Virus Genes最新文献

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.

A novel lytic phage with a broad host range was isolated from pig faeces and the complete genome was subsequently sequenced. The phage was found to lyse Staphylococcus hyicus, S. pseudintermedius, S. schleiferi and S. warneri, generating approximately 27 PFU per infected S. hyicus cell. The phage has an isometric head of 42 ± 2 nm in diameter and a noncontractile tail of 114 ± 9 nm long. The genome is 53,660 bp in size and consists of 79 predicted ORFs and one tRNA^Arg gene. The phage has been classified within the Caudoviricetes, specifically the Chaseviridae family. Its broad host range and absence of harmful genes make it suitable for use in phage therapy. In addition, a novel temperate phage was discovered that was spontaneously released from a S. hyicus isolate Pel11 from a pig with exudative epidermitis. This novel temperate phage differs from the known temperate phages in S. hyicus strains NCTC10350, MM2101 or 83/7-1B, representing a novel pathogenicity element in the S. hyicus genome.

Norovirus is the primary cause of acute gastroenteritis outbreaks, considerably impacting children under 5 years, followed by older adults and immunocompromised individuals. As an RNA virus, norovirus exhibits high genetic variability, driven by recombination events at the ORF1-ORF2 junction. This study reports the first detection of the rare norovirus GI.5 [P4] variant in Northeastern Mexico, identified in a single positive isolate (MTY0115; GenBank: PQ369661) from a sample group of 386 individuals, with a prevalence of 0.25%. Notably, norovirus GII was not detected. Phylogenetic analysis of the partial RdRp/VP1 region revealed clustering with global GI.5 [P4] sequences, revealing evolutionary relationships with isolates from Asia, Europe, and America. A recombination event was identified at position 5307 (breakpoint based on reference sequences of GI.5 [P5] and GI.4 [P4]) within ORF1, with genetic inheritance from a GI.5 [P5] isolate from Moscow, Russia, and a GI.4 [P4] isolate from France. Typing classification through sequencing of overlapping ORF1 and ORF2 regions is valuable for understanding genomic variations and their epidemiological impact on at-risk and non-risk populations.