Virus Genes最新文献

Peste des petits ruminants (PPR) continues to pose a significant challenge in endemic regions, such as India, despite ongoing vaccination efforts. Although the existing vaccines are effective, they have certain limitations, such as thermolability and the inability to distinguish between infected and vaccinated animals (DIVA). Understanding the molecular mechanisms governing host-pathogen interactions during natural infection versus vaccine-induced immunity is crucial for developing next-generation control strategies. This study conducted comparative transcriptomic analysis of peripheral blood mononuclear cells from naturally PPRV-infected goats (GSE132429, n = 16) and Sungri/96-vaccinated goats (GSE155504, n = 10) to decipher shared and distinct molecular signatures of protective immunity. Differential gene expression identified 1,874 DEGs in infected samples (238 up-regulated, 534 down-regulated) and 1,838 DEGs in vaccinated samples (286 up-regulated, 534 down-regulated). Comparative analysis revealed 12 up-regulated and 11 down-regulated hub genes shared between both conditions, demonstrating that vaccination successfully activates similar protective immune pathways as natural infection, including cytokine-cytokine receptor interaction, IL-17 signaling, and RIG-like receptor signaling. Importantly, condition-specific genes were identified that distinguish infection from vaccination: infection-specific genes like IL-6 and IL1A indicated pathological inflammation, while vaccination-specific genes included ribosomal proteins (RPS27A, RPS14, RPS29, RPS18), reflecting controlled immune memory formation. Machine learning validation of these unique hub genes achieved exceptional classification accuracy (> 90%), confirming their robust biomarker potential for DIVA applications in distinguishing PPRV-infected animals from vaccinated animals. These findings establish that current PPR vaccines effectively mimic key aspects of natural infection while maintaining distinct protective characteristics, offering potential targets for developing enhanced diagnostic tools, next-generation vaccines with DIVA capabilities, and targeted therapeutic interventions to reduce PPR burden on small ruminant populations.

Orthoreovirus mammalis (MRV) can infect a wide range of mammals, including humans and bats, and the cross-species transmission of the virus poses a potential threat to the health of humans and other animals. In this study, we identified a novel MRV strain from diarrheic pigs in Hunan Province, China. Genetic analysis revealed that the virus is a reassortant, containing segments derived from human, porcine, and mink MRVs. Designated as MRV3-HNU-XXS-2020, the strain clusters within Lineage IV of MRV3 and shows the highest nucleotide identity (98.79%) and amino acid identity (98.02%) to the MRV3 strain IND/MZ/3013789/reo derived from Indian pigs in 2017. The σ1 protein of the virus contains the amino acid residues linked to the sialic acid-binding site as well as neurotropism (198-204 NLAIRLP, 249I, 340D, 419E), suggesting a potential for broader mammalian infectivity. This study provides a basis for investigating the epidemiology, genetic evolution, and zoonotic spillover potential of MRV in mammals.

Lentinula edodes (shiitake) is a globally important edible mushroom, but viral infections can hinder mycelial growth, reduce yield, and degrade quality, leading to economic losses. This study examined viral infections in L. edodes cultivated in South Korea. We developed a CRISPR/Cas12a-based reverse transcription recombinase polymerase amplification (RT-RPA) assay for the rapid and accurate detection of L. edodes spherical virus (LeSV), the predominant mycovirus-infecting L. edodes in Korea. The optimized RT-RPA-CRISPR/Cas12a assay can be completed within 20 min at 34 °C and demonstrated 100 times higher sensitivity than RT-PCR. Field sample verification further confirmed its superior detection rate over RT-PCR. The RT-RPA-CRISPR/Cas12a method described herein has the potential to facilitate early diagnosis of LeSV infections and support disease management in L. edodes cultivation.

