Virus Genes最新文献

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.

Influenza viruses pose significant public health challenges, causing seasonal epidemics with high morbidity and mortality. This study sequenced influenza viral RNA from hospitalized patients with severe acute respiratory illness in Sri Lanka using an amplicon-based approach on the Illumina platform. Raw sequencing reads were quality checked using FASTP and Trimmomatic. Assembly was performed with SPAdes, and subtype identification was conducted using ABRIcate. Phylogenetic trees for HA and NA genes were generated in MEGA X and Geneious Prime and visualized with iTOL. Data analysis was performed using Galaxy and INSaFLU. Nineteen patient samples from different regions were successfully sequenced, identifying influenza A H1N1 (7/19), H3N2 (6/19), and influenza B (6/19). Notably, co-infection with H1N1 and the SARS-CoV-2 Omicron variant was observed, along with the co-circulation of influenza A H1N1, H3N2, and B strains in 2023. Molecular analysis revealed that all H1N1 and H3N2 strains carried mutations consistent with global strains. Influenza B strains also aligned with global trends. Key mutations affecting antigenicity and receptor binding were identified, highlighting viral evolution. This study explores the molecular evolution of influenza viruses in Sri Lanka (2021-2024) post-COVID-19. Findings underscore the need for continued molecular surveillance to inform public health strategies, particularly regarding co-infections and emerging mutations. However, this study did not assess the association between influenza genomic characteristics and disease severity; thus, future research could explore potential links between specific mutations, clades, or co-infections and clinical outcomes.

Chickenpox, caused by the Varicella Zoster Virus (VZV), presents as varicella (chickenpox) during primary infection and as herpes zoster (shingles) upon reactivation. With a high infectivity rate and transmission through airborne droplets and contact, VZV poses a significant public health challenge. While the disease is self-limiting, complications such as encephalitis and pneumonia can occur, particularly in unimmunized individuals and those with weakened immune systems. The introduction of varicella vaccination has significantly reduced incidence and complications in countries with universal vaccination programs, but India is yet to incorporate this vaccine into its national immunization schedule. In June 2023, an outbreak of varicella was reported in Biswanath district, Assam, affecting 18 individuals. The outbreak highlighted the impact of factors such as overcrowding, poor ventilation, and inadequate medical intervention. Clinical symptoms included fever, vesicular rash, and severe abdominal pain, with three fatalities linked to severe complications. Molecular and serological investigations confirmed VZV infection in the cases, and whole genome sequencing (WGS) identified the strain as belonging to Clade 5. Phylogenetic analysis revealed the strain's similarity to other Indian VZV sequences, aligning with the established VZV clade nomenclature. The outbreak investigation underscored the importance of timely medical intervention and effective vaccination strategies. Enhanced surveillance, community awareness, and a coordinated response involving various health stakeholders are crucial for managing varicella outbreaks and improving vaccination coverage. This study represents the first comprehensive genomic analysis of VZV from Northeast India, providing valuable insights into the strain circulation and reinforcing the need for vaccination and preventive measures.

Foot-and-mouth disease (FMD) is a highly infectious viral infection that has a significant economic impact on livestock farming worldwide. The adaptability of a field isolate of FMDV virus for rapid isolation and production of a high antigen titer is one of the concerns of vaccine preparation, which can delay and endanger effective control programs. During a period between 2019 and 2020, a total of 63 oral epithelial samples were collected from vaccinated cattle. These samples were first analyzed and typed to identify the virus using ELISA method. Subsequently, the field virus was isolated using two continuous cell lines, BHK-21 and IB-IS2. Cytopathic effects (CPE) were observed under an inverted microscope, and then viral titration of isolated viruses was determined. Of 63 samples received from 2019 to 2020, 50 samples (79.36%) were reported positive by type-specific ELISA and typed as follows: 32 samples (64%) were type O, and 18 samples (36%) were type A. Of 50 positive samples, 38 samples (76%) were isolated in the IB-IS2 cell culture (26 samples type O, 12 samples type A) and 12 samples (34%) were isolated in the BHK-21 cell culture (9 samples type O, 3 samples type A) during three consecutive passages. The mean virus titration of isolated viruses was 10^-3.4 TCID₅₀ in the IB-IS2 cell line and 10^-4.2 TCID₅₀ in BHK-21 cell line. 26 samples that were initially isolated on the IB-IS2 cell line but not on the BHK-21 cell line were successfully isolated on the BHK-21 cell line after three consecutive passages of culture on the IB-IS2 cell line. In these samples, an average increase of about 10^-1.08 in TCID50 was observed. Although both studied cell lines are suitable for the culture of Foot-and-mouth Disease virus, the IB-IS2 cell line is particularly suitable for the isolation of field viruses. While according to the virus titer (TCID50) produced in the BHK-21 cell line, this cell line is suitable for large-scale virus culture and appropriate for the production of inactivated vaccines.

Adenoviruses are non-enveloped, double-stranded deoxyribonucleic acid (DNA) viruses that belong to the family Adenoviridae. Human adenovirus (HAdV)-55 is associated with severe respiratory illnesses that often lead to respiratory failure and death. HAdV-55 caused a febrile respiratory illness (FRI) outbreak at a military base in the Republic of Korea. The Army Forces Capital Hospital provided DNA samples from 79 patients with FRI; among them, we obtained seven whole-genome sequences of HAdV-55 using next-generation sequencing. Phylogenetic analysis of the complete genome and penton base, hexon, and fiber gene sequences demonstrated type-specific genetic clustering among the seven HAdV-55 strains. We also demonstrated protein modeling, molecular phylogeny, and evolution based on whole-genome sequences of seven HAdV-55 isolates characterized using next-generation sequencing and bioinformatics. Additionally, HAdV-55 strains from different countries have contributed to multiple lineages and genetic evolution. Our findings provide important insights into the evolution, molecular phylogeny, protein modeling, and genome sequencing of HAdV-55 isolates. Further studies are needed to better understand the genetic variants of emerging or re-emerging HAdVs.