Archives of Virology最新文献

Group A Clostridium perfringens is a major poultry pathogen that causes necrotic enteritis. The molecular similarity of its toxins to those of other bacterial species suggests the involvement of horizontal gene transfer through mobile genetic elements or bacteriophages. Lysogenic bacteriophages play an important role in bacterial evolution through horizontal gene transfer. In the present study, we examined and compared the physiochemical characteristics, genome sequences, and tail fiber proteins of two lysogenic bacteriophages infecting C. perfringens. Bacteriophages ΦCP5(17) and ΦCP17(i) were isolated from a sewage sample and tested for their stability at different temperatures and pH conditions, and in simulated gastric fluids. The genomes of these phages were sequenced, and their morphology was examined by electron microscopy. Both phages produced circular, hazy plaques on their host bacteria and were stable up to 60°C, exhibiting optimal activity at pH 7–8. Both bacteriophages were found to have a very narrow host range, with ΦCP17(i) exhibiting a slightly broader host range than ΦCP5(17). Both phages exhibited podovirus morphology and a genome size of 17.8 kb and 17.9 kb for ΦCP5(17) and ΦCP17(i), respectively. According to the ICTV classification system, ΦCP5(17) and ΦCP17(i) belong to the genus Brucesealvirus, family Guelinviridae, and class Caudoviricetes. These phages share 95.6% genomic nucleotide sequence identity, suggesting that they belong to the same species but differ at the subspecies level. Although ΦCP5(17) and ΦCP17(i) have similar morphological and genomic features, their tail fiber proteins differ in their predicted folding patterns. Nucleotide sequence analysis indicated the absence of toxin and antibiotic resistance genes. Both phages encode a SpoVG protein, whose functional role requires further investigation.

Porcine circovirus 3 (PCV3) has emerged as a significant pathogen associated with various clinical manifestations affecting global swine populations. To investigate the prevalence and molecular characteristics of PCV3 strains, we collected 11,194 tissue samples from pigs across 650 farms of varying breeding scales in 18 cities of Henan province from March 2022 to December 2024. Detection of PCV3 was performed using a validated real-time quantitative PCR assay. The results showed that the total positive rate of PCV3 was 9.25% (1035/11,194), and PCV3 was detected on pig farms in 18 cities of Henan Province. The complete genome sequences of six PCV3 strains and the ORF2 gene sequences of four PCV3 strains were determined and analyzed. These 10 PCV3 strains shared 98% to 99.7% nucleotide sequence identity in ORF2 with PCV3 reference strains. The complete ORF2 gene sequences of these 10 PCV3 strains shared 98.4% to 99.8% nucleotide sequence identity with each other, and the encoded proteins shared 98.1% to 100% amino sequence acid identity. Phylogenetic analysis based on the ORF2 gene indicated that all 10 sequenced PCV3 strains belonged to genotype PCV3b. Notably, two amino acid mutations were identified in predicted B cell epitopes within the Cap protein of the these strains, which may affect the immunogenicity of PCV3. These data contribute to our understanding of the molecular epidemiology and evolution of PCV3 and provide a foundation for the prevention and control of PCV3 and other PCVs.

Here, we report a novel fungal virus, tentatively named “Rhizoctonia solani endornavirus 15” (RsEV15), isolated from Rhizoctonia solani AG-1 IA strain MY-JK-1. The RsEV15 genome consists of 18,934 nucleotides with a GC content of 44.5% and contains two open reading frames (ORFs). ORF1 encodes a large polypeptide of 5070 amino acids with conserved RNA-dependent RNA polymerase (RdRp), helicase (Hel), and glycosyltransferase domains. ORF2 encodes a protein of unknown function composed of 1063 amino acids. BLASTp results showed a relationship between RsEV15 and RsEV8, although their genomes share only 49.56% nucleotide sequence identity. Phylogenetic analysis based on RdRp sequences indicated that RsEV15 is a new member of the genus Alphaendornavirus (family Endornaviridae).

