Virus Genes最新文献

Henan Province is rich in livestock and poultry resources, home to well-known local breeds, including Gushi, Lushi, and Luohé Ma chickens. These breeds are of substantial agricultural and economic importance and play a pivotal role in preserving biodiversity as well as fostering genetic innovation. Avian leukosis (AL) is a major viral disease affecting the poultry industry, with the J subgroup of avian leukosis virus (ALV-J) emerging as a significant cause of economic losses. In this study, we performed reverse transcription -polymerase chain reaction (RT-PCR) identification on chickens suspected of ALV infection based on clinical symptoms and pathological changes in the parent stock breeder farm of Luohé Ma chicken in Henan Province, and isolated the virus from the samples initially identified as positive. Indirect enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescent antibody (IFA), transmission electron microscopy (TEM), and phylogenetic tree analysis were used to further determine whether ALV infection existed and its infection subtype. The results demonstrated that ALV infection did exist in the breeding farm of the Luohé chicken parents, and we successfully isolated and obtained an ALV strain, which was named HN-1. The RT-PCR results showed that only the gp85 gene sequence of the ALV-J subtype was amplified, and the nucleotide sequence was submitted to GenBank, where it was assigned the accession number PQ010741.1. Its genetic evolutionary relationship was most closely related to the ALV-J subtype strain FJ201307. In conclusion, our findings indicate the presence of ALV-J infection in this chicken farm and remind us that appropriate measures should be taken before ALV-J outbreaks to minimize economic losses.

This comment raises concerns about the validity and reproducibility of a publication by Li et al. in Virus Genes (60:488-500, 2024. https://doi.org/10.1007/s11262-024-02096-1 ; PMID: 39103702), which aimed to investigate the role of aquaporin-3 in nasopharyngeal carcinoma (NPC) and its regulation by the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1). The central criticism focuses on using the CNE-1, CNE-2, and HONE-1 cell lines, which are recognized as unreliable for NPC research. There is an alarming prevalence of publications that continue to utilize these compromised cell lines, impeding genuine advancements in understanding NPC. Beyond the cell line authenticity issue, the study lacks relevant methodological information and justification for experimental design choices. We emphasize the need for raw data availability and comprehensive methodological information to ensure reproducibility. Ultimately, this comment calls for a more rigorous and multi-faceted approach to quality control in scientific publishing and embracing Open Science principles to ensure the reliability of published research.

Transcriptions of nascent HIV-1 RNA from the integrated proviral DNA, and HBV RNAs from a stably formed minichromosome of cccDNA, are carried out by cellular RNA polymerase II, and strongly regulated by viral transactivation proteins Tat and HBx, respectively. Both Tat and HBx are intrinsically disordered proteins with promiscuous gene transactivation activities and regulate HIV-1 and HBV transcription by multiple, but similar mechanisms. The antiviral therapies of HIV-1 and HBV effectively suppress viral replication and enable the infection into latent states. The viral life cycles of HIV-1 and HBV differ significantly, but the core mechanisms of T-cell depletion are intertwined. Consequently, future therapeutic interventions must encompass a dual strategy of viral clearance and immune reconstitution. A functional cure would be achieved by combining checkpoint inhibitors, specific T-cell activators, and drugs targeting viral persistence.

