Archives Of Virology[JOURNAL]
Sun
200 papers
Molecular epidemiological investigation of viruses in Amur tigers in Northeast China.
Jiang H, Wang L, Huo S … +10 more , Qiu Y, Chen Z, Wang W, Zhang S, Chai H, Zeng X, Yang S, Xu H, Wang Y, Haitao
Arch Virol · 2026 Jun · PMID 42371188 · Publisher ↗
A systematic molecular epidemiology survey was conducted on ten viruses in 226 captive and two wild Amur tigers from Northeast China. The target viruses were: feline panleukopenia virus (FPV), feline herpesvirus-1 (FHV-1...
A systematic molecular epidemiology survey was conducted on ten viruses in 226 captive and two wild Amur tigers from Northeast China. The target viruses were: feline panleukopenia virus (FPV), feline herpesvirus-1 (FHV-1), feline immunodeficiency virus (FIV), feline leukemia virus (FeLV), canine distemper virus (CDV), feline coronavirus (FCoV), feline calicivirus (FCV), influenza A virus (IAV), hepatitis E virus (HEV), and rotavirus A (RVA). The overall infection prevalence in captive tigers was 45.6% (103/226), with FPV (25.2%) and FHV-1 (20.4%) identified as the dominant pathogens. Other viruses detected at lower frequencies were FIV (3.1%), CDV (1.8%), FCoV (0.9%), and FeLV (0.4%); FCV, IAV, HEV, and RVA were not detected. This study reports the first detection of FeLV in this subspecies. Infection prevalence exhibited marked age and regional dependence, being highest in juveniles (56.5%) and in the facilities of Shenyang (55.8%) and Harbin (52.6%). Phylogenetic analysis of partial VP2 sequences indicated that FPV strains from captive tigers formed a distinct, well-supported monophyletic clade (bootstrap = 99). In contrast, the VP2 sequence from the wild tiger (YINGCHUN) did not group within the captive tiger clade; instead, it occupied a separate position within the broader FPV cluster. FIV strains from tigers were phylogenetically interspersed with strains from domestic cats in China. Despite existing vaccination protocols, the persistent high prevalence of FPV and FHV-1 indicates suboptimal immunoprotection. These findings clarify the current viral pathogen profile in captive Amur tigers and underscore the necessity for optimizing disease management strategies, including age-stratified immunization, enhanced biosecurity, and the establishment of transboundary surveillance.
Mining viruses in public databases unveils the diversity within the Deltaflexiviridae family.
Fernandes JEA, Nagata T, Melo FL
Arch Virol · 2026 Jun · PMID 42360507 · Full text
Cloud computing platforms aided the scalability and applicability of viral mining in genomic databases. The Serratus project reported SRA accessions that may contain viral sequences. This study analyzed SRA accessions co...
Cloud computing platforms aided the scalability and applicability of viral mining in genomic databases. The Serratus project reported SRA accessions that may contain viral sequences. This study analyzed SRA accessions containing sequences similar to Tymovirales members to verify the presence of sequence data derived from viral genomes. All steps in the genome mining analysis were performed by a pipeline running on virtual machines hosted on the Google Cloud Platform. Manual curation of the pipeline output discovered 111 putative genomes in the analyzed SRAs. Among the genomes identified, four were classified as isolates within the Betaflexiviridae family, and two were putative new members of the Alphaflexiviridae family. Another four sequences were likely classified in a family not yet accepted by the ICTV. The phylogenetic reconstruction of the Deltaflexiviridae family revealed three distinct clades, one of them containing 81 genomes (34 putative new species), a second clade with 18 novel genomes (7 putative new species), and a third with one putative new species. Given the high divergence between these three groups, we suggest the establishment of a new family, "Epsilonflexiviridae", and the split of the Deltaflexiviridae family into two by establishing the family "Zetaflexiviridae". The results of this work provide insight into important aspects of the evolutionary history of the order Tymovirales and offer new ways for virus-mining projects in genomic databases.
Identification of novel hepaciviruses in rock pigeon (Columba livia [Gmelin, 1789]), rusty-margined flycatcher (Myiozetetes cayanensis [Linnaeus, 1766]), and Hispaniolan amazon (Amazona ventralis [Statius Muller, 1776]).
