Virus Genes最新文献

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.

Rift Valley fever virus (RVFV) is a newly discovered arboviral pathogen that infects humans and livestock. Numerous outbreaks have occurred in Africa and the Arab Peninsula. Epizootics of RVFV are sporadic and frequently associated with ongoing floods and excessive rainfall. This leads to the development of infected Aedes mosquitoes, which then amplify transmission by other mosquito species (like Anopheles and Culex genera). In animals, it typically results in high rates of death and abortion. In humans, Rift Valley fever (RVF) manifests as clinical symptoms that may vary in intensity from minor to severe. Common symptoms include retinitis, hepatitis, delayed onset encephalitis, and hemorrhagic illness. The possibilities for containing RVFV outbreaks are limited due to the lack of authorized human vaccinations and treatments. Although molecular detection techniques are available, they can only recognize viral nucleic acids during the short viremic phase. There are currently no specific treatments for RVFV infection. Ribavirin is one of the few therapies for viral hemorrhagic fevers, but severe adverse effects restrict its use. Significant studies have been done in recent years on using Nanotechnology to diagnose and treat viruses. This review summarizes the common and recent diagnostic and therapeutic approaches for RVFV, including nanoparticles, intravenous immunoglobulin (IVIG), stem cells, vaccines, and antibody-based therapies.

The H9N2 subtype of avian influenza virus (AIV) is a critical pathogen responsible for avian infectious diseases, inducing respiratory symptoms in poultry and exhibiting high susceptibility to coinfections, which complicates clinical diagnosis. In this study, we designed specific primers and probes targeting the hemagglutinin (HA) gene of H9N2 AIV and developed a real-time fluorescent reverse transcription recombinase-aided isothermal amplification (RT-RAA) assay through systematic optimization of reaction components and conditions. The established method demonstrated exclusive reactivity with the H9N2 subtype, yielding negative results for all other tested viral pathogens, thereby showcasing high specificity. Analytical sensitivity testing revealed the capability to detect as low as 13.5 copies/μL of H9N2 viral RNA, indicating superior sensitivity. To further validate the practical application of this method, a total of 48 clinical samples, comprising oropharyngeal and cloacal swabs, were tested using the developed RT-RAA assay. The results revealed a positivity rate of 79%, reflecting strong diagnostic performance. This study presents a rapid RT-RAA assay characterized by high specificity and sensitivity, offering a robust technical platform for the immediate identification of H9N2 AIV and facilitating epidemiological surveillance in avian populations.

Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.

MicroRNAs, abbreviated as miRNAs, have a substantial impact on viral infections through their ability to control gene expression and influence the interactions between the host and the virus. This work investigates the capacity of miRNAs to selectively inhibit the expression of rabies virus genes, specifically Nucleoprotein N, Phosphoprotein M1 and M2, Transmembrane Glycoprotein G, and L protein. The 7mer-m8 model was utilized to identify human miRNAs that target these viral genes. The interactions between the miRNAs and the genes were then assessed based on binding energy, GC content, and stability. The findings indicated that miRNAs, including miR-1279, miR-4251, miR-4288, and miR-12117, successfully target the N gene. In addition, other miRNAs target the remaining viral genes, indicating their capacity to bind and potentially inhibit viral replication. In addition, docking experiments have verified the stability of miRNA-mRNA duplexes, as evidenced by the high free energy values that indicate strong and reliable contacts between miRNA and gene. These findings indicate that certain human miRNAs have the potential to be effective therapeutic agents against the rabies virus by suppressing gene expression. This offers a new and innovative strategy to fight against this deadly infection.

Curative drugs are needed for the treatment of viral infections. Small interfering (si)RNA offer such a prospect but require the development of safe, effective and non-hepatotropic subcellular delivery systems. Here, 5 candidate siRNA molecules targeting defined sequences within the Zika Virus (ZIKV) genome were assayed for their ability to reduce ZIKV induced cytopathic effects in vitro. The protection of Huh-7 cells from ZIKV cytopathic effects was recorded after electroporation and the siRNA Feron-Zv2, resulting in 122.7 ± 5.3% cell viability (n = 3 ± standard error of the mean (SEM), 100 nM siRNA) after exposure to ZIKV relative to a virus treated control (35.2 ± 7.1% cell viability (n = 3 ± SEM)). Protection of BHK-21 cells was recorded after transfection with an attenuated anthrax toxin containing an RNA binding domain. Treatment with Feron-Zv4 resulted in 75.1 ± 2.9% cell viability (n = 3 ± SEM, 25 nM siRNA) after exposure to ZIKV. This protection was mirrored by a system containing octameric PA where a maximum of 86.2 ± 4.4% cell viability was reported (n = 3 ± SEM, 75 nM siRNA) after treatment with Feron-Zv2. Scrambled siRNA afforded no measurable protection. Here we report for the first time that siRNA delivered by either attenuated anthrax toxin or octamer forming ATx can protect mammalian cells from ZIKV cytopathic effects.

The human respiratory syncytial virus (HRSV), recently known as the human orthopneumovirus (HOPV), continues to generate new variants with the ability to cause recurrent infections. Data regarding HRSV-B evolution and genetic diversity in Riyadh, Saudi Arabia, are very limited. Therefore, the current study was designed to investigate the prevalence, genetic diversity, and evolution of HRSV-B. A total of 200 nasopharyngeal aspirate (NPA) samples from hospitalized children at King Khaled University Hospital were screened for the presence of HRSV-B. The second hypervariable region (2nd HVR) of the G gene from all 37 HRSV-B genotypes was used to study sequences and family trees. Of the 200 screened nasopharyngeal samples (NPAs), 16 (8%) were positive for HRSV-B, with a high incidence rate in the age group of 2 to 5 months. The analysis of the 2nd HVR region's sequence showed several differences, such as point mutations, different protein lengths, sequence gaps, duplication regions, and glycosylation sites. A total of 46-point mutations were reported, of which 29 changed their corresponding amino acid residues. N-linked glycosylation sites in Riyadh strains were 3, whereas O-linked glycosylation sites ranged from 22 to 32. Phylogenetic analysis revealed that Riyadh strains from the seasons 2019/20 and 2022/23 are grouped into the subclade BA-11. Other Riyadh strains from different previous seasons were clustered into different sub-genotypes (BA-9, -10, and -12). Seasonal surveillance and molecular evolution tracking of HRSV-B is essential for the early detection of viral genotypes that might cause severe illness consequences and widespread transmission.