PiVX, and TSV. The phylogenetic analysis showed close clustering of GBNV, TSV, PiVX, and CVX isolates with previously reported Indian and global isolates, indicating high genetic conservation and probable regional dissemination through shared agroecosystems and planting materials. Recombination analysis identified statistically significant recombination events in TSV (RNA1 and RNA2), GBNV (L segment), and PiVX (RdRp region), suggesting ongoing genetic reshuffling and adaptive evolution. In contrast, CVX showed no evidence of recombination. RT-LAMP assays developed for the identified viruses enabled rapid, sensitive, and field-deployable detection, confirming widespread mixed infections across surveyed regions. This study represents the first comprehensive HTS-based virome profiling of dragon fruit in India and highlights the complexity of viral infections in this crop. The integration of HTS with RT-LAMP provides a robust framework for early diagnosis, quarantine surveillance, and the production of virus-free planting material, which is essential for the sustainable expansion of dragon fruit cultivation in India.
Groundnut bud necrosis orthotospovirus: An emerging viral problem of pulse crops.
Akram M, Kumar D, Jamil A … +3 more , Pratap A, Nair RM, Dixit GP
Arch Virol · 2026 Mar · PMID 41831068 · Publisher ↗
Pulses are vital to sustainable global food systems, supplying plant-based protein, minerals, and vitamins while improving soil fertility through biological nitrogen fixation. Cultivated on ~99.26 million ha with ~99.06...
Pulses are vital to sustainable global food systems, supplying plant-based protein, minerals, and vitamins while improving soil fertility through biological nitrogen fixation. Cultivated on ~99.26 million ha with ~99.06 million tonnes annual production, their demand is rising, particularly in Asia and Africa. Yet production stability is increasingly threatened by climate variability, expanding vector niches, and predominantly rain-fed cultivation systems, where viral diseases impose major yield losses. While begomovirus-induced yellow mosaic disease remains the most destructive in Asia, the thrips-borne groundnut bud necrosis orthotospovirus (GBNV: Orthotospovirus arachinecrosis) is rapidly reshaping the viral disease scenario in Indian pulse crops. GBNV infections are now recorded in mungbean, urdbean, cowpea, French bean, field pea, and wild Vigna species, causing necrotic leaf-curl symptoms. Here, we review how GBNV has emerged as a major threat to the sustainability of pulse-based agro-ecosystems. GBNV shows considerable genetic diversity, indicating ongoing evolution and host expansion. Climate-driven changes in Thrips palmi populations and their efficient persistent-propagative transmission play a central role in disease outbreaks. Resistance breeding remains limited because no resistance genes or QTLs have been identified. Emerging management approaches such as ecosystem-based vector suppression, biocontrol and antiviral agents, and early RNA-level diagnostics, offer promising alternatives to reduce reliance on broad-spectrum insecticides. This review presents a pulse-centric sustainability framing of GBNV and outlines research priorities to strengthen surveillance, breeding, and management strategies within global pulse production systems.
Insect cypoviruses: advances in structural characterization, evolutionary genomics, and host interaction dynamics.
Gnanasekaran R, Subrahmanyam G, Ito K … +12 more , Hiranmayi D, Suraporn S, Swevers L, de Miranda JR, Dubey H, Debnath R, Shukla P, Arunkumar KP, Jiang L, Xia Q, Samova S, Moorthy SM
Arch Virol · 2026 Mar · PMID 41820676 · Publisher ↗
Cypoviruses are insect-specific, double-stranded RNA viruses belonging to the genus Cypovirus within the family Spinareoviridae. Cypoviruses primarily infect insects of the orders Lepidoptera, Diptera, and Hymenoptera. T...
