Virus Genes最新文献

A systematic survey across cotton-growing districts of Haryana revealed the occurrence of tobacco streak virus (TSV) in cotton, marking the first documentation of the virus in Northern India. Infected plants predominantly exhibited chlorosis and necrosis of leaves, with necrotic spots varying in size (small to large), color (purplish to purplish-brown), and shape (irregular or ring-like), distributed across the interlobular regions, leaf apex, or the entire lamina. Virus presence was initially detected through serological assay and subsequently confirmed as TSV by sequencing of the coat protein gene in RNA-3 segment. This finding underscores the northward emergence of TSV beyond Southern India, warranting vigilant monitoring and management to mitigate its spread in major cotton-growing regions.

Pigeon paramyxovirus-1 (PPMV-1) is a major cause of mortality in domestic and free-living pigeons worldwide and has the potential to infect chickens, posing risks to the poultry sector. This study investigated a severe outbreak of PPMV-1 in a racing pigeon loft in Srinagar, India, despite routine vaccination with the LaSota strain. Molecular screening of 30 clinical samples identified NDV in 18 birds by real-time qPCR targeting the matrix gene. Histopathology revealed characteristic viscerotropic lesions, including epithelial necrosis and congestion in the proventriculus and duodenum, sinusoidal dilation in the liver, and lymphoid depletion in the spleen, consistent with pathogenic NDV infection. Whole genome sequencing of one of the isolates FVSC-S64 showed a virulent multi-basic cleavage site motif (113-KRQKRF-117) and classified the strain as genotype XXI.1.2. Phylogenetic analysis demonstrated close clustering with pigeon-derived isolates from Pakistan and Eastern Europe, while showing marked genetic divergence from Class I and other Class II strains. Comparative analysis revealed extensive amino acid substitutions within major antigenic regions of the fusion protein, including L69M (A1-A3) and Y337H, T341S, and R349K (A5), along with substitutions in antigenic regions of the hemagglutinin-neuraminidase protein, notably D349S and G494D. Virus neutralization testing showed that sera from LaSota-vaccinated chicken developed strong homologous neutralizing responses but failed to neutralize the FVSC-S64 isolate, demonstrating a pronounced antigenic mismatch. Together, these molecular, pathological, and serological findings provide clear evidence of vaccine escape by an emergent genotype XXI.1.2 PPMV-1 strain and highlight the urgent need for genotype-matched vaccines to improve NDV control in pigeon populations.

Human cellular APOBEC enzymes were largely reported as involved in innate antiviral defenses. We previously highlighted that in SARS-CoV-2 genomes obtained in our center, nearly half of 'hyperfertile' or 'fertile' mutations while 23% of neutral/weakly deleterious mutations had APOBEC signatures. Here we determined that 29% of mutations we named 'lethal' as detected in quasispecies but not in consensus genomes have APOBEC signatures. Overall, these results do not suggest that human APOBEC acts as defense agents against SARS-CoV-2 but as 'Court Jesters', being neither friends nor foes but only enzymes whose activity can either favor or hamper viral fitness according to the Kimura theory of neutral evolution.

Influenza B virus (IBV) is a type of influenza virus. The NS1 protein is a powerful regulatory factor during the process of viral infection of host cells and plays an important role in viral replication, virulence, and innate immunity. Protein-protein interactions play an extremely important role throughout the entire life cycle of viral infection of host cells. Identifying host proteins that interact with IBV NS1 protein is of great significance for exploring the pathogenic mechanism of IBV and screening for new antiviral drugs. In this study, the NS1 protein was purified by immobilized metal affinity chromatography (IMAC) using nickel-charged resin and the known host interactome of IBV NS1 was expanded using Pull-down combined with mass spectrometry (LC-MS/MS). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein-Protein Interaction (PPI) analyses were conducted on the candidate-interacting proteins identified in the mass spectrometry results. These identified candidate-interacting proteins are mainly involved in biological processes such as protein translation, protein folding, mRNA processing, small molecule metabolism, ribosome biogenesis, and viral processes. The heterogeneous nuclear ribonucleoprotein (hnRNPA0) and the DDX39B protein of the DEAD-box RNA helicase family were further studied. Co-IP, IFA, and BiFC all confirmed that the NS1 protein of IBV interacts with the hnRNPA0 and the DDX39B proteins. We further mapped the interaction between the NS1-RBD and NS1-ED domains of NS1 protein and the hnRNPA0-GRD domain. These data provide resources for further research on the mechanism by which NS1 protein modulates host cells.

