Archives Of Virology[JOURNAL]
Sun
200 papers
Characterization and genomic analysis of a novel Vibrio harveyi Vibrio phage LRZ.
Yang Z, Ge H, Chen N … +6 more , Zhang Y, Wei H, Hu J, Fan C, Wang Y, Zhang Z
Arch Virol · 2026 Apr · PMID 41984259 · Publisher ↗
Bacteriophages (phages), viruses that specifically infect and lyse their host bacteria, hold significant potential for application in the prevention of Vibrio infections and the treatment of vibriosis for aquaculture. In...
Bacteriophages (phages), viruses that specifically infect and lyse their host bacteria, hold significant potential for application in the prevention of Vibrio infections and the treatment of vibriosis for aquaculture. In this study, a novel Vibrio harveyi phage, designated Vibrio Vibrio phage LRZ, was isolated from an abalone aquaculture farm in Lianjiang, Fujian Province. Its biological characteristics and complete genomic sequence were investigated. The results demonstrated that Vibrio phage LRZ exhibits robust tolerance to acidic/alkaline environments, as well as elevated temperatures. The phage exhibited a latent period of approximately 30 min and reached the plateau phase at approximately 190 min post-infection, with an estimated burst size of 134 plaque-forming units (PFU) per cell. Whole-genome sequencing using the Illumina platform revealed a genome length of 43,274 base pairs (bp) with a guanine-cytosine (GC) content of 39.45%. Annotation identified 51 open reading frames (ORFs), encoding proteins involved in phage structural assembly, host lysis, DNA replication, and metabolism. Bioinformatic predictions did not identify antibiotic resistance or virulence genes in the LRZ genome. BLAST comparative analysis indicated the highest similarity (75.47%) to Vibrio phage VPMS1, establishing Vibrio phage LRZ as a novel isolate of Vibrio phages. Phylogenetic analysis further confirmed its closest relationship to Vibrio phage VPMS1, placing them within the same genus in the class Caudoviricetes. Vibrio phage LRZ could serve as a valuable novel genomic resource for studying phage evolution and offers novel perspectives for the biocontrol of V. harveyi in aquaculture settings.
Viral genotype and the pace of epidemic waves: an assessment from SARS-CoV 2 genomics and wastewater surveillance data.
Jones LR, D'Andrea JS, Levite J … +2 more , Brito M, Manrique JM
Arch Virol · 2026 Apr · PMID 41973264 · Publisher ↗
The SARS-CoV-2 pandemic was characterized by multiple epidemic waves, whose geographical non-synchronicity remains not fully understood. This study aimed to characterize this phenomenon at local and regional scales. To t...
The SARS-CoV-2 pandemic was characterized by multiple epidemic waves, whose geographical non-synchronicity remains not fully understood. This study aimed to characterize this phenomenon at local and regional scales. To this end, we compared SARS-CoV-2 epidemics in a geographically isolated city (Trelew, Chubut, Argentina) with country-wide data between April 2020 and February 2022. This period encompassed distinct phases defined by non-pharmacological interventions, changes in population immunity, and shifts in dominant viral lineages. Routine daily case reports and clinical genomics data were integrated with local wastewater data collected weekly. Three epidemic waves were identified: the first hit the study site three months after the national peak, the second with a one-month delay, and the third virtually without delay. Wastewater samples analyzed for SARS-CoV-2 RNA by RT-qPCR were used in cross-correlation analyses to assess temporal relationships among datasets. These analyses confirmed a progressive reduction in epidemic asynchronicity, independent of testing or reporting practices. The gradual reduction in the delay was matched with the emergence of viral lineages with progressively higher transmissibility. The first wave was dominated by lineage B.1.499, endemic in Argentina; the second by the co-circulation of Alpha, Gamma, and Lambda variants typical of South America; and the third by the Delta and Omicron variants. These findings highlight the influence of viral evolution on the temporal synchronization of epidemic waves underscoring the relevance of integrated genomic and environmental surveillance.
Complete genome sequence of ramie marafivirus 1, a novel marafivirus infecting ramie (Boehmeria nivea).
Jiang J, Zhai L, Chen W … +8 more , Wu J, Li X, Li J, Yin K, Shi X, Tu J, Xia X, Wang Y
Arch Virol · 2026 Apr · PMID 41973252 · Publisher ↗
High-throughput sequencing (HTS) combined with reverse transcription-polymerase chain reaction (RT-PCR) revealed a novel marafivirus, tentatively named “ramie marafivirus 1” (RaMaraV1), infecting ramie (Boehmeria nivea (...
