Virus Genes最新文献

The complete genome sequence of a baculovirus isolated from larvae of the Virginia pine sawfly, Neodiprion pratti pratti, was determined from sequence data generated from two isolates of this virus obtained from virus-killed larvae harvested during a N. pratti pratti outbreak in Maryland, Virginia, and North Carolina, USA, during the 1950s. Sequence assembly and analysis of this virus, Neodiprion pratti pratti nucleopolyhedrovirus (NeppNPV), revealed a circular genome of 81,658 bp. BLASTp queries with the 89 ORFs annotated for NeppNPV indicated a close relationship with Neodiprion lecontei nucleopolyhedrovirus (NeleNPV). Pairwise nucleotide distances and phylogeny determined from alignments of baculovirus core gene homologs indicated that NeppNPV and NeleNPV are both members of species Gammabaculovirus nelecontei. NeppNPV and NeleNPV were distinguishable by differences in ORF content and indels suggestive of intramolecular recombination. Overlapping geographic ranges and shared host plants for N. pratti pratti and N. lecontei suggest the potential for cross-infections of larvae of these two sawfly species with NeppNPV and NeleNPV.

Bluetongue (BT), a significant economic disease affecting domestic and wild ruminants, requires rapid and precise diagnostic methods. The diversity of BTV serotypes, coupled with their high genetic and antigenic variability, poses substantial challenges for disease control and prevention. To address this, multiplex Magpix assays were developed for the simultaneous and accurate detection of BTV serotypes and topotypes. Primers and probes were designed to target segment 2 (Seg-2) of the BTV genome, a highly variable region that enables serotype-specific identification using probes conjugated to magnetic beads.The developed Magpix assays facilitate the identification of multiple BTV serotypes from a single sample. Five multiplex Magpix assays were created to detect eastern and western strains of 12 distinct currently circulating BTV serotypes (1, 2, 3, 4, 5, 9, 10, 12, 16, 21, 23, and 24) in India to align with the current epidemiological landscape. These assays were categorized as follows: eastern assays-E1 (1e, 2e, 4e), E2 (3e, 9e), and E3 (16e, 21e, 23e); and western assays-W1 (1w, 10w, 12w) and W2 (2w, 5w, and 24w). The detection limits varied across assays, with E1 showing a higher detection limit (500 pg) compared to E2 (50 pg), E3 (50 pg), W1 (5 pg), and W2 (5 pg). Importantly, the assays exhibited no cross-reactivity with other related viruses.These five multiplex Magpix assays provide an effective diagnostic tool for identifying circulating BTV strains in India. Additionally, the system offers flexibility for expansion to include more serotypes as needed, enhancing its utility for BT surveillance and control. In summary, the introduction of these advanced diagnostic methods presents a significant opportunity for more strategic and effective management of BTV, thereby ensuring better protection for both livestock and the livelihoods dependent on them.

Orbiviruses are emerging pathogens of public and veterinary health concern. This study reports the discovery and genomic characterization of a novel orbivirus in adult ticks collected from African savanna elephants (Loxodonta africana) in Kafue National Park, Zambia. Six ticks were identified through genetic analyses; one Rhipicephalus maculatus and five Amblyomma tholloni. Salivary gland and blood meal samples were dissected for virus characterization. Total nucleic acids were extracted and reverse-transcribed, and libraries were prepared for deep sequencing. De novo assembly of trimmed sequences recovered four novel viruses designated "zaloxo" to indicate their association with Zambian elephants (genus Loxodonta), abbreviated ZXLV-1 to ZXLV-4. ZXLV-1, a member of the genus Orbivirus, belongs to the same subclade of dsRNA orbiviruses as bluetongue virus, epizootic hemorrhagic disease virus, and African horse sickness virus. ZXLV-2 and ZXLV-3 are most closely related to dsRNA Totiviridae and ssDNA Circoviridae viruses, respectively. ZXLV-4 belongs to the genus Alphapolyomavirus, dsDNA viruses which are ubiquitous in mammals but have unclear associations with disease. While the pathogenicity of these viruses remains unclear, these results suggest that a hidden diversity of viruses likely exists in elephant ectoparasites, warranting attention from the perspective of both health and conservation.

Celavirus is a genus within the family Potyviridae, currently comprising a single recognized species, Celavirus apii, represented by celery latent virus (CeLV), and one additional potential member, Striga-associated poty-like virus 2 (SaPlV2). The Celavirus genome is highly divergent from those of other potyvirids, and its polyprotein architecture remains incompletely resolved. In this study, we conducted systematic mining of publicly available transcriptome datasets and identified eight novel celavirus-like viral genome contigs from five distinct sources, including Chrysanthemum × morifolium, Leucadendron linifolium, L. muirii, Dalzellia ubonensis, and mycorrhizal protocorms formed by Serapias vomeracea and Tulasnella calospora. Based on sequence comparisons and species demarcation criteria, these genome contigs likely represent four novel viral species. Phylogenetic analysis placed all novel viruses in a monophyletic clade with CeLV and SaPlV2, distinct from all other approved genera in the family Potyviridae. Conserved functional domains typical of potyvirid polyproteins, including CI, NIa-Pro, and NIb, were identified, whereas other canonical domains such as P1, HC-Pro, and CP were not detected, likely due to high sequence divergence. These findings expand the known diversity of Celavirus and offer new insights into its genome organization, host associations, and evolutionary position within the Potyviridae.

This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.

Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.

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.

The H3 avian influenza virus (AIV) is a common avian pathogen, widely prevalent among domestic poultry and wild birds. In China, H3N8 AIVs led to two confirmed cases of human infection in 2022, followed by a deadly case in 2023. In 2019, an H3N8 AIV was identified in chickens monitored within live poultry markets of eastern China. To investigate the genetic connections between these eastern Chinese AIV strains and other influenza viruses, we sequenced all gene segments of these strains and performed a comparative analysis with sequences retrieved from the GenBank database. We performed phylogenetic analysis and molecular characterization of the virus and then assessed the viral growth kinetics and pathogenicity in mice. The results demonstrated that the H3N8 AIV possesses genetic features of H3, H4, H7, and H10 AIVs, which have been identified in ducks and chickens in China. The strain could stably replicate in DF-1, MDCK, and A549 cells. In animal experiments, the strain demonstrated moderate pathogenicity and replicated in mice without prior adaptation. In conclusion, a reassortment occurred between AIVs from diverse avian hosts, and the ongoing dissemination of H3N8 AIVs may pose a threat to human health.

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.