Kawano S, Kishimoto M, Imai S … +3 more , Tanaka T, Moriishi K, Horie M
Arch Virol · 2026 Jun · PMID 42360501 · Publisher ↗
Recent advances in sequencing technology and transcriptome mining have revealed highly divergent hepaciviruses in birds. However, only a limited number of avian hepaciviruses have been identified to date, leaving their d...
Recent advances in sequencing technology and transcriptome mining have revealed highly divergent hepaciviruses in birds. However, only a limited number of avian hepaciviruses have been identified to date, leaving their diversity and evolutionary history poorly understood. Moreover, deep phylogenetic gaps among known avian hepaciviruses suggest that additional lineages remain undiscovered. Here, we screened publicly available RNA-seq data and identified three previously undescribed hepaciviruses from rock pigeon (Columba livia), rusty-margined flycatcher (Myiozetetes cayanensis), and Hispaniolan amazon (Amazona ventralis), named rock pigeon hepacivirus (RpHV), rusty-margined flycatcher hepacivirus (RfHV), and Hispaniolan amazon hepacivirus (HaHV). Although these three viruses meet the ICTV species demarcation criteria relative to their closest known relatives, the NS5B-based criterion was not satisfied between RfHV and HaHV. Notably, however, their genome sequence identity is low at 43.2%, and their hosts differ at the order level, suggesting that their classification warrants further consideration. Our phylogenetic analysis showed that avian hepaciviruses, including those found in this study, are monophyletic, but phylogenetic incongruence was observed between avian hepaciviruses and their hosts, suggesting past cross-species transmission among avian hepaciviruses. Overall, this study provides novel insights into the diversity and evolution of hepaciviruses.
Structural insights into DENV-2 NS2B-NS3 protease and inhibition by glutathione-coated gold nanocluster.
Zhu H, Niu W, Xu Y … +11 more , Li Z, Xia D, Chen S, Zhang B, Wang J, Yang H, Gao X, Chen Y, Gong Y, Cao P, Zhou Y
Arch Virol · 2026 Jun · PMID 42337180 · Publisher ↗
Dengue virus (DENV) continues to pose a significant global health threat, with increasing infection rates and limited treatment options. The viral NS2B-NS3 protease (NS2B-NS3pro), a highly conserved two-component enzyme...
Dengue virus (DENV) continues to pose a significant global health threat, with increasing infection rates and limited treatment options. The viral NS2B-NS3 protease (NS2B-NS3pro), a highly conserved two-component enzyme essential for polyprotein processing and replication, is a key target for antiviral drug development. Here, we report the 2.25 Å-resolution crystal structure of DENV serotype 2 (DENV-2) NS2B-NS3pro, in which a PEG fragment is bound within a solvent-exposed pocket between β10, β11, β14 and β15 of NS3. This structure reveals a previously unrecognized solvent-exposed PEG-binding pocket, which may represent a putative ligand-binding surface for future validation and inhibitor-design studies. We also show that the glutathione-coated gold nanocluster (GSH-AuNC) directly inhibits DENV-2 NS2B-NS3pro. Bio-layer interferometry and fluorescence-based protease assays indicate that the nanocluster binds NS2B-NS3pro with a dissociation constant of 15.64 µM and inhibits its catalytic activity with an IC of 16.04 µM, consistent with a direct inhibitory effect at the in vitro enzymatic level. Molecular dynamics simulations further suggest that GSH-AuNC is predicted to interact with the catalytic triad of NS2B-NS3pro, forming stable electrostatic and van der Waals interactions that may interfere with substrate access. Collectively, these findings provide an in vitro structural and biochemical basis for targeting DENV-2 NS2B-NS3pro and may inform future development of small-molecule or nanomedicine-based inhibitors, although cell-based antiviral efficacy, cytotoxicity, and cellular uptake remain to be evaluated.
Genomic characterization of three novel Shiga toxin-producing Escherichia coli lytic phages.
Juarez AE, Krüger A, Lucchesi P
Arch Virol · 2026 Jun · PMID 42337171 · Publisher ↗
Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens. In response to the need for safe biocontrol strategies, lytic phages have emerged as promising tools for STEC control. This study analyses geno...
Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens. In response to the need for safe biocontrol strategies, lytic phages have emerged as promising tools for STEC control. This study analyses genomic features of three novel phages, L73, PG3 and A4.3, isolated from cattle farms using STEC strains as hosts. L73 and PG3 were classified as Tequatrovirus, while A4.3 as Vequintavirus. Genomic analyses revealed no markers of lysogeny, antimicrobial resistance, or virulence. Phylogenetic and comparative analyses confirmed close relationships to reference phages of each genus, while also revealing distinct genetic differences. These phages constitute genomically well-supported candidates for future evaluation as STEC biocontrol agents.
Molecular characterization of a novel partitivirus isolated from Fusarium solani, the causal agent of tobacco root rot.
Wu X, Wang Y, Guo R … +6 more , Wang YR, Li SJ, Zhou XP, Zhong J, Xiao YS, Liu TB
Arch Virol · 2026 Jun · PMID 42337121 · Publisher ↗
In this study, a novel double-stranded RNA (dsRNA) mycovirus, tentatively designated Fusarium solani partitivirus 4 (FsPV4), was isolated from the Fusarium solani strain GF7, a phytopathogenic fungus responsible for toba...
In this study, a novel double-stranded RNA (dsRNA) mycovirus, tentatively designated Fusarium solani partitivirus 4 (FsPV4), was isolated from the Fusarium solani strain GF7, a phytopathogenic fungus responsible for tobacco root rot. The genome of FsPV4 consists of two dsRNA segments, referred to as dsRNA1 (2312 bp in length) and dsRNA2 (2213 bp in length). The dsRNA 1 and dsRNA 2 were predicted to encode an RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. Sequence analysis revealed that the RdRp of FsPV4 showed significant sequence similarity to the RdRps of partitiviruses, with Aplosporella javeedii partitivirus 1 being the best match (identity: 60.76%). Phylogenetic analysis of the RdRp showed that FsPV4 clustered robustly within the genus Betapartitivirus of the family Partitiviridae. This represents the first report of a betapartitivirus infecting F. solani, providing a potential candidate for the biological control of F. solani-mediated plant diseases.
Identification of candidate serotype-specific B-cell epitopes from dengue virus non-structural proteins using an integrated in silico approach.
Subramanian P, Shanmugaraj B, Ramalingam S
Arch Virol · 2026 Jun · PMID 42323433 · Publisher ↗
Dengue is a vector-borne disease transmitted through mosquitoes that pose serious health issues globally. Dengue infection is caused by dengue virus (DENV) that circulates as four serotypes in endemic regions and accurat...
Dengue is a vector-borne disease transmitted through mosquitoes that pose serious health issues globally. Dengue infection is caused by dengue virus (DENV) that circulates as four serotypes in endemic regions and accurate serotype differentiation is hindered by widespread serological cross-reactivity. DENV is composed of three structural and seven non-structural proteins and in the current study, all seven non-structural (NS) proteins were analyzed using an integrated in silico approach to identify candidate serotype-specific B-cell epitopes carrying potential diagnostic relevance. Multiple sequence alignment, pairwise identity assessment, and phylogenetic relationship of all four DENV serotype amino acid sequences were carried out. Linear B-cell epitopes were predicted using the BepiPred tool with parameters optimized to balance sensitivity and specificity and the ABCPred tool for further sequence-based epitope prediction. This was later followed by structure-based surface epitope prediction using ElliPro. The predicted epitopes were subsequently subjected to a two-step conservancy analysis to evaluate intra-serotype conservation and pan-serotype divergence. The multiple sequence alignment showed that high sequence conservation (~ 98-99%) was observed overall across NS proteins, yet specific aminoacid substitutions were identified that enabled serotype-level discrimination. Initial B-cell epitope prediction resulted in 355 epitopes and 1067 epitopes from BepiPred and ABCPred respectively. Antigenicity, allergenicity and toxicity filters were applied to retain potential antigenic epitopes. Further, initial stringent filtering criteria (≤ 75% intra-serotype conservation and ≤ 30% pan-serotype minimum identity) were applied to increase serotype-specific strictness of the candidate epitopes. Altogether all non-structural proteins yielded 121 epitopes from the BepiPred, ABCPred and ElliPro tools with stricter 50-75% intra-serotype conservation, and ≤ 25% pan-serotype minimum identity. Also, few of the predicted epitopes were in concordance with previous in silico or experimentally validated antigenic regions reported, supporting their biological relevance. Overlap with surface epitopes and stringent filtering suggest that the DENV NS proteins are made of distinct antigenic regions that makes them as potential candidates for serotype-specific differentiation. This workflow for epitope prediction and filtering provides a computational basis for utilizing epitopes for future experimental validation and diagnostic assay development.