High-throughput sequencing (HTS) combined with reverse transcription-polymerase chain reaction (RT-PCR) revealed a novel marafivirus, tentatively named “ramie marafivirus 1” (RaMaraV1), infecting ramie (Boehmeria nivea (L.) Gaudich.) plants in China. The complete genome of RaMaraV1 consists of 6,607 nucleotides (nt) and shares the highest nt sequence identity (65.4%) with Artemisia argyi albinism-associated virus (AAAaV), a recently identified marafivirus. The RaMaraV1 genome structure is typical of marafiviruses, containing a conserved 16-nt marafibox motif and a large open reading frame (ORF) encoding a polyprotein with five predicted domains. The coat protein (CP) of RaMaraV1 shares 23.9–65.4% amino acid (aa) sequence identity with those of reported marafiviruses, which is below the species demarcation threshold for the genus Marafivirus. Phylogenetic analyses based on the sequences of the complete genome and polyprotein revealed that RaMaraV1 clustered closely with viruses of the genus Marafivirus. Collectively, these results suggest that RaMaraV1 is a novel virus in the genus Marafivirus.
Urine as a complementary specimen for RT-qPCR detection of Oropouche virus.
de Azevedo SSD, Có ACG, Tavares EA … +9 more , Bonela LAS, Sant'Anna JG, Marinho P, Goulart JP, Covre LP, Rodrigues IR, Gomes DCO, Delatorre E, Ribeiro-Rodrigues R
Arch Virol · 2026 Apr · PMID 41973242 · Full text
Oropouche fever is an emerging arboviral disease in South America, for which reliable molecular diagnostic specimens throughout the course of infection are essential for surveillance and clinical management. This study a...
Oropouche fever is an emerging arboviral disease in South America, for which reliable molecular diagnostic specimens throughout the course of infection are essential for surveillance and clinical management. This study aimed to compare the diagnostic performance of RT-qPCR in paired urine and serum samples and to evaluate temporal trends in cycle threshold (Ct) values according to time since symptom onset. A retrospective analysis was conducted on 41 paired serum–urine samples (one pair per patient) collected within 15 days after symptom onset. RT-qPCR results were classified as detectable or undetectable, with Ct values recorded when available. Positivity rates were compared using McNemar’s test, inter-matrix agreement was assessed with Cohen’s kappa, and paired Ct values were analyzed using the Wilcoxon signed-rank test. Temporal trends were evaluated according to clinical phases defined by time since symptom onset: acute phase (0–7 days) and early convalescent phase (8–14 days), and univariable logistic regression was used to assess the effect of time on detection probability. Urine samples showed a significantly higher positivity rate (75.6%, 31/41) than serum samples (43.9%, 18/41; McNemar p = 0.037), with poor agreement between matrices (Cohen’s kappa ≈ − 0.52). While serum Ct values increased over time), indicating declining detectability, urine Ct values remained showed no significant temporal trend throughout the two clinical phases. No significant association was observed between days since symptom onset and urine detection probability within 15 days. These findings suggest that urine may serve as a complementary specimen for molecular detection of Oropouche virus, particularly when serum testing occurs later in the course of infection.
Genomic analysis of jumbo coliphage fEgEco12.
Badawy S, Skurnik M
Arch Virol · 2026 Apr · PMID 41968149 · Full text
Avian pathogenic Escherichia coli (APEC) infections are associated with major economic losses, cause perihepatitis, pericarditis, septicemia and even systemic infections in the poultry industry. APEC infections have usua...
Avian pathogenic Escherichia coli (APEC) infections are associated with major economic losses, cause perihepatitis, pericarditis, septicemia and even systemic infections in the poultry industry. APEC infections have usually been controlled by antibiotics, resulting in an increased prevalence of antibiotic-resistant E. coli. Concerns have been increased that transfer of antibiotic-resistant APEC via the food chain may cause risks for extra-intestinal infection of humans related to zoonotic transfer and increased difficulties in the treatment of human infections caused APEC-related E. coli types. With the occurrence of antibiotic resistance reaching a crisis point, it is important to find alternative treatments for multidrug-resistant infections. The use of phages to control pathogens is a promising therapeutic option for antibiotic replacing, therefore, novel phages specific for APEC were isolated in this study. Phage fEgEco12 was isolated from the hospital sewage water sample during a search for candidates for phage therapy applications against APEC. The phage morphology was studied by transmission electron microscopy, and the host range was analyzed with a Bioscreen C analyser. The phage genomic DNA was isolated, sequenced and annotated. Phage stability, phage adsorption and one step growth curve experiments were carried out to characterize its biological properties. Genomic analysis revealed that fEgEco12 is a lytic jumbo phage with genome size of 374,733 bp encoding 670 predicted genes. No genes associated with lysogeny, bacterial virulence, or antibiotic resistance were identified. The phage had myovirus morphology and a narrow host range. Comparative genomic analysis revealed that fEgEco12 and phage Ecwhy_1 belong to a new species in jumbo phage genus Asteriusvirus. fEgEco12 is a novel jumbo bacteriophage that is considered safe for phage therapy.
