Virus Genes最新文献

Human retroviruses such as HIV-1 and HTLV-1 hijack host cellular mechanisms for their replication, survival, and pathogenesis, often causing profound genomic instability. This review explores the dual role of homologous recombination (HR), explicitly mediated by the recombinase RAD51, in the context of retroviral infections. RAD51 is central to high-fidelity repair of DNA double-strand breaks, yet its activity is manipulated differently by HIV-1 and HTLV-1. In HIV-1 infection, RAD51 expression is elevated by viral proteins like Tat and Vpr, promoting DNA repair and enhancing viral transcription through interactions with NF-κB, thereby supporting viral persistence. Conversely, HTLV-1 suppresses RAD51-mediated HR via viral proteins such as p30 and Tax, promoting error-prone DNA repair pathways that contribute to oncogenesis. These contrasting effects may underscore RAD51's functional plasticity as both a facilitator of viral replication and a potential antiviral restriction factor. Furthermore, the therapeutic modulation of RAD51 activity-especially in combination with PARP inhibitors offers promising avenues for treating retrovirus-associated malignancies such as adult T-cell leukemia/lymphoma. This review highlights RAD51 as a pivotal connection in the interplay between genome stability and retroviral pathobiology.

Rabies, a neglected tropical zoonotic disease caused by the rabies virus (RABV), results in fatal encephalitis in both humans and animals. India, a high-burden country, accounts for nearly 30% of global rabies-related deaths. Robust surveillance combined with large-scale genomic sequencing of RABV is essential to monitor viral spread, evolution, and diversity, critical for developing targeted interventions. However, the lack of comprehensive whole genome data on Indian RABV isolates hampers detailed molecular epidemiological analysis. In this study, 630 RABV-positive samples from diverse hosts and regions across India were sequenced using an amplicon-based Illumina workflow. Phylogenetic analysis identified the Arctic-like 1a lineage as predominant, exhibiting high genetic homogeneity. Additionally, Arctic-like 1b and the Indian subcontinent lineages were detected, indicating the presence of co-circulating strains. Geographic clustering observed at the state level suggested localised transmission with limited inter-state viral movement. Mutation and selection pressure analyses revealed conserved amino acid substitutions in the glycoprotein, without alterations in key antigenic sites. These findings underscore the feasibility and significance of large-scale genomic surveillance of RABV in India, pivotal for informing effective rabies control strategies and advancing the global goal of eliminating dog-mediated human rabies deaths by 2030.

Genomic surveillance of respiratory viruses is an expanding field. As of 2024, only 110 (near-) complete genomes of human parainfluenza virus type 2 (HPIV2) were available in GenBank, none being from France. Here we aimed to obtain and analyze HPIV2 genomes from residues of HPIV2 RNA-positive respiratory samples from patients diagnosed in university hospitals of Marseille, Southern France, between 2017 and 2022. Prior to next-generation sequencing (NGS), an in-house PCR-based enrichment strategy was implemented with primers chosen with PrimalScheme. NGS used Illumina technology on a NovaSeq 6000 instrument. HPIV2 genomes were generated from NGS reads by mapping and de novo assembly using CLC Genomics. Mutations were identified by NextClade, and phylogeny was performed by MEGA and NextClade. Seventy-seven near-complete (≥ 90% coverage) genomes and 239 genomes with ≥ 70% coverage were recovered from 318 HPIV2 RNA-positive samples. Two major genotypes, G1a (n = 129 genomes) and G3 (110), were identified, and five subgenotypes, namely G1a.5 (n = 23 genomes), G1a.8 (68), G3.4 (4), G3.5 (7), and G3.7 (23), were newly proposed. Genotype-specific mutations were in the L gene (encoding RNA polymerase) for G1a (T14612A/T11981A/T12374C) and the hemagglutinin-neuraminidase-encoding gene for G3 (G8171A/A14057G/10367G). Subgenotype G3 was only detected in 2019. Subgenotype G1a was absent during the 2021-2022 winter, before becoming majority again during autumn 2022. Although preliminary, this work increased by 70% the number of HPIV2 genomes available worldwide and produced the first genomes from France. It shows an evolution of genotypes, with significant genetic diversity, and of their distribution. It justifies the genomic surveillance of this virus.

Bovine parvovirus 2 (BoPV-2), officially classified as Ungulate copiparvovirus 1 by the ICTV, and Bopivirus A, a recently recognized picornavirus, are poorly characterized viruses sporadically reported in cattle worldwide. Here, we describe the first detection of BoPV-2 and Bopivirus A in Iran-and potentially the Middle East-through RNA-seq analysis of a diarrheic neonatal calf. Four BoPV-2 contigs (82-85% nucleotide identity; 91-100% amino acid identity) were identified, clustering within the Ungulate copiparvovirus 1 clade, while the Bopivirus sequence grouped with Chinese strains BoP8 and BoP9, supporting its classification within lineage A2. Both viruses were confirmed by phylogenetic analyses based on partial RdRp (3Dpol) and ORF regions. The concurrent detection of these viruses in a single calf suggests possible co-circulation in early-life gastrointestinal infections, highlighting the complexity of the calf virome. Notably, RNA detection of the DNA virus BoPV-2 in fecal material indicates potential intestinal replication and shedding, raising questions about its transmission dynamics. These findings expand the geographic range of BoPV-2 and Bopivirus A and underscore the value of metagenomic surveillance for uncovering under-characterized viral agents contributing to neonatal calf diarrhea.