Newcastle disease (ND) is a serious poultry disease in Ethiopia. F gene sequences have shown that the velogenic Newcastle disease virus (NDV) sub-genotype VII.1.1 is prevalent in Ethiopia and other East African countries. However, the F gene sequence alone is not enough to fully understand the pathogenicity, antigenicity, and epidemiological characteristics of NDVs. Whole-genome characterizations of currently circulating virus strains are needed to understand the molecular basis of the pathogenicity and antigenicity differences between vaccine and field strains. In this study, we obtained the complete genome sequences of seven NDV sub-genotype VII.1.1 isolated from chicken farms in Ethiopia and compared them with closely related NDVs and vaccine strains. Whole-genome sequencing revealed that all isolates have genome length of 15,192 nucleotides and are composed of six genes in the order 3'-NP-P-M-F-HN-L-5'. Phylogenetic analysis of the whole genomes showed that sub-genotype VII.1.1 can be classified into three distinct lineages and that the Ethiopian isolates in this study clustered within lineage 1. Unique amino acid substitutions were identified in all six genes of the Ethiopian isolates when compared to closely related NDV strains and commonly used vaccine strains. Some of these substitutions have been linked to antigenic variation. Although sub-genotype VII.1.1 is widespread in Ethiopia and other horn of African countries, to the best of our knowledge, this is the first report describing its whole-genome characteristics in this region. The findings in this study are expected to support effective ND control strategies in the region.

Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.

In this study, we report the discovery of a novel virus, Yunxiao leafhopper virus 1 (YXLeV1), found in the insect vector Recilia dorsalis, a significant pest of rice crop. The complete genome of YXLeV1, consisting of 14,115 bp, was sequenced and analyzed. The whole viral genome shares only 36.32% identity with the RNA-dependent RNA polymerase (RdRp) of Hubei diptera virus 11, belonging to genus Alasvirus. It contains four open reading frames encoding a nucleoprotein (N), a hypothetical protein (p78) of unknown function, a glycoprotein (G), and an RNA-dependent RdRp. The N, G, and RdRp proteins of YXLeV1 share 22.0%, 34.05%, and 36.32% amino acid sequence identity with the corresponding sequence of Hubei diptera virus 11. As per the genus demarcation criteria of the family Xinmoviridae, viruses sharing less than 60% amino acid identity in the RdRp sequence with known members are considered to belong to new genera, so the observed 36.32% identity between YXLeV1 and Hubei diptera virus 11 supports the classification of YXLeV1 as the first member of a novel genus, which we propose to name Recilivirus. Phylogenetic analysis further confirms that YXLeV1 is distantly related to Hubei diptera virus 11, the sole member of the genus Alasvirus, and forms a separate clade supporting its classification as a member of a new genus. Given the ecological significance of R. dorsalis as a vector, this discovery adds to the catalog of viruses associated with this species and contributes to our understanding of virus vector associations.

Hepatitis B Virus (HBV) infection is a global health concern. HBV genotypes differ in disease potential and geographical distribution. These genotypes impact the diagnostic and preventive strategies. Furthermore, limited data are available on Torque Teno Virus (TTV) co-infections with HBV. Hence, this study evaluated HBV infection prevalence, genotype distribution, and the presence of TTV among HBV-positive patients. During the study period, a total of 1820 serum samples were collected and tested for HBsAg using ELISA method. Of this, 43 (2.36%) were HBsAg positive. These HBsAg-positive samples were further subjected to conventional PCR followed by Sanger sequencing for HBV and TTV genotype detection. In this study, only HBV genotypes D (subgenotype D2) (97%) and A (subgenotype A1) (3%) were detected. 15% of HBV-infected patients were positive for TTV in which genotype 1A was detected in 66.67% of cases and 1B in 33.33% of cases. To the best of our knowledge, this study represents the first of its kind from Puducherry to document Torque Teno Virus (TTV) co-infection in HBV-positive cases from the non-renal transplant population. This study underscores the significance of HBV genotypes and TTV co-infection in HBV patients. Further studies and surveillance are needed to monitor circulating HBV genotypes and explore TTV's role in co-infection, particularly its pathogenesis and clinical implications.