Characterization of a novel phage BUCT800 against Acinetobacter baumannii and its biofilm removal efficiency.
Liu Y, Zhang L, Li Y … +4 more , Zhang J, Zhang J, Tong Y, Li M
Arch Virol · 2026 Apr · PMID 41963712 · Publisher ↗
Acinetobacter baumannii (A. baumannii) poses a significant global public health threat. As natural antimicrobial agents, phages hold enormous potential for controlling the spread of A. baumannii by targeting environmenta...
Acinetobacter baumannii (A. baumannii) poses a significant global public health threat. As natural antimicrobial agents, phages hold enormous potential for controlling the spread of A. baumannii by targeting environmental pathogens. In this study, we report the isolation and characterization of a novel phage, BUCT800, from wastewater, which specifically lysed ST2-type A. baumannii and forms transparent plaques surrounded by a halo. We analyzed its physiological properties, genomic features, and biofilm removal efficacy. The phage exhibited an optimal MOI of 0.01 and a latent period of about 15 min, and favorable thermal and pH stability. The genome of phage BUCT800 is 42,018 bp in length, with a G + C content of 39%. BLAST analysis showed that it shares the highest similarity with Acinetobacter phage vB_AbaP_APK26, with a query coverage of 89% and a percent identity of 94.72%. Genomic analysis revealed that BUCT800 belonged to the class Caudoviricetes, family Autoscriptoviridae, and did not harbor any known antibiotic resistance or virulence genes. Phage BUCT800 exhibited varying biofilm removal efficiencies against different bacterial strains. Phage BUCT800 at a titer of 1 × 108 PFU/mL removed 72.4% of the T2347 biofilm. Collectively, these findings underscored the substantial potential of phage BUCT800 as an environmental disinfectant.
P3, P3N-PIPO and 6K1 from soybean mosaic virus strain N are involved in host specificity for systemic infection in cultivated and wild soybeans.
Wang Y, Xu W, Hu R … +4 more , Penicks AK, Pruitt D, Fernandez E, Hajimorad MR
Arch Virol · 2026 Apr · PMID 41963537 · Publisher ↗
Soybean mosaic virus-N (SMV-N) and clover yellow vein virus (ClYVV-No.30) are two recognized potyviruses with distinct host ranges and host specificities. Both infect systemically wild soybean (Glycine soja) whereas SMV-...
Soybean mosaic virus-N (SMV-N) and clover yellow vein virus (ClYVV-No.30) are two recognized potyviruses with distinct host ranges and host specificities. Both infect systemically wild soybean (Glycine soja) whereas SMV-N, but not ClYVV-No.30, infects systemically cultivated soybean (G. max) as well. In contrast, ClYVV-No.30, but not SMV-N, infects systemically broad bean (Vicia faba). To investigate whether P3, P3N-PIPO, and 6K1 from SMV-N play role in host specificity for systemic infection, each was replaced precisely with those from ClYVV-No.30 including the corresponding NIaPro protease recognition sequences at the junctions between P3-6K1 or 6K1-CI cistrons. A second set of SMVN/ClYVV-No.30 chimeras were also synthesized with the P3, P3N-PIPO, and 6K1 from ClYVV-No.30 but with NIaPro protease recognition site at P3-6K1 or 6K1-CI junctions from SMV-N. Regardless of the origin of NIaPro recognition sites, none of the SMV-N-derived chimeras gained the ability to infect systemically broad bean. On the contrary, unlike parental SMV-N, all SMV-N-derived chimeras lost the ability to infect systemically cultivated and wild soybeans. Site-directed mutagenesis of SMV-N NIaPro recognition site at P3-6K1 junction showed replacement of one of the amino acids with the corresponding residue from ClYVV-No.30 at proximal C-terminus of P3 abolished systemic infection of the SMV-N-derived mutant in both cultivated and wild soybeans. Our data suggest that in addition to processing of the NIaPro recognition site at the P3-6K1 junction, P3N-PIPO and 6K1 are also involved in systemic infection of cultivated and wild soybeans by SMV-N.
Establishment of grass carp (Ctenopharyngodon idella) fibroblast cell line and its application in elucidating pathogenic mechanisms of pathogen infection.
