Archives of Virology最新文献

A potyvirus (isolate AMLV-CQ) infecting culantro (Eryngium foetidum L.) imported from Vietnam was identified by RT-PCR. The complete genome sequence of AMLV-CQ was determined to be 9,549 nucleotides in length. It contains a large open reading frame encoding a 3,082-amino-acid putative polyprotein, flanked by 5´ and 3´ untranslated regions (UTRs) of 77 and 226 nt, respectively. AMLV-CQ is closely related to five other completely sequenced potyviruses, sharing 68-69% nucleotide and 69-70% amino acid sequence identity. However, the coat protein (CP) gene shares 89% nucleotide and 93% amino acid sequence identity with that of a partially sequenced potyvirus, Ammi majus latent virus (isolate AMLV-WF17). These results suggest that AMLV-CQ and AMLV-WF17 are isolates of the same species. To our knowledge, this is the first report of a complete genome sequence of an AMLV isolate, and culantro was identified as a new natural host for this virus. In addition, a one-step RT-PCR assay was developed that provides a rapid, robust, and highly sensitive approach for the detection of AMLV.

Human adenovirus (HAdV), a leading cause of pediatric acute respiratory infections (ARIs), exhibited altered transmission patterns during the period of time in which COVID-19 nonpharmaceutical interventions (NPIs) were being applied. In this study, we investigated the molecular and clinical characteristics of pediatric HAdV infections in Hangzhou across two epidemiological phases: the 2022 group (March 2022–February 2023), representing a period of strict NPIs with initial post-policy adjustment, and the 2023 group (March 2023-February 2024), reflecting resumption of normal social activities. The retrospective analysis included 55,772 children (aged 0–16 years) with respiratory infections from the Children's Hospital of Zhejiang University School of Medicine. HAdV was detected via PCR‒capillary electrophoresis. Hexon gene sequencing and phylogenetic analysis were performed on 105 randomly selected HAdV-positive samples. In the 2022 group, the positivity rate of HAdV was 4.12% (579/14,049), whereas in the 2023 group, it was 3.59% (1,497/41,723). The peak HAdV infection rate occurred in May 2022 (6.39%, 61/955) and November 2022 (5.32%, 102/1,918). A sustained epidemic trend emerged after Oct. 2023, with a 6.08% (230/3,785) rate occurring in February 2024. HAdV-positive children were predominantly aged 3–6 years (P < 0.001), with no significant difference in the proportion of male and female patients (P > 0.05). The primary coinfections involved Mycoplasma pneumoniae. Pneumonia was the most common clinical diagnosis. Phylogenetic analysis classified 92.6% of the circulating strains as HAdV-B, with a small proportion of HAdV-C. These results offer vital evidence for optimizing the prevention and control of pediatric HAdV infections.

The corn leafhopper Dalbulus maidis (DeLong & Wolcott) (Hemiptera: Cicadellidae) is a major pest of corn in the Americas, transmitting pathogens that cause corn stunt disease. Using high-throughput sequencing and PCR-based assays, we identified and characterized two novel large-genome pestiviruses (LGPs), chicharrita del maiz pestivirus 1 (ChMPV1) and 2 (ChMPV2), from D. maidis populations collected in Texas, Oklahoma, Missouri, and Iowa. Genome analysis revealed long polyproteins with conserved "Pestiviridae" domains, and virus incidence varied geographically (0–43%). Phylogenetic analysis placed both viruses within the newly proposed family "Pestiviridae". These findings expand the known insect virome and provide tools for future studies on insect virus–vector–plant pathogen interactions.

Feline coronavirus (FCoV) has two biotypes: feline enteric coronavirus (FECV), which typically causes mild intestinal infections, and feline infectious peritonitis virus (FIPV), a virulent form associated with a fatal systemic and infectious disease in cats, known as feline infectious peritonitis (FIP). The differentiation between FECV and FIPV has been linked to specific mutations, most notably M1058L and S1060A, in the spike (S) protein. These mutations are believed to enhance macrophage tropism and facilitate systemic dissemination. However, the precise contribution of these mutations to FIPV virulence remains uncertain, as they have also been reported in non-FIP cases. Here, we report three FIP-positive cases (3/20; 15%) in domestic cats in Hanoi, Vietnam, in which the virus carried the M1058L mutation, while none had the S1060A substitution. These findings contribute to the ongoing debate regarding the role of spike protein mutations in FIP pathogenesis and underscore the need for continued genomic surveillance. Further research is needed to elucidate the molecular determinants involved in the FECV-to-FIPV transition, with potential implications for improving diagnosis, treatment, and prevention strategies for feline infectious peritonitis.

In this study, we investigated infectious canine hepatitis (ICH), caused by canine adenovirus 1 (CAdV-1), in 125 bear carcasses submitted for examination. CAdV-1 is known to cause severe disease in domestic dogs and in wild canids and bears. Using molecular and/or histopathological methods, CAdV-1 infection was confirmed in 12 cases: 11 in sloth bears (Melursus ursinus) and one in an Asiatic black bear (Ursus thibetanus). Affected captive bears exhibited acute onset of high fever, jaundice, bloody vomitus, and foul-smelling diarrhoea, followed by death. Necropsy revealed widespread congestion and petechial-to-ecchymotic haemorrhages across multiple visceral organs. Histopathological examination showed marked vascular changes, including engorged blood vessels, oedema, and haemorrhages. Intranuclear basophilic inclusion bodies were observed in endothelial cells, hepatocytes, and Kupffer cells. Immunohistochemistry confirmed the presence of CAdV-1 antigen in endothelial cells of various organs, as well as in hepatocytes and Kupffer cells in the liver. Molecular analysis identified a strain closely related to CAdV-1 isolates previously reported in domestic dogs and other carnivores in various parts of the world. The virus was successfully isolated in MDCK cells from sloth bear samples. Among 99 live sloth bears tested, 41.4% were seropositive for CAdV-1 antibodies. Our findings confirm the susceptibility of these bear species to CAdV-1 and highlight the need for ongoing surveillance, as well as the importance of vaccination in captive bear populations to prevent the spread of this disease.