The Polymycoviridae family is an expanding group of mycoviruses, generally characterized by atypical capsids and segmented double-stranded (ds) RNA genomes. Polymycoviruses have been associated with various changes in their hosts' traits, such as shifts in spore production, changes in pigmentation, and alterations in growth and virulence, either enhancing or reducing them. Here, we report the complete genome sequence of a polymycovirus identified in an entomopathogenic, fungicolous, and keratinophilic, filamentous ascomycete species Lecanicillium aphanocladii, isolated from a patient with foot dermatophytosis (Tinea pedis). The virus, denominated Lecanicillium aphanocladii polymycovirus 1 (LaPmV1), has six genomic dsRNA segments. Phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) sequences revealed that LaPmV1 is closely related to the previously reported Beauveria bassiana polymycovirus 4. Virus-curing studies revealed that LaPmV1 regulates pigmentation and decreases sporulation in its host while not affecting mycelial growth in vitro. LaPmV1 has also been shown to slightly increase the host's susceptibility to certain common antifungals, including itraconazole, voriconazole, and posaconazole.

Viruses have long been known to infect various arthropod hosts, playing crucial roles in their ecology and evolution. While viral diversity has been well studied in insects, knowledge of viruses in arachnids remains limited. This study investigated the DNA virome of Androctonus mauritanicus (Moroccan black thick-tailed scorpion) to expand our understanding of viral diversity in non-insect arthropods and explore the evolutionary relationships of scorpion-associated viruses. Samples of Androctonus mauritanicus collected from the region of Marrakech, Morocco, were subjected to high-throughput DNA sequencing via the Illumina X Ten platform. After the assembly, a complete circular viral genome of 136,386 bp in size with a GC content of 31.75% was identified that bears protein homology to the Ascovirus and Toursvirus genes and was provisionally named Androctonus mauritanicus toursvirus (AmTV). AmTV genome annotation resulted in 144 predicted ORFs, including proteins involved in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism, and apoptosis. Phylogenetic analysis revealed that AmTV is basal to the Toursvirus genus of the Ascoviridae family and forms a sister clade with Dasineura jujubifolia toursvirus 2a (DjTV-2a) and Diadromus pulchellus ascovirus 1a (DpTV-1a). Comparative genomic analysis revealed that AmTV shares 97 genes with DjTV-2a (average amino acid identity: 43.72%) and 95 genes with DpTV-1a (average amino acid identity: 44.30%), but the genomic structure of AmTV differs significantly from that of both viruses, indicating that these viruses diverged early in their evolutionary history. These findings imply that toursviruses might infect a wider variety of hosts than previously understood, providing insights into the evolution of the Ascoviridae family. The discovery of the presence of viruses in scorpions, a group of arthropods often overlooked in viral studies, broadens our understanding of host-virus interactions and highlights the importance of expanding viral surveillance to new arthropod and arachnid species.

Koala retrovirus (KoRV) causes multiple disease phenotypes in koalas, including carcinogenesis. The study aimed to assess oncogene expression in spleen tissues from ten deceased koalas coinfected with different subtypes and peripheral blood mononuclear cells (PBMCs) from two subclinically coinfected koalas with KoRV-A and KoRV-B. Initially, KoRV subtyping involved amplifying endogenous KoRV-A, and exogenous KoRV-B, -C specific env gene fragments, followed by sequencing. Using quantitative real-time polymerase chain reaction (RT-qPCR), we examined five oncogenes (BCL2, BAX, BCL2L1, BCL3, and MYC) in spleen and PBMCs from dead and alive koalas coinfected with multiple KoRV subtypes, respectively. Significant (p < 0.05) increases in BCL2 and BAX oncogene expression were observed in deceased koalas that were coinfected with multiple KoRV subtypes compared with healthy koalas. Thus, this study highlights a potential link between KoRV subtype infections, oncogene expression, and koala diseases.