Molecular characterization and whole-genome sequencing-based genetic evolution of coxsackievirus A16 in Taiyuan City, 2023-2025.
Wang Y, Xu J, Zhao L … +8 more , Li Y, Xu Y, Gao R, Guo X, Niu M, Zuo Z, An T, Wang J
Arch Virol · 2026 Jun · PMID 42322358 · Publisher ↗
Coxsackievirus A16 (CVA16) is a major causative agent of hand, foot, and mouth disease (HFMD) in China. Based on 35 CVA16-positive strains isolated in Taiyuan (2023-2025), we characterized the post-pandemic evolutionary...
Coxsackievirus A16 (CVA16) is a major causative agent of hand, foot, and mouth disease (HFMD) in China. Based on 35 CVA16-positive strains isolated in Taiyuan (2023-2025), we characterized the post-pandemic evolutionary dynamics. Genomic analysis revealed the highest conservation in VP4 and the lowest in the 3' UTR. Temporally, a shift from B1a/B1b co-circulation to a three-lineage pattern (including a novel B1c subgenotype) was observed. Intertypic recombination was the primary driver, specifically targeting the 5'UTR and VP1/2A junction (B1a with EV71; B1b with CVA4; B1c with both). Crucially, the core P1 capsid region remained intact and recombination-free, preserving major antigenic determinants. Complementing this, positive selection acted on four internal structural residues (VP1‑T97I, VP2‑D139T, VP3‑I2V, VP3‑M126T), stability predictions indicated these substitutions moderately reduced capsid stability, suggesting adaptive tuning of assembly kinetics rather than antigenic drift. Three B1b-specific markers including L23M, I235V and T240A in VP1 further supported temporal adaptation, with no significant geographic divergence between northern and southern strains during overlapping time periods. This study clarifies that CVA16 evolution is driven by non-coding recombination and subtle structural refinement, providing molecular evidence for the sustained antigenic relevance of current vaccine candidates.
A novel hexasegmented virus isolated from the phytopathogenic fungus Verticillium nonalfalfae.
Miljanić V, Sabanadzovic S, Aboughanem-Sabanadzovic N … +3 more , Jakše J, Radišek S, Štajner N
Arch Virol · 2026 Jun · PMID 42321439 · Full text
In this study, we describe a novel virus, tentatively named Verticillium nonalfalfae virus M (VnaVM), identified in the phytopathogenic fungus Verticillium nonalfalfae isolated from hop (Humulus lupulus L.). The VnaVM ge...
In this study, we describe a novel virus, tentatively named Verticillium nonalfalfae virus M (VnaVM), identified in the phytopathogenic fungus Verticillium nonalfalfae isolated from hop (Humulus lupulus L.). The VnaVM genome consists of six double-stranded RNA (dsRNA) segments ranging from 1051 to 2401 bp. DsRNAs 1-3 encode an RNA-dependent RNA polymerase (RdRp), a hypothetical protein and a methyltransferase (MTR), respectively, while dsRNA6 encodes a proline-alanine-serine-rich protein (PASrp). These four proteins share less than 58% amino acid identity with homologs encoded by viruses in the family Polymycoviridae. Products encoded by dsRNAs 4 and 5 show no similarity to known proteins, and their roles in the viral life cycle are unknown. Phylogenetic analysis of RdRp amino acid sequences, together with genome organization and pairwise identity values, supports classifying VnaVM as a representative of a novel species within the genus Multimycovirus (family Polymycoviridae). To our knowledge, this is the first report of a polymycovirid infection in a member of the genus Verticillium.
Molecular epidemiology of DS-1-like G1P[8] rotavirus strains in Vietnam, 2012-2016: Evolutionary dynamics of an unusual rotavirus reassortant.