Vesicular stomatitis virus (VSV) is a zoonotic infectious disease that severely impacts the livestock economy. Infection causes vesicle formation, epithelial cell lysis, and severe interstitial edema, accompanied by inflammatory cell infiltration. It can also infect humans and result in a 3 to 5-day illness characterized by fever, headache, fatigue, and muscle aches. (Phosphoribosyl pyrophosphate synthetase 2) PRPS2, a core rate-limiting enzyme in purine and pyrimidine nucleotide biosynthesis, is a key regulator of nucleotide metabolism. In this study, we found that knockdown of PRPS2 significantly attenuated VSV-GFP infection efficiency and suppressed viral replication. Conversely, overexpression of PRPS2 promoted VSV-GFP replication. Further mechanistic exploration revealed that PRPS2 knockdown enhanced IRF3 phosphorylation and upregulated the transcription of IFN-β, CXCL10, and ISG56. This study demonstrates that PRPS2 likely regulates the host innate immune response by modulating IRF3 phosphorylation, thereby influencing VSV replication. These findings reveal the role of PRPS2 in host antiviral immunity and deepen the theoretical understanding of VSV-host interactions.

One challenge in utilizing the Measles virus (MV) for cancer therapy is the number of virus particles required, nearly a million times greater than the amount reported for vaccination. This study aims to design and develop a cell line with increased production capacity to supply the required amounts of MV in oncolytic virotherapy. The sphingosine kinase 1 (SphK1) gene was inserted into a pIRES2-EGFP plasmid and transiently transfected into four cell lines: MRC-5, HEK293, Vero, and A549. Fluorescent light intensity was measured using flow cytometry, and the MV production titer was determined using the TCID50 method. Transient transfection of pIRES2-EGFP-SphK1 was associated with increases in MV yield of approximately 3 logs in HEK293, 2 logs in Vero and A549, and 1 log in MRC-5 cells compared to controls and has impacted the morphology of MRC-5 cells. The top 100 genes co-expressed with SphK1 were identified with the ARCHS4 RNA-seq data resource, and functional enrichment with EnrichR suggested involvement in interleukin and cytokine signaling, extracellular matrix organization, and stress responses. The observed results indicate that augmenting the expression of the SphK1 gene may enhance MV production and influence cellular behavior, although effects appear to be cell line-dependent. A better understanding of cell-specific S1P signaling and cytoskeletal regulation could assist in optimizing cell lines for scalable virotherapy production.

Dengue is a major public health problem that affects millions of people globally. The present study used microarray data to identify differentially expressed genes (DEGs) during dengue clinical conditions. The microarray datasets GSE84331, GSE18090, GSE43777, and E-MTAB-3162 were downloaded and analyzed using statistical analysis (Unpaired t-test). This was followed by Machine Learning (ML) and Deep Learning (DL) techniques with recursive feature elimination and genetic algorithms implemented to identify the potential biomarkers. Further, functional enrichment, platelet signaling, and protein-protein interaction (PPI) network analysis were performed to explore the potential diagnostic markers associated with dengue. Among all ML/DL models, the Random Forest algorithm outperformed on baseline data and identified 27 DEGs in the dengue fever (DF) vs. control (C) group and 13 DEGs in filtered data of the severe dengue (SD) vs. DF group. Likewise, the Support Vector Machine with Genetic Algorithm (SVM-GA) hybrid model outperformed the SD vs. C group and identified 79 DEGs. Based on the analysis, the study identified seven hub genes such as PIK3R1, GATA3, ZFPM, SKAP1 (involved in hemostasis, platelet activation, aggregation, and production), TP63, ZBTB20, and ZEB2 (abnormal hard palate morphology) for dengue diagnosis. Further, the hub genes may facilitate the development of reliable diagnostic potential; their prognostic utility requires further validation in larger, more diverse cohorts.

In the present study, the full-genome sequence of a novel potyvirus, provisionally named "Sauropus androgynus potyvirus 1" (SAPV1), was determined using a combination of high-throughput sequencing (HTS) contig assembly, reverse transcription polymerase chain reaction (RT-PCR), and rapid amplification of cDNA ends (RACE) PCR. The full-genome sequencing of SAPV1, excluding the 3' poly(A) tail, was 10,365 nucleotides long and encoded a large polyprotein comprising 3,315 amino acids. Maximum likelihood phylogenetic analysis based on the multiple sequence alignment of the polyprotein sequence revealed that SAPV1 clustered with the genus Potyvirus as a monophyletic clade, with its closest evolutionary relative being the Plum pox virus (PPV). BLAST searches revealed that the polyprotein sequence of SAPV1 shares the highest amino acid sequence identity of 45.6% with known viruses, with the highest being PPV. According to the species demarcation criteria of the family Potyviridae and the phylogenetic analysis, we propose that SAPV1 represents a novel member of the genus Potyvirus, infecting Sauropus androgynus, a plant widely used in medicine and the food industry.

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.