Human astroviruses (HAstV) are a significant viral pathogen contributing to acute gastroenteritis. This study investigated the molecular diversity of human astroviruses in Riyadh, Saudi Arabia. A total of 1043 stool samples were collected from patients with acute gastroenteritis between July 2022 and June 2023 across five hospitals. Initial screening for HAstV was performed using real-time PCR, followed by PCR amplification and sequencing of the ORF1 capsid region for genotyping. HAstV was detected in 16 (1.53%) of the samples. Among the HAstV-positive cases, 8 patients (50%) were male and 8 (50%) were female. The highest detection rate was observed in the 0-18-year age group (12 cases, 75%). The highest number of infections were recorded in winter (10 cases, 62.5%), followed by autumn and spring (3 cases each, 18.75%). The circulation of two distinct HAstV genotypes, HAstV-1 (93.75%) and HAstV-5 (6.25%), was recorded. Maximum-likelihood phylogenetic reconstruction confirmed the placement of 12 sequences within the HAstV-1 clade, showing low intra-clade divergence. The clear separation of genotypes may underscore the ongoing genetic diversification of HAstV in the region. These findings highlight the importance of molecular surveillance for detecting emerging and circulating genotypes that may influence transmission dynamics or clinical impact.

Introduction: OCI is defined as the presence of hepatitis C virus (HCV) RNA in hepatocytes or peripheral blood mononuclear cells (PBMCs) and the absence of HCV RNA in serum. Two types of OCI are distinguished based on the presence or absence of anti-HCV antibodies: seropositive and seronegative.

Objective: This study aimed to determine the prevalence of seronegative OCI and identify its genotypes in blood donors (BDs) and hospital patients (HPs) from Argentina.

Methodology: Peripheral blood and serum samples were collected from a total of 177 BDs and HPs. All individuals were non-reactive for HCV markers. The samples were analyzed by RT-nested-PCR. In addition, RT-qPCR was performed only on the serum samples. Other serological tests were conducted in all serum samples, and biochemical markers were realized only in Oci-positive serum samples.

Results: Fifteen samples were OCI-positive by RT-qPCR in PBMCs, with an overall prevalence of 8.5%; it was 3.0% BDs and 11.7% HPs, respectively. Genotypes 2 and 3 were identified in all OCI sequences. None of the serum samples were RNA HCV positive. Moreover, two of the total OCI positive were HIV positive, and one had elevated liver enzyme levels.

Conclusion: This study is being conducted for the first time in Argentina and sets a precedent regarding the presence of seronegative for OCI in these populations. Further research is needed in different populations and with a larger number of samples to understand the true prevalence of OCI in the country.

Japanese encephalitis virus (JEV) remains a major health threat across Asia, yet the contribution of genotype-specific variation in the multifunctional NS5 protein to viral fitness is not fully resolved. This study evaluated how sequence differences among JEV genotypes G1-G5 shape NS5 stability and, in turn, replication potential. A unified in-silico workflow combined physicochemical profiling, residue-level substitution mapping, and atomistic molecular dynamics to compare structural stability and conformational behavior across genotypes, with a focus on substitutions predicted to modulate enzymatic performance. Analyses revealed that G5 NS5 maintains a balanced electrostatic environment and persistent hydrogen-bonding networks, yielding greater structural stability than other genotypes. In contrast, G4 NS5 presented a charge imbalance and reduced stability. Simulations consistently supported the robustness of G5 dynamics, with specific substitutions, including Y65, M59, E182, and T191, contributing to improved packing, favorable local interactions, and putative gains in catalytic efficiency. These molecular attributes align with heightened replication capacity and provide a mechanistic rationale for the recent prominence of G5 strains relative to G1-G4. Comprising together, our results demonstrate that genotype-linked substitutions in NS5 directly influence protein stability, replication efficiency, and adaptive potential. Translationally, prioritizing G5-informed NS5 features may guide the design of small-molecule inhibitors and vaccine antigens with broader protective value.