Tam PT, Vu MH, Hoa-Tran TN … +17 more , Dao THA, Nguyen TA, Duong TH, Dang TTH, Nguyen TT, Hoang HM, Nguyen TVH, Nguyen TH, Varja G, Sarah T, Bines JE, Donato CM, Hasebe F, Kodama T, Abe H, Nakagomi T, Nakagomi O
Arch Virol · 2026 Jun · PMID 42310243 · Publisher ↗
The segmented genome of Rotavirus alphagastroenteritidis facilitates the emergence of unusual reassortants, increasingly documented in the post-vaccine era. However, their long-term evolutionary dynamics and population-l...
The segmented genome of Rotavirus alphagastroenteritidis facilitates the emergence of unusual reassortants, increasingly documented in the post-vaccine era. However, their long-term evolutionary dynamics and population-level persistence remain poorly understood. We investigated G1P[8] strains detected through hospital-based surveillance in northern and central Vietnam from 2012 to 2016. Electropherotyping, whole-genome sequencing, and phylogenetic analyses were performed to define genomic constellations and reconstruct evolutionary dynamics of DS-1-like reassortants. We documented four-year circulation patterns of DS-1-like G1P[8] strains, emerging in 2012/2013, peaking in mid-2014, and declining by 2016. Among 44 strains exhibiting short electropherotypes, at least three sequential genotype constellations (A-C) were identified: Constellation A likely arose in northern Vietnam through inter-genogroup reassortment between Wa-like G1P[8] (VP7/VP4) and DS-1-like G2P[4] strains; A related variant in central Vietnam suggested regional transmission from contemporaneous strains reported in Thailand and Japan; Constellation B involved acquisition of a Wa-like NSP2 gene; Constellation C included additional reassortment with bovine-like NSP2 and NSP4 genes from a co-circulating G8P[8] strain. No significant differences in clinical severity were observed between DS-1-like and Wa-like infections, and no cases of either genotype were detected among fully vaccinated children. Overall, this study describes a stepwise reassortment process involving intergenogroup, intragenogroup, and potential zoonotic events. Genomic diversification in this setting was not associated with increased virulence or evidence of immune escape. These findings highlight the need for continued genomic surveillance and broader sampling to better resolve the evolutionary dynamics of rotavirus reassortants.
Enhanced virucidal activity of quaternary ammonium compound-thymol combinations: influence of mucin and mucoadhesive polymers.
Ahmady A, Mickleburgh I, Bryant N … +2 more , Carnell GW, Blacklaws BA
Arch Virol · 2026 Jun · PMID 42310234 · Full text
The COVID-19 pandemic highlighted the potential of oral antiseptic agents to reduce viral transmission. Strategies that enhance and sustain antiviral activity in the oral cavity may further support control of respiratory...
The COVID-19 pandemic highlighted the potential of oral antiseptic agents to reduce viral transmission. Strategies that enhance and sustain antiviral activity in the oral cavity may further support control of respiratory viruses. In this study, we evaluated the virucidal activity of selected antiseptic agents against influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), individually and in combination, under controlled in vitro conditions. Cetylpyridinium chloride (CPC), benzethonium chloride (BZT), thymol, and tannic acid were assessed using a quantitative suspension assay in the presence of mucin and representative mucoadhesive polymers. Dynamic light scattering and zeta potential analyses were performed to characterize interactions between active agents and mucin or polymers. CPC, BZT, and thymol exhibited dose-dependent viral inactivation. CPC reduced IAV and SARS-CoV-2 titres by approximately 4 log₁₀ at > 200 µg/mL and 25 µg/mL, respectively, while thymol achieved comparable reductions at 1000 µg/mL and 750 µg/mL. Tannic acid showed minimal virucidal activity. Notably, CPC-thymol and BZT-thymol combinations achieved > 4 log₁₀ reductions at substantially lower concentrations than individual agents, indicating enhanced virucidal activity and improved cytocompatibility. Mucin markedly attenuated the virucidal activity of CPC-thymol combinations; however, selected polymers partially preserved antiviral efficacy under mucin-rich conditions. Physicochemical analyses suggest that electrostatic, hydrophobic, and hydrogen-bonding interactions contribute to these effects. These findings demonstrate the enhanced antiviral activity of quaternary ammonium compound-thymol combinations and highlight the influence of mucosal components and macromolecules interactions in modulating oral antiseptic activity.
Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica.