An J, Yuan M, Yi P … +3 more , Xu X, Wen C, Hu B
Arch Virol · 2026 Apr · PMID 41961147 · Publisher ↗
We successfully established and characterized a fibroblast cell line derived from the epidermal tissue of grass carp (Ctenopharyngodon idella), designated as Ctenopharyngodon idella epidermal fibroblast (CIEF). The cell...
We successfully established and characterized a fibroblast cell line derived from the epidermal tissue of grass carp (Ctenopharyngodon idella), designated as Ctenopharyngodon idella epidermal fibroblast (CIEF). The cell line was maintained in M199 medium supplemented with 20% fetal bovine serum under standard culture conditions (28 °C, 5% CO2), exhibiting characteristic fibroblast-like morphology. CIEF cells have demonstrated stable proliferation through 38 successive passages and retained viability after cryopreservation. Species confirmation was achieved through 18 S ribosomal RNA sequencing, verifying the cell line’s origin from grass carp. Cytogenetic analysis revealed a diploid chromosome count of 48, consistent with the species’ karyotype. Dual immunofluorescence demonstrated co-expression of fibroblast-specific markers α-smooth muscle actin (α-SMA) and fibroblast-specific protein 1 (FSP1), confirming cellular identity. The cell line exhibited sensitivity to major piscine pathogens, showing pronounced cytopathic effects (CPE) following challenge with Aeromonas hydrophila, Aeromonas veronii, and grass carp reovirus (GCRV). Ultrastructural analysis via transmission electron microscopy revealed pathogen-induced cellular alterations, including increased apoptotic bodies and phagocytic vesicles, accompanied by significant organelle damage particularly affecting endoplasmic reticulum and mitochondrial structures. Quantitative real-time PCR analysis demonstrated activation of antimicrobial immune responses post-infection, coupled with observed mitochondrial membrane potential depolarization. This established in vitro model provides a valuable platform for investigating host-pathogen interactions, pathogenic mechanisms, and cellular responses to aquatic pathogens in cyprinid species.
Expanding insights into plant rhabdovirus diversity through the discovery of viruses representing 32 putative novel species.
Botermans M, de Koning PPM, Westenberg M … +35 more , Adams IP, Mansour KB, Chabi-Jesus C, de Krom C, Dullemans AM, Festus R, Fowkes AR, Fox A, Freitas-Astúa J, Hajizadeh M, Hellin P, Knierim D, Krenz B, Maclot F, Malandraki I, Maliogka VI, Margaria P, Massart S, Meekes ETM, Menzel W, Oplaat C, Orfanidou CG, Ramos-González PL, Roenhorst JW, Ros VID, Seal SE, Silva G, Silva Dos Santos G, Tzanetakis IE, van der Vlugt RAA, van Gemert J, Varveri C, Verbeek M, Winter S, Giesbers AKJ
Arch Virol · 2026 Apr · PMID 41951987 · Full text
Plant-infecting rhabdoviruses (family Rhabdoviridae, subfamily Betarhabdovirinae) include several viruses that cause important crop diseases and are subject to phytosanitary regulation. Despite their agricultural and eco...
Plant-infecting rhabdoviruses (family Rhabdoviridae, subfamily Betarhabdovirinae) include several viruses that cause important crop diseases and are subject to phytosanitary regulation. Despite their agricultural and ecological importance, the diversity of plant rhabdoviruses and their impact on plant health remain poorly understood. Here, we report 32 tentative novel species of plant-infecting rhabdoviruses, identified via high-throughput sequencing and spanning nine established genera. The virus sequences originated from diverse hosts and geographic regions, revealing extensive diversity within the family Rhabdoviridae. Several viruses were detected independently in the same host species across multiple countries, demonstrating the practical value of data sharing for confirming host associations and gaining insight into the geographic distribution of these viruses. Our study highlights the underexplored diversity of plant rhabdoviruses and demonstrates the value of coordinated, collaborative virus discovery. With HTS now widely accessible, the challenge has shifted from virus discovery to making sequence data and metadata publicly available, and to conducting the time-consuming biological characterization often deprioritized in favour of viruses with immediate phytosanitary relevance. As a result, many findings remain unreported, leaving valuable data dormant on servers. By sharing genomic data prior to publication, we present an efficient approach to accelerate virus reporting, enable comparative analyses and advance understanding of virus diversity. We hope this collaborative effort will encourage further exploration of plant viruses, including those from hosts without discernable symptoms, supporting virus biology, taxonomy, pest risk assessments, and plant health policies.
Genome characterization of a novel betaflexivirus from the wild tea plant Camellia taliensis.