Cypoviruses are insect-specific, double-stranded RNA viruses belonging to the genus Cypovirus within the family Spinareoviridae. Cypoviruses primarily infect insects of the orders Lepidoptera, Diptera, and Hymenoptera. These viruses replicate in midgut epithelial cells, forming polyhedrin-based occlusion bodies. Cypovirus genomes typically consist of 10-16 linear double-stranded RNA (dsRNA) segments that encodes distinct viral proteins; however, the number of genomic segments may vary among species. Each genomic segment encodes a functionally specialized distinct viral protein, with high intra-species conservation but notable divergence between species, reflecting genomic plasticity and evolutionary divergence. This review presents a comprehensive comparative genomic analysis of representative Cypovirus species, focusing on segment-wise assignments. Segment 1 universally encodes the major capsid protein, while segment 2 encodes the RNA-dependent RNA polymerase (RdRP) and segment 3 encodes the minor capsid protein. Segments 4 and 5 typically encode enzymes with methyltransferase and guanylyl transferase, which are essential for RNA capping. Segments 6 to 8 encodes for other structural or accessory proteins. Segment 9 frequently encodes a non-structural protein and segment 10 consistently encodes structural polyhedrin protein. Conserved protein domains and sequence motifs are identified across cypovirus genomic segments. Analysis of nonsynonymous to synonymous substitutions (Ka/Ks ratios) reveals evidence of both purifying and positive selection in viral genomic segments. Phylogenetic analysis demonstrates lineage diversification and species-specific clustering. Genotypic and phenotypic variability among viral strains correlates with host insect species, co-infection and geographic isolation, whereas functional convergence in protein roles is observed across species. This study consolidates electrophoretic migration patterns and genomic demarcation criteria for Cypovirus species into a practical reference framework that enables rapid species identification without the need for complete genome sequencing. The current review provides structural, genomic, and evolutionary insights that collectively advance the current understanding of cypovirus biology and diversity.
Genetic diversity of Apis mellifera filamentous virus in bees sampled in the USA and Jamaica.
Bandoo RA, Kraberger S, Ozturk C … +5 more , Zhu Q, Smith B, Krupovic M, Cook C, Varsani A
Arch Virol · 2026 Mar · PMID 41811537 · Publisher ↗
Apis mellifera filamentous virus (AmFV) is a large filamentous virus with a ~500 kb double-stranded DNA genome identified in honeybees and a handful of other winged insects. Since its first identification almost 50 years...
Apis mellifera filamentous virus (AmFV) is a large filamentous virus with a ~500 kb double-stranded DNA genome identified in honeybees and a handful of other winged insects. Since its first identification almost 50 years ago, only a few nearly complete AmFV genomes have been sequenced. Genomic regions of AmFV have been identified using gene-specific primers as part of the viral screening surveys for honeybee viruses. Here, we assembled a complete AmFV genome from honeybees from the USA which shares 94.4-96.4% intergenomic similarity with previously published AmFV genomes. A distinct variation observed within this genome compared with others available in public databases is a unique inversion and translocation of an ~11,000 bp genomic region. In addition to assembling a full genome, we screened 250 honeybees and 20 Nomia solitary bee samples collected in the USA, and 120 honeybees collected in Jamaica for AmFV using DNA polymerase gene-specific primers. The incidence rate of AmFV infection in Nomia solitary bees sampled in the USA was 20%, whereas in the honeybees, the incidence ranged from 0% to 80% for the samples collected at different locations in the USA and from 13.3% to 58% at two locations in Jamaica. Analyses of the DNA polymerase sequences (n=84 from this study and n=43 from other studies) revealed three phylogenetically supported genotypes (I, II, III). AmFV genotype I is found in samples collected in France and the USA. Genotype II has a broad geographical range detected in samples collected in Bangladesh, China, South Korea, Cyprus, Hungary, Switzerland, and the USA. Genotype III is in samples collected from South Africa, Jamaica, Argentina, and the USA. Thus, all three AmFV genotypes are circulating in bees in the USA. To better understand the origin, diversity, and host range of AmFV at a global level, it is essential to increase the screening of various pollinators as well as Varroa mites which parasitize bees. Furthermore, given that the available AmFV genomes all belong to genotype II, and the fact that we identified large tracts of translocation/rearrangement in an AmFV genome, there is need for sequencing of additional genomes to elucidate the drivers of AmFV diversity.
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