Biter R, Regney M, Schmidt AE … +12 more , Swanson N, Elrod M, Lescroël A, Burnham C, Jongsomjit D, Winquist S, Pennycook J, Ainley DG, Dugger KM, Ballard G, Kraberger S, Varsani A
Arch Virol · 2026 Jun · PMID 42298252 · Publisher ↗
Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach t...
Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua (Stercorarius maccormicki) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake (Rissa tridactyla), Larus smithsonianus papillomavirus 1 from American herring gull (Larus smithsonianus) and Fratercula arctica papillomavirus 1 from Atlantic puffin (Fratercula arctica), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp. and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins (Pygoscelis adeliae), Weddell seals (Leptonychotes weddellii), Antarctic fur seals (Arctocephalus gazella), leopard seals (Hydrurga leptonyx) and emerald notothen (Trematomus bernacchii).
Characterization of a divergent isolate of rice stripe virus from volunteer durum wheat in France.
Marais A, Faure C, Huang A … +2 more , Comte R, Candresse T
Arch Virol · 2026 Jun · PMID 42295510 · Publisher ↗
A highly divergent isolate of rice stripe virus (RSV, Tenuivirus oryzaclavatae) was identified by high-throughput sequencing (HTS) of volunteer durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) plants collected...
A highly divergent isolate of rice stripe virus (RSV, Tenuivirus oryzaclavatae) was identified by high-throughput sequencing (HTS) of volunteer durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) plants collected in summer 2023 in Loir-et-Cher (France). The complete sequence of all four genomic RNAs was obtained from a single plant, showing a genomic organization similar to that of known RSV isolates but with significant indel polymorphism in non-coding regions. Genomic RNAs showed between 81.6% (RNA4) and 88.3% (RNA3) nucleotide identity with RSV reference isolates, while encoded proteins showed between 86.3% (NSvc2) and 97.4% (L and NSvc4 (movement protein)) with those of the reference RSV isolate. The 97.4% identity in the L protein should be compared with the average pairwise identity of 99.0% +/- 0.1% among all RSV isolates present in GenBank, as well as with the ICTV species demarcation threshold of 5% divergence. This demonstrates that the French wheat variant is indeed an RSV isolate but a highly divergent one, which questions our current understanding of RSV geographic distribution, diversity and evolution history.
Identification and characterization of an endogenous pararetrovirus in Gentiana triflora plants.
Isogai M, Tezuka S, Abe A … +2 more , Takamura Y, Yaegashi H
Arch Virol · 2026 Jun · PMID 42295471 · Full text
Deep sequencing and de novo assembly of small RNAs (sRNA analysis) provide a powerful approach to detect plant RNA and DNA viruses. Here, using sRNA analysis of Gentiana triflora (gentian) plants affected with kobu-sho d...
Deep sequencing and de novo assembly of small RNAs (sRNA analysis) provide a powerful approach to detect plant RNA and DNA viruses. Here, using sRNA analysis of Gentiana triflora (gentian) plants affected with kobu-sho disease, a serious disease of gentian, we found caulimovirus-like sequences, provisionally designated as gentian caulimovirus-like sequence (GCVS). Analysis of the complete nucleotide sequence indicated that GCVS is a novel virus with a genomic structure and organization typical of members of genus Caulimovirus (family Caulimoviridae). Based on Southern blot hybridization and rolling circle amplification analyses, GCVS seems to be integrated into the genomes of a wild gentian plant and three F₁ gentian cultivars and their respective parents and without any episomal viral forms in plants. Consistently, no episomal virus was detected in gentian plants with kobu-sho disease. To confirm GCVS integration in the gentian genome, we used a BLASTn analysis of the gentian draft genome (4,374 contigs; total: 3,657,985,820 nucleotides [nt]) using the GCVS sequence as a query and identified 1,929 GCVS-derived fragments (total: 3,116,680 nt) across 280 contigs. All fragments were shorter than the full-length GCVS genome (8,125 nt), and more than 90% were less than 4,000 nt long. Open reading frames in these fragments encoded proteins containing numerous amino acid substitutions and were frequently disrupted by premature stop codons. Collectively, these features indicate that GCVS represents a non-infectious endogenous pararetrovirus, defined as a pararetroviral sequence that has been integrated into the host genome and is no longer capable of autonomous replication or infection.
