Archives of Virology最新文献

A new badnavirus was discovered in nettle plants (Urtica dioica L., family Urticaceae) with vein banding symptoms using high-throughput sequencing. This virus was provisionally named "nettle badnavirus 1" (NBV 1). The complete NBV 1 genome consists of 7598 bp and contains three overlapping open reading frames. NBV 1 found to be was most closely related to green Sichuan pepper vein clearing-associated badnavirus, sharing 73.9% nucleotide sequence identity in the whole genome. These two viruses showed 76.3% nucleotide sequence identity in the region of the genome encoding RT-RNase H. This is lower than the species demarcation cutoff (80%) for the genus Badnavirus of the family Caulimoviridae, suggesting that NBV 1 is a new member of this genus. Phylogenetic analysis based on full-length badnavirus genome sequences showed that NBV 1 belongs to the same clade as a badnavirus whose genome was found to be integrated into chromosome 6 of the nettle genome, sharing 78% identity. Using PCR, NBV 1 was detected in a symptomless nettle plant growing next to symptomatic ones. It is therefore likely that the observed vein banding was due to an idaeovirus or a partitivirus, which were shown to be coinfecting the symptomatic plant. These findings expand the list of viruses infecting nettle.

The coronavirus disease of 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can alter the expression levels of host microRNAs (miRNAs). Increasing evidence suggests that circulating miRNAs can potentially play an important role in the diagnosis and prognosis of respiratory infectious diseases, especially COVID-19, and might serve as sensitive indicators of disease before the emergence of clinical symptoms. Here, we review the potential of circulatory microRNAs as novel biomarkers for different aspects of COVID-19. Recent studies have suggested that they can be useful not only for COVID‐19 prognosis but also for prediction of disease severity and mortality among intensive care unit (ICU) and ward patients. Moreover, extracellular vesicle (EV) miRNAs can be associated with antibody titer after COVID-19 vaccination. This review provides an overview of miRNA‐based biomarkers.

Penicillium exsudans strain RCEF7900, obtained from leaf litter, was found to harbor two double-stranded RNA (dsRNA) elements, designated as dsRNA1 and dsRNA2, with lengths of 1,816 bp and 1,625 bp, respectively. dsRNA1 encodes a 572-amino-acid RNA-dependent RNA polymerase (RdRp) protein (65.29 kDa), while dsRNA2 encodes a 503-amino-acid coat protein (CP) (56.73 kDa). A BLASTp search indicated that dsRNA1 and dsRNA 2 together constitute the genome of a novel partitivirus, which we have named "Penicillium exsudans partitivirus 1" (PePV1). Phylogenetic analysis based on RdRp amino acid sequences revealed that these genome segments belong to a member of a new species within the proposed genus “Zetapatitivirus” of the family Partitiviridae, with the RdRp showing the most sequence similarity (79.72% identity) to that of Sonifin virus. This is the first report of a zetapatitivirus from P. exsudans, expanding our understanding of mycoviral diversity in this fungal species.

Members of the fungal genus Stagonosporopsis are important plant pathogens that can cause severe disease on a wide range of economically important plants and crops. Here, a novel victorivirus, tentatively named "Stagonosporopsis citrulli victorivirus 1" (SciVV1), was isolated from S. citrulli isolate HS2-8. The SciVV1 genome is 5,163 nucleotides in length, with a predicted GC content of 63.85%, and contains two open reading frames (ORF1 and ORF2), which overlap at an AUGA sequence. ORF1 and ORF2 are predicted to encode a coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). A phylogenetic tree based on RdRp amino acid (aa) sequences showed that SciVV1 clustered together with members of the genus Victorivirus in the family Pseudototiviridae. Our results indicate that SciVV1 is a novel victorivirus. This is the first report of the complete genome sequence of SciVV1 infecting S. citrulli.

Bovine viral diarrhea (BVD), caused by bovine viral diarrhea virus (BVDV), has a significant economic impact on affected farms worldwide. For effective disease control, it is crucial to select an appropriate vaccine based on the specific genotype of BVDV. Therefore, developing a rapid and reliable assay to detect and genotype BVDV is imperative for controlling the spread of disease. In this study, we developed a TaqMan assay to detect and genotype BVDV types 1 and 2 directly in bovine serum without extraction of RNA. The direct BVDV TaqMan assay effectively detected both BVDV1 and BVDV2 with confirmed specificity and showed no cross-reactivity with any of the other viruses tested, including bovine respiratory syncytial virus, bovine coronavirus, Akabane virus, bovine herpesvirus 1, bovine parainfluenza virus 3, bovine immunodeficiency virus, and bovine leukemia virus. The assay could detect the virus in serum samples with a titer as low as 10² TCID₅₀/mL in two out of three trials for BVDV1 and all three trials for BVDV2, indicating that its sensitivity is equivalent to that of virus isolation. Our findings represent a significant advancement in BVDV detection and typing directly from bovine serum.