Tomato spotted wilt virus (TSWV) is a harmful pathogen that causes severe disease in tomato, pepper, and other horticultural and agronomic crops. Its genome comprises three linear single-stranded RNA molecules (segments L, M, and S), which are unequally packed in nucleocapsids. Although its genome structure and molecular mechanism of infection are well understood, the evolutionary dynamics of this virus require further analysis to determine the most probable viral ancestor, the date of divergence, the ancestral geographical source of dispersal, and the demographic history of TSWV. For this, we employed a Bayesian framework to analyze whole-genome sequences of 136 isolates of TSWV obtained from different sites worldwide with a sampling window of 35 years, and phylodynamic analysis was performed separately for segments L, M, and S. Our results showed that the mutation rates of the different genome segments ranged from 1.678 × 10^− 4 to 2.444 × 10^− 4 substitutions/site/year. Although the estimated time to the most recent common ancestor varied depending on the dataset used, the most probable date of TSWV divergence was around 1768 CE. Our phylogeographic analysis yielded concordant results for the three genome segments, indicating that the TSWV population originated in South Korea and, from there, first expanded to Europe and then to North America and other continents. Past population dynamics analysis showed that the virus experienced two major population expansions that coincided with the expansion of the agricultural frontier and the emergence of new species of insect vectors.

To enhance preparedness against existing and new zoonotic viruses such as Hendra virus, Nipah virus, and other paramyxoviruses, screening tools and efficient diagnostic methods are needed. Here, we established a conventional nested pan-PCR assay using previously described primers for screening of human and bat samples. Additionally, we developed specific real-time RT-PCR (RT-qPCR) assays to detect Nipah virus and Hendra virus genotypes 1 and 2. Both PCR methods demonstrated good performance and could be used for screening of paramyxoviruses. Human serum and cerebrospinal fluid samples from 558 Finnish patients and 60 serum samples from Kenyan patients were screened using the nested-pan-PCR assay, and all were negative. In addition, we screened 340 synanthropic bat samples collected during 2021 and 2023 from Kenya, resulting in the discovery of two parajeilongviruses in Angolan free-tailed bat (Mops condylurus) samples.

A new double-stranded RNA mycovirus, tentatively named "Sclerotinia sclerotiorum victorivirus 2" (SsVV2), was isolated from Sclerotinia sclerotiorum strain DT-110. The complete genome of SsVV2 is 5135 nucleotides in length and contains two open reading frames (ORF1 and ORF2) that overlap at the tetranucleotide AUGA (positions 2546-2549). ORF1 and ORF2 were predicted to encode a coat protein (CP, 755 amino acids) and an RNA-dependent RNA polymerase (RdRP, 836 amino acids), respectively. BLASTp analysis identified Sclerotinia nivalis victorivirus 1 (SnVV1) as the closest match to SsVV2, with their RdRPs sharing 75.7% amino acid sequence identity. Phylogenetic analysis based on the RdRP and CP of victoriviruses further support the clustering of SsVV2 with SnVV1. These results confirm that SsVV2 as a new member of the species Victorivirus nijyusani, genus Victorivirus, family Pseudototiviridae.

Alternaria alternata orfanplasmovirus 1 (AaOrfV1), a previously unreported orfanplasmovirus, was discovered in strain TG155-3 of Alternaria alternata f. sp. mali in this study. The genome of AaOrfV1 consists of two positive-sense single-stranded RNA segments. RNA1, which is 3122 nucleotides in length, encodes a protein with 973 amino acids. BLASTp analysis showed that this protein had the highest sequence similarity (62.79% identity) to the RNA-dependent RNA polymerase of downy mildew lesion associated orfanplasmovirus 4. RNA2, with a length of 2,485 nucleotides, encodes a protein with 785 amino acids that showed the highest similarity (44.02% identity) to a hypothetical protein of downy mildew lesion associated orfanplasmovirus 7. Phylogenetic analysis indicated that AaOrfV1 clusters with other reported orfanplasmoviruses, supporting its classification as a new member of the proposed family "Orfanplasmoviridae". This is the first report of the complete genome sequence of an orfanplasmovirus from Alternaria alternata f. sp. mali. These findings significantly enhance our understanding of orfanplasmoviruses and the diversity of mycoviruses in A. alternata.

Multidrug-resistant Klebsiella pneumoniae requires alternative therapies. In this study, we characterized two novel phages, PKP K9 (a siphovirus) and PKP Kh11 (a myovirus). Both showed genomic safety and exhibited excellent reproduction and physicochemical tolerance. A cocktail containing both phages had a broad combined host range (85.7%, 72/84) and showed potent in vitro activity with distinct dose-dependent inhibition modes. In a Galleria mellonella infection model, each phage individually and the two combined provided complete prophylactic and therapeutic protection against lethal challenge. The PKP K9/PKP Kh11 cocktail demonstrates significant therapeutic potential against multidrug-resistant K. pneumoniae.