The global public health is still at risk due to the COVID-19 pandemic, which was caused by SARS-CoV-2. Disease severity varies among patients and is influenced by mutations in the viral genome, particularly within the spike protein's receptor-binding domain (RBD). This study aimed to investigate the association between RBD mutations and disease severity and to shed light on the fundamental molecular mechanisms. Nasopharyngeal and oropharyngeal samples were obtained from 70 COVID-19 patients in Iran, including 35 mild and 35 deceased cases. The RBD region of the spike protein gene underwent amplification through reverse transcription-polymerase chain reaction (RT-PCR) and was subsequently sequenced using Sanger sequencing. The impact of RBD mutations on binding affinity to human ACE2 (hACE2) was assessed by molecular docking analyses. Sequence analysis identified seven nonsynonymous mutations within the RBD region. The N501Y mutation, which was the most prevalent, showed a significant correlation with disease severity. Molecular docking revealed that the N501Y substitution enhanced binding affinity to hACE2 by increasing hydrophobic interactions and altering the interaction patterns of neighboring residues. This study demonstrates that the N501Y mutation has an independent association with increased severity of COVID-19, likely due to its effect on strengthening the RBD-hACE2 interaction. Further studies involving larger cohorts and diverse populations are necessary to confirm these results and to explore their potential implications for disease management and therapeutic strategies.

Classical swine fever virus (CSFV) is a pathogen that affects pigs and wild boars. This contagious RNA virus is a high threat to swine industries throughout the world because it has high mortality and morbidity rates, leading to economic losses. Although some studies have analyzed whole-genome sequences, but often focus on isolates from only a few countries, while others started with whole-genome analysis before narrowing down to specific gene region like E2. In addition, several studies have predominantly focused on isolated geographic regions. Our study leverages a global dataset of 220 CSFV whole-genome sequences retrieved from the NCBI repository along with two CSFV complete genome sequence from our laboratory (Accession Number: MH734359.1 and OR4282229.1) and carefully curated to 66 sequences. The refined dataset was subjected to Bayesian analysis along with selection pressure analysis. The outcome of this experiment, the mean substitution rate was estimated at 2.06 × 10^-3 substitutions/site/year with the Highest Posterior Density (HPD) (95% HPD 6.8012 × 10^-4 to 3.3044 × 10^-3), and the estimated average time to the most recent common ancestor (tMRCA) for the analyzed dataset was the year 1877 (95% HPD 1833.8181-1932.3176). Among the curated dataset, 2 CSFV complete genome sequences (Accession Number: MH734359.1 and OR428229.1) from our laboratory showed a Chinese origin. In addition, pervasive and episodic selection pressure revealed that both had ongoing diversifying natural positive selection, which could lead to increased genetic diversity and possibly emergence of the new lineage. This potential information could be used for future evaluation of strategies to control emerging new genotypes of CSFV with high mortality and morbidity.

Gastric cancer (GC) ranks as the fourth most common cancer worldwide and is a leading cause of cancer-related deaths globally. The development of GC is influenced by multiple factors. This study aimed to detect the presence of Epstein-Barr virus (EBV) and JC virus (JCV) in cancerous, non-malignant, and control tissue samples using polymerase chain reaction (PCR) methodology. In this descriptive cross-sectional study, we analyzed 150 paraffin-embedded tissue samples collected over a seven-month period from laboratory archives in East Azerbaijan province. The samples comprised three groups: GC tissues (n = 50), non-malignant gastric tissues (n = 50), and control tissues (n = 50). PCR was performed to detect EBV and JCV. Then, Southern blot analysis was performed for EBV and JCV in PCR positive cases. Data analysis was conducted using SPSS version 18 software with chi-square testing. Among the cancer samples (mean age 61.7 ± 12.01 years), PCR analysis detected EBV in 5 samples (10%) and JCV in 2 samples (4%). The EBV-positive and JCV-positive cases had mean ages of 63.6 ± 13.31 and 61 ± 18.38 years, respectively. No viral DNA was detected in either the non-malignant or control groups. Southern blot analysis was positive in all PCR positive cases. As cancer incidence continues to rise, understanding its risk factors becomes increasingly critical. Our findings demonstrate the presence of EBV and JCV in GC tissues from this geographical region, suggesting their potential role in gastric carcinogenesis. However, the relationship between oncoviruses and GC risk remains understudied. Further research is warranted to elucidate the molecular mechanisms by which these viruses may contribute to GC development.