A novel ampelovirus, designated “arachis ampelovirus 1” (ArAV1), was identified through high-throughput sequencing in forage peanut (Arachis pintoi). The ArAV1 genome sequence, confirmed by Sanger sequencing, comprises 12,940 nucleotides and contains seven open reading frames (ORFs), indicating a typical ampelovirus genome structure. The HSP70 homolog, RdRp, and CP proteins were found to exhibit less than 75% amino acid sequence identity to those of other ampeloviruses. Phylogenetic analysis based on amino acid sequences of the HSP70 homolog and the RdRp showed that pineapple mealybug wilt-associated virus 1 is the most closely related to ArAV1, whereas analysis based on CP amino acid sequences revealed that the pineapple mealybug wilt-associated virus 3 is the closest relative of ArAV1. These analyses suggest that ArAV1 is a member of a new species within the genus Ampelovirus, for which we propose the binomial name “Ampelovirus arachii”. 

The emergence of extended-spectrum-beta lactamase (ESBL)-producing E. coli sequence type 131 (ST-131) in urinary tract infections is a serious public-health threat. Here, we describe the isolation and characterization of a novel bacteriophage, PSK1, which exhibits antibacterial activity against multiple clinical strains of E. coli ST-131 with the O25:H4 serotype. This phage demonstrated strong lytic activity, achieving a 2-log reduction in infectivity at a multiplicity of infection (MOI) of 1, and complete growth inhibition at an MOI of 10 or 100. It was found to be stable for 24 hours in artificial urine and also exhibited stability at various pH values and temperatures, suggesting its potential use as a therapeutic agent for infections of the urinary tract and other tissues. PSK1 was found to have a latent period of 15 minutes and a burst size of 360 plaque-forming units (PFU) per infected cell. Transmission electron microscopy revealed a podovirus morphotype, with a capsid diameter of 104.97 ± 3.3 nm and a tail length of 33.56 ± 2.7 nm. The PSK1 genome is a double-stranded DNA molecule with a length of 39,615 base pairs, containing 61 open reading frames, encoding 25 proteins (41%) with a predicted function and 36 (59%) with no predicted function. PSK1 exhibits a purely lytic growth cycle and lacks any known virulence, antibiotic resistance, lysogeny, or mycotoxin genes. Lipopolysaccharide (LPS) inhibition assays showed that infection was blocked only by O25:H4-specific LPS, confirming the serotype specificity of this phage. A phylogenetic dendrogram based on proteomics analysis showed that PSK1 clustered with members of the family Autotranscriptaviridae, subfamily Studiervirinae, and genus Kayfunavirus, whose members employ a T7-like direct terminal repeat for genome packaging. Our data suggest that phage PSK1 is a strong candidate for bacteriophage therapy against uropathogenic E. coli ST-131 with the O25:H4 serotype.

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne infectious disease that was first identified in South Korea in 2013. To investigate the SFTS virus (SFTSV) genotypes in Gyeonggi Province, SFTSV detected in 126 patient serum samples collected between 2017 and 2022 was subjected to genetic analysis. Among SFTSV genotypes A to F, SFTSV genotype B was the most common, found in a total of 101 cases (80.2%). Within genotype B, there were 85 cases of subgenotype B-1 (67.5%) and 16 cases of subgenotype B-2 (12.7%), but no cases of subgenotype B-3. Five cases of genotype F (3.9%), one of genotype C (0.8%), and one of genotype D (0.8%) were identified. No genotype A or E strains were found. Of the 108 patients for whom epidemiological information was available, 16 (14.8%) died, 75 (68.5%) recovered, and the outcome was unknown for 18 (16.7%) patients. Although the number of samples tested was not large enough to allow a concrete conclusion, subgenotype B-1 showed the highest fatality rate (16.5%). The high prevalence and lethality of SFTSV subgenotype B-1 in a local region of South Korea showed that continuous monitoring of SFTSV genotypes is necessary.

