Archives of Virology最新文献

A novel positive single-stranded RNA virus, tentatively named “Pholiota nameko narnavirus 1” (PnNV1), has been identified in the edible fungus Pholiota nameko strain N1. The complete genome of PnNV1 is 2254 nucleotides in length, containing a single large open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp) of 682 amino acids (aa) with a molecular mass of 77.81 kDa. BLASTp analysis indicated that PnNV1 exhibited the highest sequence similarity (30.80% identity) to Rhizoctonia solani narnavirus 18. Sequence alignments and phylogenetic analysis based on RdRp sequences indicated that PnNV1 can be classified as a new member of the family Narnaviridae. To our knowledge, this is the first mycovirus reported in Pholiota nameko.

The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List (https://ictv.global/msl), the Virus Metadata Resource (https://ictv.global/vmr), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm (Singelaviria), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae, assigned to the realm Varidnaviria. Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae. Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae, realm Monodnaviria). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota, in the kingdom Trapavirae (realm Monodnaviria), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Patients with chronic hepatitis B (CHB) are at risk of developing hepatocellular carcinoma (HCC) during treatment with nucleos(t)ide analogs (NAs). Several factors, including abnormal ALT levels during NA treatment, are associated with HCC risk; however, the mechanisms of ALT abnormalities remain unknown. Here, deletions in the preS1/2 region of the hepatitis B virus (HBV) genome were evaluated in the context of persistent ALT abnormalities after NA treatment. Out of the 198 patients with CHB who had been treated with NAs, 40 who had been treated with entecavir, tenofovir disoproxil fumarate, or tenofovir alafenamide fumarate as the first-line therapy and from whom serum samples had been collected before NA treatment were selected for analysis of the infecting virus. Total DNA was extracted from the samples and subjected to nested PCR to detect deletions in the preS1/2 region of the HBV genome. Patients for whom deletions were found in ≥ 40% of the amplicons were classified as the "high-del" group, and the others were the "low-del" group. The preS1/2 region was amplified from 39 (97.5%) of the 40 samples, and a deletion was found in 19 of these patients (48.7%). The cumulative incidence of HCC was found to be significantly higher in the high-del group than in the low-del group (25% vs. 7% at 2 years, P = 0.021). The high-del group also had significantly higher ALT levels than the low-del group after 1 year of NA treatment (35 vs. 26 U/L, P = 0.020). In summary, patients with CHB with frequent preS1/2 deletions showed higher ALT levels after NA treatment and a higher risk of developing HCC.

Vibrio alginolyticus is a zoonotic pathogenic bacterium that causes various diseases in marine animals, including Penaeus vannamei. Phage therapy, as a natural antibiotic, offers a novel approach to the prevention and control of vibriosis. In this study, we isolated, identified, and characterized a novel bacteriophage targeting V. alginolyticus, designated as PV48. PV48, a short-tailed bacteriophage isolated from the Ningbo aquaculture farm, possesses the ability to lyse V. alginolyticus strains that affect shrimp. It displays stability over a range of temperatures (30–50°C) and pH values (4–10). The latent period and burst size for phage PV48 were determined to be 20 minutes and 15.6 PFU/cell, respectively. Whole-genome sequencing revealed that PV48 has a dsDNA genome with a length of 43,398 bp and a G + C content of 49.54%. The phage genome contains 44 open reading frames (ORFs). Comparative genomic analysis suggested that PV48 might represent a new species within the genus Maculvirus. Phylogenetic analysis indicated a close evolutionary link between PV48 and other Vibrio-targeting phages, suggesting a shared viral lineage. This study lays the groundwork for the application of V. alginolyticus bacteriophage in aquaculture.

The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).

Human papillomavirus (HPV) 16 variants can differ in their oncogenic potential. Here, we investigated the effect of the amino acid substitutions H78Y and L83V in the E6 oncoprotein of HPV16 on early immune escape and p53 degradation in vitro. Although E6 inhibits the RIG-I-IRF-3-IFN-β pathway, this inhibition was not affected by the H78Y substitution. We found that the L83V mutation did not significantly affect p53 and p21 expression, cell migration and proliferation, or resistance to apoptosis. We therefore conclude that the H78Y and L83V substitutions in E6 had no phenotypic effect on early immune escape and p53 degradation, respectively, in our model.

Equid alphaherpesvirus type 1 (EHV-1) is a neurotropic virus known to manipulate host cytoskeletal structures to facilitate infection and spread. In this study, we examined the susceptibility of primary murine astrocytes to neuropathogenic and non-neuropathogenic EHV-1 strains, focusing on the role of the actin and microtubule cytoskeleton. Infection induces morphological changes and remodeling of actin and microtubule networks. Viral antigen was localized along actin filaments and microtubules, indicating their likely role in intracellular viral trafficking. Cytoskeletal inhibitors significantly reduced viral DNA levels. Both EHV-1 strains exhibited limited replication, suggesting that EHV-1 may establish abortive infection in murine astrocytes.

Bacteriophages play crucial roles in microbial ecosystems and have potential for biotechnological applications. However, our understanding of culturable phages remains limited. In this study, we characterized six novel Escherichia coli phages isolated from pig farm wastewater and urban sewage, using comprehensive genomic, morphological, and host-range analysis. Using multiple comparative approaches, including gene-sharing network analysis, average nucleotide identity (ANI), and nucleotide intergenomic similarity (NIS), we demonstrated that five of these phages form a distinct group within the subfamily Stephanstirmvirinae, potentially representing a novel genus, for which we propose the name "Wecvirus”. We further propose that these phages, each of which exhibits a unique host range pattern, should be classified in two distinct species within the proposed genus. This host specificity is reflected in differences in the amino acid sequences of tail fibers, which are crucial for infection. The remaining phage, which was not classified as a wecvirus, exhibited characteristics that challenged the current classification criteria, highlighting the need for more-flexible taxonomic approaches. These findings expand our understanding of phage diversity within the subfamily Stephanstirmvirinae and contribute to the evolving phage taxonomy framework.

Foot-and-mouth disease virus (FMDV) poses a major threat to the global livestock economy. In this study, we analyzed 951 complete genome sequences of FMDV from 66 countries/regions reported from 1958 to 2023, using phylogenomics, recombination detection, and entropy analysis to elucidate its evolutionary dynamics. The phylogeny confirmed the grouping of isolates within the seven established serotypes (O, A, Asia1, C, SAT1, 2, and 3) with strong geographic clustering, and distinct subgenotypes were identified within serotypes O, A, Asia1, and SAT1. The genetic similarity was high (> 90%) within the serotypes but low (< 75%) between them, with the P1 capsid region showing the highest divergence. Interestingly, 117 probable recombination events were detected, predominantly involving serotypes O (n = 41) and A (n = 38), with 58.1% being inter-serotypic. Recombination hotspots were identified in non-structural regions (P2/P3), and the recombination frequency was markedly higher among the Asian and African isolates. Shannon entropy analysis revealed elevated amino acid variability in the structural proteins, notably VP1, of serotypes O and A. The study demonstrates that recombination is an important driver of FMDV diversity and adaptability, significantly affecting vaccine efficacy and outbreak patterns. These findings emphasize the critical need for global genomic surveillance to inform vaccine selection and control strategies.