Xiao J, Chen J, Zhang C … +5 more , Long J, Yu Y, Yu Y, Han Y, Liu R
Arch Virol · 2026 Apr · PMID 41945179 · Publisher ↗
The wild tea species Camellia taliensis is an important genetic resource and a close relative of cultivated tea plants. In this study, metatranscriptomic sequencing of asymptomatic leaves of C. taliensis led to the ident...
The wild tea species Camellia taliensis is an important genetic resource and a close relative of cultivated tea plants. In this study, metatranscriptomic sequencing of asymptomatic leaves of C. taliensis led to the identification of a previously undescribed virus. This virus, which is tentatively named as Camellia taliensis betaflexivirus 1 (CtBV1), possesses a monopartite positive-sense RNA genome of 6,564 nucleotides (nt). The genome contains two overlapping open reading frames (ORFs), flanked by a 37-nt 5′ untranslated region (UTR) and a 128-nt 3′ UTR. The larger ORF encodes a polyprotein containing conserved domains typical of members of the family Betaflexiviridae, including viral methyltransferase, RNA helicase, RNA-dependent RNA polymerase, and coat protein. Phylogenetic analysis based on the replication-associated protein placed CtBV1 in a clade with viruses belonging to the genus Capillovirus, including apple stem grooving virus and cherry virus A. Pairwise amino acid sequence comparisons showed that CtBV1 shares less than 80% identity with these viruses in the replication-associated protein, supporting the classification of CtBV1 as a novel species within the family Betaflexiviridae. The discovery of CtBV1 expands the currently known diversity of viruses associated with Camellia species and provides new information on viruses infecting wild tea germplasm.
Evolutionary and phylogenetic insights from global canine astrovirus genomes.
Qiu Y, Lai L, Wang M … +4 more , Yuan H, Wu J, Wang P, Li M
Arch Virol · 2026 Apr · PMID 41945171 · Publisher ↗
Through a comprehensive analysis of the complete genomes of 74 global CaAstV strains, this study systematically untangles their evolutionary relationships and driving mechanisms. The research establishes a population str...
Through a comprehensive analysis of the complete genomes of 74 global CaAstV strains, this study systematically untangles their evolutionary relationships and driving mechanisms. The research establishes a population structure comprising three major groups (GI, GII, GIII), with the GIII group exhibiting the highest genetic diversity due to high-frequency recombination events and further subdividing into three subgroups (GIII-1, -2, -3). Recombination is confirmed as a key evolutionary driver, with 88.9% (16/18) of the events concentrated within the GIII group, and hotspots identified in the ORF1ab and ORF2 regions. Profound group-specific amino acid variations are identified within the capsid protein (ORF2), with significant homology differences observed among the groups. Furthermore, phylogenetic analysis reveals a Japanese raccoon origin GII strain exhibiting high homology with the GII group, providing critical evidence for cross-species transmission. This study constructs a clear genotyping framework for CaAstV and elucidates the complete evolutionary pathway from recombination-driven diversity to protein adaptive variation, thereby laying a crucial foundation for its epidemiological research.
The emergence and evolutionary advantage of the novel epidemic norovirus GII.17 lineage.
Peng W, Gao J, Liu Y … +2 more , Liu S, Xue L
Arch Virol · 2026 Apr · PMID 41945140 · Publisher ↗
Human norovirus (HuNoV) is a major causative agent of non-bacterial gastroenteritis. During the winter of 2014/2015, the GII.17 Kawasaki variant emerged abruptly in Asia, temporarily surpassing the predominant GII.4 geno...
Human norovirus (HuNoV) is a major causative agent of non-bacterial gastroenteritis. During the winter of 2014/2015, the GII.17 Kawasaki variant emerged abruptly in Asia, temporarily surpassing the predominant GII.4 genotype and driving a significant epidemic surge. Since 2022, GII.17 has again caused sustained large-scale outbreaks due to the re-emerged of this genotype. To unravel the evolutionary advantages of these emerging GII.17 strains, we systematically evaluated the genetic variation mechanism of the GII.17 HuNoV capsid protein and their potential impact on viral prevalence. Phylogenetic analysis revealed that the novel GII.17 lineages originated from the clade C of GII.17, with an amino acid distance of 2.6% from clade C. This lineage was provisionally designated as C2. Its time of most recent common ancestor was 2020, with an average evolutionary rate of 5.47 × 10− 3 substitutions/site/year. Amino acid multiple sequence alignment analysis revealed that there were no new insertions or deletions in the C2 compared with the earlier variant C. Through the prediction of positive selection sites and B-cell epitopes, it was determined that the prevalence of C2 might not be due to an increase in epitopes but might be due to mutations in existing epitopes. Among 12 key amino acid mutations, sites 297, 374, and 409 in the P2 domain were the key amino acid sites for the prevalence of the new GII.17 lineage.