Human adenovirus (HAdV) is a common cause of acute respiratory infections, affecting both the upper and lower respiratory tract. In this study, we retrospectively analyzed the epidemiology of HAdV by using data from the National Community Viral Surveillance System in Taiwan from 2019 to 2023. The average detection rate during this period was 3.4%, with the highest detection rate observed in 2023, at 6.6%, which is more than 3–4 times the detection rate observed from 2020 to 2022. In this study, a total of 1,565 HAdV isolates were sequenced from 2019 to 2023, and six species and 17 HAdV types were identified. Among these, HAdV-B3 and HAdV-C2 were the most prevalent types. HAdV infections occurred year-round in Taiwan, with statistical analysis revealing that 91.9% of cases affected children under nine years of age, with no significant difference between males and females. Although HAdV infections are typically mild and self-limiting, some patients presented with severe complications, such as pneumonia and central nervous system (CNS) symptoms. Additionally, several patients with HAdV infection were coinfected with other respiratory pathogens. Our findings indicate that the prevalent HAdV types in Taiwan are genetically diverse and coexist in the community, emphasizing the need for continued epidemiological surveillance. Given the significant role of HAdV in acute respiratory disease, further investigation into its molecular epidemiology and clinical characteristics is essential for the development of effective prevention and control strategies.

Viral hemorrhagic septicemia virus (VHSV) is a single-stranded RNA virus that infects both freshwater and marine fish. In Korea, VHSV genotype Ⅳa infects cultured olive flounder (Paralichthys olivaceus) annually. As a prevention strategy against infectious viral diseases, this study aimed to develop a multi-epitope DNA vaccine using in silico methods and evaluate its efficacy in vivo in olive flounder. Cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes of the VHSV glycoprotein were predicted using bioinformatic tools and assembled with the linkers AAY, GPGPG, and KK, respectively. This multi-epitope sequence (359 bp) was then cloned into the pcDNA3.1(+) vector for use as a DNA vaccine, and this construct was named "pMulti". To evaluate the efficacy of the multi-epitope DNA vaccine, olive flounder were vaccinated with PBS, pcDNA3.1(+), or pMulti. The persistence and transcript levels were confirmed up to 28 days post-vaccination (dpv). Moreover, HTL-associated immune-related genes, including MHCII and IFN-γ, were significantly upregulated at 3 dpv. Immunoglobulin M (IgM) production was confirmed by ELISA at 14, 21, and 28 dpv. The protective efficacy of the vaccine was tested by challenging fish with 1×10⁴ PFU of VHSV at 21 dpv, and the relative percent survival (RPS) of pMulti-vaccinated fish was 40% in experiment 1 and 23.08% in experiment 2. Moreover, the hazard ratio for the pMulti vaccine was significantly lower than that for PBS and pcDNA3.1(+) (2.08 and 2.65, respectively). Although these findings demonstrate the potential of multi-epitope-based vaccines against VHSV IVa, additional research involving in vivo evaluation of a subunit vaccine through protein expression is essential for a more conclusive assessment of efficacy.

We tested whether rice root aphids (RRA; Rhopalosiphum rufiabdominale) and cannabis aphids (CAs; Phorodon cannabis) acquire hop latent viroid (HLVd) from infected cannabis plants (Cannabis sativa). One of eight groups of RRAs and four of eight groups of CAs feeding on infected plants tested positive for HLVd, as shown using a multiplex reverse transcription polymerase chain reaction assay. We found no evidence that HLVd-infected CAs transmitted HLVd to viroid-free cannabis plants, possibly because the amount of HLVd transmitted remained below the detection threshold. Further research is needed to determine whether CAs or RRAs are able to transmit HLVd to cannabis plants.

Metarhizium acridum is a well-established specialist entomopathogenic fungus that primarily targets arthropods within the order Orthoptera. In this study, we investigated the genomic characteristics of a novel mycovirus infecting M. acridum, named “Metarhizium acridum unirnavirus 1” (MaUV1). Its genome is 2,907 bp in length and contains two open reading frames (ORFs), encoding a protein of unknown function and an RNA-dependent RNA polymerase. The identified ORFs showed sequence similarity to those of “Botryosphaeria dothidea non-segmented dsRNA mycovirus” and “Nigrospora oryzae mycovirus 1”. Phylogenetic analysis revealed that MaUV1 belongs to the recently established genus Unirnavirus, family Amalgaviridae. This is the first report of an amalgavirus infecting a member of the genus Metarhizium and the first report of a mycovirus infecting M. acridum.