The role of DPP4 in viral infections: from receptor biology to antiviral target.
Aguilera-Flores C, Arias CF
Arch Virol · 2026 Jun · PMID 42287495 · Full text
Dipeptidyl Peptidase 4 (DPP4) is a type II transmembrane serine protease with diverse physiological roles in metabolic regulation and immune modulation. Beyond its native functions, DPP4 has emerged as a critical host fa...
Dipeptidyl Peptidase 4 (DPP4) is a type II transmembrane serine protease with diverse physiological roles in metabolic regulation and immune modulation. Beyond its native functions, DPP4 has emerged as a critical host factor exploited by a range of viruses to drive infection and pathogenesis. This review synthesizes the multifaceted interactions between DPP4 and viral pathogens. We examine the structural basis for direct receptor binding by coronaviruses such as MERS and PHEV, as well as the dual-receptor entry mechanism used by human astroviruses. Additionally, the review explores how viruses such as HIV-1 and HCV exploit DPP4's enzymatic and non-enzymatic functions to modulate T cell activation and promote viral persistence. Finally, we evaluate pharmacological perspectives, including DPP4 inhibitors, monoclonal antibodies, and soluble decoy receptors as host-directed therapies. By mapping these diverse viral strategies, this article provides a comprehensive framework for understanding DPP4 as a moonlighting protein and a promising target for broad-spectrum antiviral interventions.
Identification of a capsid-derived Zika virus epitope with high IgG discriminatory performance.
Dos Santos ALC, Lopes SR, Amaral RP … +4 more , Malaquias LCC, Dos Santos Nunes Ferreira A, de Oliveira DB, Coelho LFL
Arch Virol · 2026 Jun · PMID 42283882 · Full text
The identification of specific serological targets for Orthoflavivirus zikaense (ZIKV) remains challenging due to the high degree of structural similarity and antibody cross-reactivity among co-circulating arboviruses, p...
The identification of specific serological targets for Orthoflavivirus zikaense (ZIKV) remains challenging due to the high degree of structural similarity and antibody cross-reactivity among co-circulating arboviruses, particularly dengue virus (DENV). In this context, immunoinformatics-based approaches may contribute to the rational selection of candidate epitopes with potentially improved analytical specificity. In the present study, five conserved ZIKV peptides previously identified through an immunoinformatic pipeline were experimentally evaluated as candidate serological targets. Peptide reactivity was assessed by indirect ELISA using human serum samples positive for anti-ZIKV IgM and IgG antibodies. Distinct reactivity patterns were observed between antibody classes. IgM assays showed limited analytical discriminatory capacity, particularly due to reduced specificity for some peptides. In contrast, IgG-based analyses revealed more favorable analytical profiles. Among the peptides evaluated, a peptide identified in the capsid (PEP03) exhibited the most favorable analytical performance, with an area under the ROC curve (AUC) of 0.9183 (95% CI: 0.8301-1.000). An absence of detectable reactivity was observed among sera from DENV-positive patients, and minimal reactivity with chikungunya virus (CHIKV) positive samples under the experimental conditions employed. Other peptides tested in this study demonstrated variable analytical profiles, reinforcing the importance of rational epitope selection for serological applications. Overall, these findings provide preliminary analytical evidence that structurally derived ZIKV epitopes may exhibit distinct IgM and IgG recognition patterns and support the continued evaluation of capsid-derived epitopes as candidate targets for serological applications (IgG detection) in regions where multiple arboviruses co-circulate.
Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.
Chen X, Fang Z, Li S … +6 more , Wu Q, Liu W, Xiang L, Liu Q, Tan L, Weng Q
Arch Virol · 2026 Jun · PMID 42283754 · Publisher ↗
Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome...
Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome places it within the genus Ghunavirus (family Autographiviridae). Notably, its genome lacks auxiliary metabolic genes (AMGs), in contrast to AMG-rich profiles reported in cave metagenomic surveys and underscoring the necessity of isolation-based approaches to complement environmental sequencing data.
A new putative carlavirus identified by metagenomic analysis in a wild weed in Angola.
Amoia SS, Giampetruzzi A, Antònio LF … +2 more , Tomàs Pais da Cunha A, Minafra A
Arch Virol · 2026 Jun · PMID 42277454 · Full text
A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery...