Identification and characterization of a putative novel tri-segmented rhabdovirus infecting Humulus scandens.
Wang J, Li Y, Zhang Y … +3 more , Zhang S, Cao M, Yang C
Arch Virol · 2026 Apr · PMID 41944889 · Publisher ↗
A putative novel tri-segmented rhabdovirus, tentatively named Humulus trirhavirus 1 (HuTRV1), was identified from mosaic and chlorotic leaves of Humulus scandens in Shenyang, Liaoning, China. Using high-throughput sequen...
A putative novel tri-segmented rhabdovirus, tentatively named Humulus trirhavirus 1 (HuTRV1), was identified from mosaic and chlorotic leaves of Humulus scandens in Shenyang, Liaoning, China. Using high-throughput sequencing, RT-PCR and RACE, HuTRV1 was found to comprise three genomic segments (RNA1, RNA2, RNA3) of 6,674, 4,417, and 4,094 nucleotides (nt) respectively. Its genome organization resembles that of Chenopodium trirhavirus 1 identified from Chenopodium album in China, containing eight open reading frames (ORFs) encoding putative L, N, P2-P4, and P6-P8 proteins. All these proteins shared less than 58.6% nt and 51.9% amino acid (aa) sequence identity with other known rhabdoviruses. Phylogenetic analysis of the L protein sequences confirmed the close relationship of HuTRV1 with trirhaviruses in a distinct clade in the family Rhabdoviridae. These results suggest that HuTRV1 represents a new Trirhavirus species, for which we propose the name Trirhavirus humuli.
Out of Asia: feline stool-associated circular DNA virus (FeSCV) in Brazilian domestic cats.
Pierucci LS, Catozo RG, Kobayashi LL … +4 more , de Souza Silva SO, da Hora AS, Brandão PE, Taniwaki SA
Arch Virol · 2026 Apr · PMID 41925880 · Full text
Feline stool-associated circular DNA virus (FeSCV), was identified in Japan (2018) and China (2021) but has not yet been detected outside Asia. In this study, 137 fecal or rectal swab samples from 83 cats were screened f...
Feline stool-associated circular DNA virus (FeSCV), was identified in Japan (2018) and China (2021) but has not yet been detected outside Asia. In this study, 137 fecal or rectal swab samples from 83 cats were screened for circoviruses and FeSCV, with detection of two putative novel Cyclovirus species and 19.3% (16/83) of FeSCV. A higher incidence of FeSCV in kittens and young adults, and FCoV-positive cats with clinical signs of feline infectious peritonitis were observed. Further investigation will clarify the virus pathogenicity and its association with other pathogens.
Global prevalence of hepatitis E virus in swine: a systematic review and meta-analysis (1999-2025).
Venkataramappa M, Rafeeka CAJ, Patil SS … +8 more , Jogaiah M, Velankar A, Naik N, Mallappa A, Srinivas KG, Suresh KP, Hiremath J, Nayakwadi S
Arch Virol · 2026 Mar · PMID 41910780 · Publisher ↗
Pigs are reservoirs for zoonotic HEV genotypes 3 and 4. In this systematic review and meta-analysis of 176 studies (93,024 samples; 1999–2025), the pooled global HEV prevalence was 28% under a fixed-effects model and 32%...
Pigs are reservoirs for zoonotic HEV genotypes 3 and 4. In this systematic review and meta-analysis of 176 studies (93,024 samples; 1999–2025), the pooled global HEV prevalence was 28% under a fixed-effects model and 32% under a random-effects model, with high heterogeneity (I² = 99.5%). Diagnostic method, sample size, country, and continent significantly influenced prevalence estimates, with higher prevalence in ELISA-based studies (28%) than RT-PCR–based studies (11%). Regionally, prevalence was highest in North America (21%) and lower in Asia and Africa (10%). Sensitivity analyses confirmed the robustness of pooled estimates, supporting strengthened One Health surveillance and food safety measures globally.
Red clover RNA virus 1: functional analysis of ORF2 protein, associations with co-infecting viruses, and seed transmission.
Lazareva EA, Lezzhov AA, Chergintsev DA … +5 more , Tolstyko EA, Selifonov IV, Atabekova AK, Morozov SY, Solovyev AG
Arch Virol · 2026 Mar · PMID 41906034 · Publisher ↗
A previously undescribed group of related plant viruses has recently been identified within the Benyviridae family. This group is called reclovirids, named after the type species, red clover RNA virus 1 (RCRV1). The sing...