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term ‘quasispecies’ to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (> 10% sample) variants. The composition of variants differed in samples from different plants and among tissue types of a single plant. Single-nucleotide polymorphisms (SNPs), mostly in the form of substitutions, were the primary source of variation; in this study, SNPs were observed in approximately 10% of the viroid genome. The results of the three experiments indicate that CVd-VII follows the quasispecies model as reported for other viroids and that variability occurs in viroid populations in different tissue types and host species.

In India, plants from the non-cultivated, horticultural, and agricultural categories are commonly infected with various begomoviruses, most of which produce yellow mosaic, bright yellow mosaic, or curling symptoms on leaves. In this study, the complete genome of a new bipartite begomovirus causing yellow mosaic disease (YMD) in butterfly pea (Clitoria ternatea L.) was characterized using rolling-circle amplification followed by restriction digestion, cloning, and sequencing to obtain the full-length DNA-A (2727 nt) and DNA-B (2648 nt) sequences. The DNA-A and DNA-B components have a genome organization that is typical of the Old World bipartite begomoviruses, and the common regions (95 nt) of DNA-A and DNA-B share 91% nucleotide sequence identity, which is well above the threshold (>85%) for them to be considered cognate components. Both DNA molecules contain a begomovirus nonanucleotide motif, conserved iterons, and a putative stem-loop structure. The DNA-A of this virus was found to be most similar to that of Cajanus scarabaeoides yellow mosaic virus (CsYMV), with 82.61% nucleotide sequence identity, which is far below the species demarcation threshold (< 91%) for begomoviruses, whereas the DNA-B sequence showed the most similarity (77.16% identity) to that of Rhynchosia yellow mosaic virus (RhYMV). In phylogenetic analysis, both DNA-A and DNA-B were formed a clade with the corresponding genome segments of other YMD-causing begomoviruses. Based on these characteristics, this virus, for which the name “butterfly pea yellow mosaic virus” (BpYMV) is proposed, should be considered a member of a new species in the genus Begomovirus.

In this review, we discuss different super-resolution microscopy (SRM) techniques employed to study viral structures and virus composition with nanometric resolution. We describe the basic principles of the different microscopy methods utilized to break the light diffraction limit, enabling the study of protein composition in viral structures. Finally, we demonstrate for the first time the differential spatial distribution of two structural proteins in an individual baculovirus using single-molecule super-resolution microscopy. We discuss the future of these powerful methods for virology, medicine, and biotechnology applications.

In this case study, we describe an outbreak of highly pathogenic avian influenza (HPAI) virus subtype H7N3 in an ecological reserve in Chiapas, Mexico, affecting captive and wild birds. The virus was detected mainly in plain chachalacas displaying respiratory and gastrointestinal clinical signs and death within 24 hours. Mortality in white-fronted parrots and a clay-colored thrush was also recorded. We describe control strategies implemented to prevent virus dissemination and active surveillance within the risk area. Phylogenetic analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.

The disease caused by goose parvovirus (GPV) affects young goslings and ducks and leads to substantial losses for farmers due to high mortality rates, reaching 70-100% in naive flocks. Here, we present the results of a study focusing on the historical virulent GPV LIV-22 strain, which was isolated in the USSR in 1972. An attenuated GPV LIV-22 vaccine strain that was generated by continuous passaging in goose embryonic fibroblasts was also studied. Phylogenetic analysis placed both GPV LIV-22 strains in the classical GPV group, close to the vaccine and low-pathogenic strains. However, several individual changes in the GPV LIV-22 VP1 gene highlight the uniqueness of the evolution and adaptation mechanism of GPV LIV-22 strains. Transmission electron microscopy (TEM) revealed severe ultrastructural changes in goose hepatocytes and enterocytes as early as 24-48 h postinfection, confirming abrupt GPV pathogenesis. This description of some of the essential characteristics of the GPV LIV-22 virulent and vaccine strain will be useful for studying GPV evolution and molecular pathogenesis.