A reverse genetics system for the feline panleukopenia virus (FPV) strain JL2280 was successfully established in this study. By optimizing the cloning strategy for the terminal hairpin structures, a full-length infectious clone, pFPV, harboring a KpnI genetic marker was constructed. The recombinant virus (rFPV) was successfully rescued in CRFK cells and exhibited replication kinetics, pathogenicity, and morphological characteristics comparable to those of the wild-type virus.To evaluate the potential of FPV as a live vector, a recombinant virus expressing enhanced green fluorescent protein (EGFP), designated rFPV-EGFP, was generated by inserting a P2A-EGFP cassette downstream of the NS1 gene. The rFPV-EGFP virus mediated efficient EGFP expression in infected cells; however, the fluorescence intensity gradually diminished with serial passages.The reverse genetics platform developed herein provides a valuable tool for investigating the genomic functions, pathogenic mechanisms, and evolution of FPV. Furthermore, the successful rescue of rFPV-EGFP demonstrates the preliminary feasibility of FPV as a live vector for foreign gene expression. Nevertheless, strategies such as optimizing insertion sites or modifying the viral backbone are required to enhance the stability of exogenous protein expression. This study lays the groundwork for the development of novel FPV-based genetically engineered vaccines and antiviral therapeutics.

Enterovirus G (EV-G) comprises 20 genotypes (G1-G20) associated with various disease conditions in pig populations. Recombination among homologous EV-G drives virus evolution; however, recombination with a virus from a heterologous family is a rare event. Currently, two types of recombinant EV-G strains containing torovirus papain-like cysteine protease (PLCP) at the 2C-3A junction (Type I) and in place of structural proteins (Type II) are reported. The present study was conducted to reveal the RNA virome in diarrheic piglet feces, retrieving the genome coding for a complete polyprotein of EV-G1. The detected EV-G1 strain represents the first Type I recombinant from India. The polyprotein of the strain exhibiting 97% amino acid identity was closely related to the Chinese strain. The molecular clock analysis estimated that EV-G1-PLCP likely emerged around 1989 in Japan (95% HPD), the inferred substitution rate in study strain was a mean evolutionary rate of 1.23 × 10⁻³ substitutions per site per year. Furthermore, the EV-G1-PLCP strain was found to originate from South Korean, Chinese, and Japanese strains with breakpoints at nucleotide (nt) positions 1323 and 4725. Genetic and phylogenetic analysis of VP1 and PLCP of the study strain demonstrated its closeness to EV-G1-PLCP strains from South Korea KOR/KNU-1811/2018/G1-PLCP. The present study advances the knowledge about the genetic evolution of EV-G from gaining virulence genes from different virus families.

Ungulate tetraparvovirus 1 (UTPV1), or bovine hokovirus, has been described in cattle but remains poorly characterized in Southeast Asia. In this study, we report the first detection and genomic characterization of UTPV1 in water buffalo (Bubalus bubalis) from Vietnam. Skin swab samples were collected from a buffalo with nodular lesions in northern Vietnam in 2024, and total nucleic acids were subjected to metagenomic sequencing. Analysis of Illumina MiSeq reads revealed the presence of both lumpy skin disease virus (LSDV) and UTPV1. The near-complete UTPV1 genome (NIVR-B12-2024) shared 90.7-93.3% nucleotide identity with reference strains but did not cluster with genotypes I or II, instead forming a distinct lineage. Phylogenetic analyses supported its independent position, and recombination detection indicated potential genetic exchange between Asian and South American strains. Several amino acid substitutions were identified in the NS1 protein, suggesting ongoing viral diversification. This study provides the first molecular evidence of UTPV1 in water buffalo and in Vietnam, expanding the recognized host range and geographic distribution of this virus. The findings highlight the value of non-invasive sampling and metagenomic sequencing for livestock surveillance and underscore the need for continued monitoring to evaluate the epidemiological significance and potential health risks of UTPV1 in Southeast Asia.