A previously undescribed group of related plant viruses has recently been identified within the Benyviridae family. This group is called reclovirids, named after the type species, red clover RNA virus 1 (RCRV1). The single genomic RNA of most reclovirids contains two main open reading frames (ORFs): a large, well-conserved 5′-proximal ORF1 that encodes a viral replicase and a less conserved 5′-distal ORF2 that encodes a polypeptide of unknown function with a C4-type zinc finger motif. In this study, the ORF2 proteins of RCRV1 and a Gymnadenia rhellicani virus, another reclovirid, are found to be unable to serve as viral movement proteins (MPs) in a complementation assay and fail to suppress RNA silencing induced by double- and single-stranded RNA. Transcriptomic analysis of an RCRV1-infected plant revealed the presence of two other, previously unknown viruses of the Rhabdoviridae and Qinviridae families. Further analysis of publicly available sequencing data demonstrated that two independently studied RCRV1-infected plants both contained co-infecting viruses. In one case, RCRV1 was found together with a virus of genus Varicosavirus, family Rhabdoviridae, which has no MP gene, suggesting that, in the absence of its own MP and MP provided by the co-infecting virus, RCRV1 likely does not move cell to cell in infected plants. Additionally, RCRV1 is shown to be transmitted by seeds. Taken together, the presented data support the view that reclovirids are vertically transmitted persistent viruses.
Isolation and characterization of a novel lytic bacteriophage Ecolivirus Myo-P293 targeting avian pathogenic Escherichia coli.
Xu H, Qi Q, Zhu Y … +4 more , Wu E, Yan G, Lu Y, Feng Y
Arch Virol · 2026 Mar · PMID 41906021 · Full text
A novel lytic bacteriophage, Ecolivirus Myo‑P293 (P293), targeting avian pathogenic Escherichia coli (APEC), was isolated from duck farm sewage in Jiangsu, China. P293 formed clear plaques approximately 2 mm in diameter...
A novel lytic bacteriophage, Ecolivirus Myo‑P293 (P293), targeting avian pathogenic Escherichia coli (APEC), was isolated from duck farm sewage in Jiangsu, China. P293 formed clear plaques approximately 2 mm in diameter and displayed the characteristic morphology of Myoviridae family, with an icosahedral head (~ 70 nm) and a contractile tail (~ 100 nm), as observed under transmission electron microscopy. Adsorption assays showed that over 70% of phages adsorbed to host cells within 5 min. One-step growth analysis revealed a latent period of approximately 30 min and a burst size of 244 ± 36 PFU per infected cell. P293 exhibited stability across a pH range of 5–9 and at temperature between 20 and 40 °C, but its infectivity was significantly reduced when exposed to temperature ≥ 60 °C or 60% ethanol. The phage effectively disrupted mature E. coli biofilms, achieving approximately 45% clearance after 24 h of treatment, and also inhibited biofilm formation in a dose-dependent manner. Whole-genome sequencing of P293 revealed an 89.5 kb double-stranded DNA genome encoding 95 open reading frames (ORFs), including modules related to structure, replication, lysis, and host interaction. Approximately 40% of the encoded genes are annotated as hypothetical proteins. Phylogenetic and comparative genomic analyses placed P293 within the unclassified Felixounavirus clade, closely related to Escherichia phage wV8 and Salmonella phage Felix O1, while displaying distinct tail fiber gene signatures associated with host specificity. These findings support the potential of P293 as a candidate for phage-based biocontrol strategies against APEC in poultry production.
Epidemiological and evolutionary analysis of porcine circovirus type 2 within pig populations in central China during 2021-2024.
Li JX, Li H, Wang FS … +6 more , Li YY, Wang GC, Zhang HL, Ding XY, Zheng LL, Ma SJ
Arch Virol · 2026 Mar · PMID 41888445 · Publisher ↗
Porcine circovirus type 2 (PCV2) is a major swine pathogen associated with immunosuppression and diverse clinical syndromes, posing a persistent threat to the pig industry. Updated epidemiological and molecular data are...
