Archives of Virology最新文献

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.

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.

The non-polio-enteroviruses are ubiquitous pathogens infecting over a billion people in the world. An alarming number of enterovirus-associated acute flaccid paralysis, encephalitis, hand, foot, and mouth disease, conjunctivitis and diarrhoea cases are reported worldwide. Despite their clinical significance, vaccine development has been hindered due to lack of suitable in vitro models for preclinical investigations. The present study was undertaken to develop a cell line assembled organotypic model of human intestine for replication of enteroviruses. An enterovirus specific PSGL1 receptor was introduced in intestinal epithelial HCT-8 cell line employing CRISPR/cas9 gene editing. It was co-cultured with human colon (CCD-18) and endothelial (HUVEC) cell lines with peripheral blood mononuclear cells in hanging drops and rotating wall vessel bioreactor to yield three-dimensional organoids. Histological analysis of the organoids showed presence of columnar epithelium cells with prominent intracytoplasmic mucin, hyperchromatic nuclei and presence of CK, CK20, MUC 2 and Villin markers characteristic of epithelial cells. Infection with Enterovirus A71 (EV-A71) demonstrated significantly higher viral titre in organoids compared to individual cell lines. Collectively, these findings determine, for the first time, a cell line–derived enteric organoid model that supports robust enterovirus replication, offering a cost-effective and physiologically relevant system for virology research and preclinical applications.

The outbreak of COVID-19 caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 poses an ongoing threat to global public health security. The continuous evolution of viruses (e.g., Delta, Omicron) has increased the risk of viral transmissibility, infectivity, and the risk of immune escape. As highly conserved structural proteins of viruses, nucleocapsid proteins (N proteins) play a central role in the viral life cycle, and the study of their functional mechanisms and targeted therapeutics is crucial for the development of antiviral strategies. In this paper, we systematically describe the structural characterization, functional mechanism, and targeted therapy of the SARS-CoV-2 N protein, analyze its key roles in viral packaging, replication, and immune escape, and discuss the challenges and future directions of drug development for the N protein.

Lumpy Skin Disease Virus (LSDV) remains a significant threat to cattle health and productivity. This study investigated the pathogenesis of the LSDV Pendik field strain in cattle to assess its suitability as a challenge virus for LSD vaccine efficacy trials. Two calves aged between six and nine months were inoculated intravenously, and four were inoculated intradermally with the virus. Clinical signs were monitored for 28 days, and blood, nasal, and conjunctival swab samples were collected at predetermined intervals to detect viral DNA by real-time PCR. Positive tissue samples obtained at necropsy were subjected to virus isolation using the bovine dermis (LB9.D) cell line. Among the intravenously inoculated calves, one developed subclinical infection while the other exhibited generalized disease. Of the intradermally inoculated animals, two developed generalized lesions and two showed localized skin lesions. Fever occurred between 3- and 23-days post-inoculation, and viral DNA was detected in blood samples from three animals between 7 and 21 dpi. Nasal and conjunctival shedding was confirmed in all infected cattle, being most prominent on day 19. Viral DNA was detected in the skin, lung, liver, heart, spleen, rumen, kidney, testis, and hair root, and the virus was successfully isolated from the skin, hair root, heart, lung, rumen, kidney, and nasal swabs. Two animals were humanely euthanized during the study due to severe clinical progression. These findings demonstrate that the LSDV Pendik strain is pathogenic in cattle and is suitable for use as a standardized challenge strain in LSD vaccine efficacy evaluations.

Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of antimicrobial-resistant infections in the Philippines. Here, we report the genome sequence of Klebsiella phage vB_VIPKPNMC05, which targets a multidrug-resistant (MDR) K. pneumoniae strain with capsule type K8. VIPKPNMC05, isolated from environmental water, has a siphovirus morphology and exhibits a broad lytic activity against several strains of K. pneumoniae, K. quasipneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The linear double-stranded DNA genome (34,476 bp; 51.0% G + C content) encodes 58 protein-coding sequences (CDS), 37 of which are involved in phage morphogenesis, DNA replication, transcription regulation, and host lysis. Notably, a receptor-binding protein (RBP) with a putative depolymerase (Dpo) was identified. Structural prediction using AlphaFold 3 showed that the tailspike protein (TSP19) forms a homotrimer structure with a conserved C-terminal pectin lyase domain. The TSP module is conserved among Enterobacteriaceae-infecting phages and may have been acquired through horizontal gene transfer. Whole-genome comparisons revealed 52–54% similarity to known phages, suggesting that VIPKPNMC05 represents a distinct lineage. Based on taxonomic analysis, we propose that VIPKPNMC05 belongs to a novel phage family, Pituviridae. The absence of virulence, toxin, and antimicrobial resistance genes, along with its broad host range and lytic lifestyle, suggests possible therapeutic and biotechnological potential of VIPKPNMC05. To our knowledge, this is the first report of a newly discovered phage family from the Philippines, underscoring the importance of local phage bioprospecting for therapeutic applications.

The giant freshwater prawn, Macrobrachium rosenbergii, has experienced significant economic losses due to the stunt growth in the past decade. In this study, random primer amplification was utilized in the slow-growth prawns to discover a novel Macrobrachium rosenbergii circular rep-encoding single-stranded (CRESS) DNA virus (MrCV) in Zhejiang, China. The MrCV genome is 2426 nt long, with two open reading frames (ORFs) encoding the replication protein (Rep) and capsid protein (Cp). The identity of the MrCV Cp (< 56.23%) and Rep (< 48.06%) sequence was compared to the reported CRESS DNA virus sequences. The existence of several highly conserved motifs of HUH endonuclease and superfamily 3 helicase domain in Rep protein were characterized and a GRS domain was found. Phylogenetic analysis of the Rep protein sequences and whole genome sequence revealed that MrCV is located in a branch consist of genomoviruses, circoviruses and unclassified viruses. A nested-PCR method was established to analyze the clinical slow-growth prawns, which were all MrCV-positive. Quantitative PCR results showed that MrCV viral load was significantly higher in the retarded growth prawns than that of sexual precocity, and presented a negative correlation to the prawn weights. The prevalence of MrCV in different life stages of M. rosenbergii was investigated and MrCV could be detected in zoea, postlarva and prawns. The present results reveal a high prevalence of MrCV in M. rosenbergii and suggest that this pathogen may associated with the retarded growth in M. rosenbergii.

Kyasanur Forest Disease (KFD) is a tick-borne zoonotic disease in India that causes fatal hemorrhagic fever in humans. Despite its complex network of hosts and vectors, the interspecific interactions shaping its disease ecology remain underexplored. We aimed to identify these interactions and pathways aiding disease spread within connected landscapes and across geographic barriers. Through a systematic review and meta-analysis, we mapped KFD locations, vectors’ feeding niches, and disease hosts. We found 53 KFD associated species from Western Ghats (active disease location) and 27 potentially associated species from Andaman and Nicobar Islands (KFD seroprevalence location). Each tick’s host ranges revealed unique interactions and potential transmission patterns among host animals. We challenge the current notion of KFD as an endemic primate disease, since primates are absent in the majority of the islands of Andaman and Nicobar with seroprevalence. Here, small mammals could be local hosts, while birds may act as potential dispersers across geographic barriers.

Foot-and-mouth disease virus (FMDV) is a highly contagious pathogen that is controlled mainly by the use of inactivated vaccines, but vaccine production is limited by inefficient cell culture systems. The RNA helicase DDX5 has been implicated in viral replication, but its role in FMDV infection remains unclear. Here, we generated a DDX5-knockout PK-15 cell line using CRISPR/Cas9 to investigate its impact on FMDV replication. DDX5 knockout cells exhibited enhanced FMDV replication, with increased viral protein expression, RNA levels, and titers compared to wild-type cells. Meanwhile, RNA sequencing (RNA-seq) analysis indicated that DDX5 knockout suppressed key proinflammatory cytokines (CXCL2/8/14, CCL2/4/5) and impaired IFN-α/β and ISG (ISG15/20, IRF3, IFIT3) responses postinfection. RT-qPCR was performed to determine the expression level of differentially expressed genes, and the results were consistent with the RNA-seq data. Altogether, the results of this study suggest that DDX5 restricts FMDV replication by modulating host innate immunity. The DDX5 knockout cell line provides a useful model for studying FMDV pathogenesis and improving vaccine development.