A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery of a putatively novel carlavirus, tentatively named 'Seles weed carlavirus'. The complete genome sequence, consisting of 8,597 nucleotides, poly-A tail excluded, exhibited the typical organization of members of the genus Carlavirus, including the replicase polyprotein (ORF1); the triple gene block (ORFs 2-4); the coat protein (ORF5) and an RNA-binding protein (ORF6). The replicase polyprotein and coat protein gene regions of the newly described virus shared the highest amino acid sequence identity with the corresponding sequences of cowpea mild mottle virus (51.40%) and Hainan betaflexivirus (63.08%), respectively. The infection was further confirmed by RT-PCR with multiple specific targeted primer pairs, whose related amplicons were cloned and sequenced.
The complete nucleoprotein gene molecular characterization of Akabane Virus in Türkiye.
Pekmez K, Kaplan M, Çağırgan AA … +1 more , Arslan F
Arch Virol · 2026 Jun · PMID 42277345 · Publisher ↗
Akabane virus (AKAV), a member of the Peribunyaviridae family, is an important arbovirus causing reproductive disorders and congenital abnormalities in ruminants. This study aimed to molecularly characterize AKAV isolate...
Akabane virus (AKAV), a member of the Peribunyaviridae family, is an important arbovirus causing reproductive disorders and congenital abnormalities in ruminants. This study aimed to molecularly characterize AKAV isolates from different regions of Türkiye and assess their phylogenetic relationships using complete N gene sequences. A total of seven AKAV-positive samples, obtained from sheep fetuses and one Culicoides imicola specimen, were analyzed. Viral RNA was extracted, and the full-length N gene (702 nucleotides) was amplified and sequenced. Sequence analysis showed 519 conserved nucleotide sites and 183 conserved amino acid residues. Among genogroup Ib isolates, nucleotide similarity ranged from 95.72% to 100%, and amino acid similarity from 98.29% to 100%. A total of 47 nucleotide and 6 amino acid substitutions were identified; however, none were located within predicted epitope regions. Seven potential B-cell epitopes in the N protein were predicted and found to be conserved across all isolates. Phylogenetic analysis revealed that all Turkish isolates clustered within genogroup Ib and formed a distinct clade with Israeli isolates from 2018, while older Israeli and Japanese strains grouped separately within the same genogroup. Overall, AKAV strains circulating in Türkiye show high genetic similarity and conserved antigenic regions, contributing to a better understanding of the virus's molecular epidemiology.
Genomic characterization of Actinidia totivirus 1 (AcToV1), a novel member of the genus Totivirus infecting kiwifruit.
Zhu M, Chen W, Wei Y … +6 more , He F, Zhang W, Tang X, Xin D, Liu H, Song S
Arch Virol · 2026 Jun · PMID 42271104 · Publisher ↗
Kiwifruit (Actinidia spp.) has long been appreciated for its desirable flavor and high nutritional value. In this study, leaf samples with chlorotic mottling symptoms were collected from kiwifruit plants in Hanzhong, Sha...
Kiwifruit (Actinidia spp.) has long been appreciated for its desirable flavor and high nutritional value. In this study, leaf samples with chlorotic mottling symptoms were collected from kiwifruit plants in Hanzhong, Shaanxi Province of China. Using high-throughput sequencing, a novel totivirus tentatively designated Actinidia totivirus 1 (AcToV1) was identified. Its complete genome sequence was determined using RT-PCR and RACE techniques. The genome of AcToV1 is 5,060 nucleotides in length and contains two open reading frames (ORFs), encoding a coat protein (CP) of 793 amino acids and an RNA-dependent RNA polymerase (RdRp) of 841 amino acids. It also features a typical slippery heptanucleotide motif, a conserved element characteristic of the genus Totivirus. AcToV1 shares the highest genome-wide nucleotide sequence identity of 57.6% with Panax notoginseng virus A (PnVA; GenBank accession NO. KT388111). Its CP and RdRp also exhibit the highest amino acid sequence identities to PnVA, at 44.0% and 56.7%, respectively. Phylogenetic analysis further supported that AcToV1 clusters closely with PnVA and Hubei toti-like virus 2 (HTLV2). Therefore, AcToV1 be considered a new species of the genus Totivirus.
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