Porcine circovirus type 2 (PCV2) is a major swine pathogen associated with immunosuppression and diverse clinical syndromes, posing a persistent threat to the pig industry. Updated epidemiological and molecular data are essential for effective disease control. In this study, a total of 14,436 samples collected from 18 cities in Henan Province, central China, between 2021 and 2024 were examined for PCV2 using real-time PCR. Prevalence was analyzed according to year, season, region, and farm source, and farm-level infection rates were also assessed. In addition, 30 PCV2 whole genomes were sequenced and genetically characterized. Overall, PCV2 was detected in 22.32% (3,222/14,436) of samples and was present in all surveyed cities, with prevalence ranging from 6.47% to 49.93%. Temporal analysis revealed a peak in 2022 and a consistently lower prevalence in the third quarter. Significant geographic heterogeneity was observed across regions. PCV2 prevalence was highest in samples from diseased pigs, followed by slaughterhouses, whereas commercial and breeding farms showed lower detection rates. Multivariable logistic regression confirmed that region, season, and farm type were independently associated with PCV2 positivity. Phylogenetic analysis based on ORF2 sequences showed that PCV2d was the predominant genotype, alongside PCV2a and PCV2b, and sequence comparison revealed notable divergence from commonly used vaccine strains. These findings demonstrate that PCV2 remains widely circulating in central China, with distinct epidemiological patterns and ongoing genetic evolution, underscoring the need for continuous surveillance and optimized vaccination strategies.
Exploring ASFV tolerance in Indian pigs: A genetic and relative expression study of the STING1 gene.
Arutkumaran S, Deb R, Shanmathi S … +8 more , Das PJ, Sengar GS, Pegu SR, Singh I, Kumar S, Meera K, Rajkhowa S, Gupta VK
Arch Virol · 2026 Mar · PMID 41886019 · Publisher ↗
African Swine Fever (ASF) causes severe economic losses in the global pig industry, characterized by high mortality rates and lack of an effective vaccine. Interestingly, India's indigenous Doom pig breed has displayed t...
African Swine Fever (ASF) causes severe economic losses in the global pig industry, characterized by high mortality rates and lack of an effective vaccine. Interestingly, India's indigenous Doom pig breed has displayed tolerance to ASF, remaining seropositive without detectable viremia. This study investigated the genetic basis of ASFV tolerance, focusing on the STING1 gene, a key component of the cGAS-STING antiviral signaling pathway. In-silico docking identified a potential ASFV protein binding site within exon 5 of STING1. A non-synonymous SNP (CGG/TGG; R→W) at position 148 in this region was selected for genotyping. We genotyped 119 pigs, representing tolerant (Doom), susceptible, and ASFV-infected groups, using allele-specific PCR and Sanger sequencing. Doom pigs and most other breeds, including ASFV-infected samples, displayed a conserved GG genotype. Susceptible Manipuri Black and Ghoongroo pigs, however, displayed both AA and GG genotypes, yet still succumbed to the disease. A significant downregulation (0.436-fold) of STING1 was observed in ASFV-infected spleen tissue, indicating active immune evasion by the virus. The lack of a unique allele in Doom pigs compared to susceptible breeds indicates that ASFV tolerance is unlikely to be associated with this STING1 SNP. Therefore, genome-wide studies are recommended to identify markers truly associated with ASFV tolerance in this resilient breed.
Analysis of the APOBEC3 footprint across the Anelloviridae family.
De Maio FA, Bellusci CP, Challiol ME … +2 more , Barrio DA, Iglesias NG
Arch Virol · 2026 Mar · PMID 41886009 · Publisher ↗
APOBEC3 proteins are cytidine deaminases that induce cytosine to thymine changes in the DNA strands they recognize as substrates. Editing mediated by these cellular factors modifies sequences in specific nucleotide conte...
APOBEC3 proteins are cytidine deaminases that induce cytosine to thymine changes in the DNA strands they recognize as substrates. Editing mediated by these cellular factors modifies sequences in specific nucleotide contexts, leaving a pattern called APOBEC3 footprint. Viruses of the Anelloviridae family possess single-stranded DNA genomes susceptible to these enzymes. This study examined evidence of APOBEC3 activity in a sample of anelloviruses representative of both the nucleotide diversity and the broad host range of this viral family. Reference sequences from 173 anellovirus species classified into 34 genera, associated with different mammals and birds, were analyzed. Higher levels of editing were found in anelloviruses from Primates, both in the negative (genomic) DNA strand and in the positive DNA strand, compared to cases corresponding to Carnivora, Rodentia or birds. Furthermore, a positive correlation was detected between editing signals on both strands, verified exclusively in Primates. In this same group, a negative correlation was observed between viral genome size and APOBEC3 footprint intensity. When analyzing anelloviruses by genus, those present in hominids, such as Betatorquevirus, Gammatorquevirus, and Hetorquevirus, stood out for their high levels of editing. A notable exception was Alphatorquevirus, which showed lower levels, comparable to those of phylogenetically more distant genera associated with non-primate hosts. In turn, a marked contrast was detected between the editing patterns of some Gyrovirus species obtained from humans and those from birds. Taken together, the results suggest a differential impact of APOBEC3 proteins in anelloviruses, which depends on the host type and viral genome size.
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