The use of microbial insecticides in crop fields has been very limited, especially in developed countries, compared with that of synthetic (chemical) insecticides, even though the former are friendly to vertebrates (including humans and livestock), most beneficial insects, plants, and the environment. This lower use rate is attributable mainly to their more expensive commercial production and lower effectiveness compared to synthetic insecticides. The combined use of microbial insecticides and synergistic agents would strengthen the potency of these insecticides and decrease the amounts of the microbial insecticides used. This, in turn, would lead to lower costs and wider adoption. Therefore, it is important to develop an efficient method of the combined use. Natural synergists are generally less harmful to vertebrates and the environment than synthetic synergists. Here, I review recent studies on two major natural synergists derived from insect viruses: the proteins enhancin and fusolin. Enhancin originates from baculoviruses that infect insects, while fusolin is found in the insect virus group entomopoxviruses and in baculoviruses; the fusolin in baculoviruses is also referred to as GP37. In addition, I discuss prospects for the development of technologies for the use of the proteins in the fields, including the improvement of gene expression systems and genetically modified plants, and the engineering of the two proteins.

This study aimed to investigate the prevalence and phylogenetic characteristics of Human T-cell lymphotropic virus type 1 (HTLV-1) among blood donors in Jiroft Province, southeast Iran, a region previously under-studied regarding this virus. A total of 405 blood donor samples were collected from six cities within Jiroft Province. Serum samples were screened for HTLV-1 antibodies using the ELISA method, while peripheral blood mononuclear cells (PBMCs) were analyzed via PCR targeting the long terminal repeat (LTR) and TAX regions of the virus. The study identified 6 out of 405 blood donors (1.5%) as positive for HTLV-1. Prevalence was higher among females (1.6%) compared to males (1.2%), with the age group of 46-64 years showing the highest positivity rate (4%). Phylogenetic analysis revealed that the LTR sequences of HTLV-1 in Jiroft were comparable to those circulating in Mashhad Province, with nine single-nucleotide polymorphisms (SNPs) identified in the LTR region of the isolates. The findings highlight the necessity for routine HTLV-1 screening among blood donors in Jiroft to ensure blood safety and mitigate the risk of transmission through transfusions. This study provides essential baseline data on HTLV-1 prevalence in Jiroft and contributes to the understanding of its genetic diversity, emphasizing the need for further research in this area.

Foot-and-mouth disease (FMD) is a highly contagious viral disease of even-toed animals. Rapid, early, and accurate diagnosis of the disease is important for the swift control of FMD. Although PCR-based assays are being used routinely for the effective diagnosis of FMD, these assays require sophisticated equipment, dedicated manpower, and complex procedures for the detection of amplified viral-genome. Colorimetric isothermal amplification assay with a sharp contrast in colour changes for the positive amplification of viral-genome would be qualified for quick and simple diagnosis of FMDV in both laboratory and field. Here, we report the development and evaluation of FMDV 2B-NSP coding region-based colorimetric RT-LAMP assay for pan-serotypic detection of viral-genome. Addition of 1 mg/ml of bovine serum albumin (BSA) as an additive, could reduce the detection time of the RT-LAMP assay from 60 to 30 min/reaction. Analytical sensitivity test showed that the RT-LAMP assay can detect up to 1000 copies of FMDV genome/reaction, simultaneously, the assay was found specific for the detection of FMDV genome as revealed on testing with serotypes O, A and Asia1 circulating in India during the last two decades. In addition, analysis of 312 clinical samples from various field outbreaks of FMDV in the country showed that RT-LAMP assay exhibited a sensitivity of 96.07%, and a specificity of 100% with an overall accuracy of 97.12%. Therefore, owing to the naked eye distinct visualization of amplified product (pink to yellow colour change), the RT-LAMP assay may facilitate rapid screening of FMD-suspected clinical samples without the use of hazardous DNA-binding dyes and simultaneously prevents aerosolization of amplified product, and subsequent carry over contamination in the diagnostic laboratory.