Virus Genes最新文献

Rhynchosia minima grown at Indian Institute of Pulses Research, Kanpur, India, showed yellow mosaic symptoms on leaves and were suspected to be caused by begomovirus(es). Leaves from five different plants (Rhm1-Rhm5) were tested for the presence of four viruses in PCR. PCR assays revealed the presence of mungbean yellow mosaic India virus in four samples, whereas one sample (Rhm2) was negative. Processing of Rhm2 sample using rolling circle amplification and restriction digestion indicated the presence of DNA molecules of ~ 2.6-2.7 kb. These molecules were sequenced after cloning and found to be of 2741 and 2658 nucleotides in size. BLAST analysis revealed that DNA-A (OQ269467) and DNA-B (OQ269468) molecules of rhynchosia yellow mosaic virus (RhYMV) with 99.09% and 93.74% nucleotide similarity with DNA-A (KP752090) and DNA-B (KP752091) of the RhYMV isolate, respectively. These sequences had a genome organization typical of legume-infecting Old World bipartite begomoviruses. Full genome sequences obtained from Rhm2 are, therefore, considered to be an isolate of RhYMV, designated as RhYMV-IN-Knp. The phylogenetic analysis revealed that RhYMV-IN-Knp was grouped with other isolates of RhYMV followed by Cajanus scarabaeoides yellow mosaic virus. DNA-A of RhYMV-IN-Knp showed two recombination events. The Old World bipartite begomovirus squash leaf curl China virus (AM260205) was identified as the major parent, whereas New World bipartite begomovirus rhynchosia golden yellow mosaic Yucatan virus (EU021216) was identified as the minor parent. RhYMV holds the potential of infecting cultivated legume crops, therefore regular monitoring is crucial especially for pigeonpea breeding programs.

Lumpy skin disease (LSD), a viral disease of cattle, can be acute, subacute, or inactive. It is distinguished by fever and the abrupt emergence of firm, confined cutaneous nodules that usually necrotize. Similar lesions may occur in the skeletal muscles and the mucosae of the digestive and respiratory tracts. It is an enzootic, rapidly explorative, and sometimes fatal infection, characterized by multiple raised nodules on the skin of infected animals. LSDV has a large genome, it is employed as a vaccine carrier, generating a new complex with other viral genes by homologous recombination. This review summarizes our current knowledge of lumpy skin disease (LSD), its impact on animal health, host-pathogen interaction, etiology, signs or symptoms, prevention, and treatment strategies.

Influenza virus neuraminidase inhibitors (NAIs) drug usage can result in NAI resistance, especially in children and individuals with weakened immune systems. The aim of the present study was to identify NAI-resistant variants of IBV and to introduce probable novel mutations, phylogenetic study, and its epitope mapping based on NA gene in patients from Shiraz, Iran. A cross-sectional study was conducted between 2017 and 2018 on symptomatic children. A real-time PCR was run for IBV screening. Then, making use of direct sequencing, amplified 1401 bases of NA gene and phylogenetic tree reconstructed. Epitopes were predicted using ABCpred server. From among a total of 235 specimens, 9.7% were identified with IBV infection. Of them, sequence of NA gene for 17 isolates were analyzed. Phylogenetic analysis showed that 15 isolates belonged to Yamagata clade 3 Wisconsin/01-like subclade and 2 were related to Victoria clade 1 Brisbane/60-like subclade (Vic-1A-2). NA gene sequence analysis showed a total of 52 substitutions in which 27 were for B_Vic and 37 were for B_Yam isolates and 19 were novel substitutions. Only one substitution (S198N) was found in NA active site and T49M, I120V, N198S, N219K, S295R, D320K N340D, E358K, D384G, and D463N were found as probable resistance variants to NAIs. Epitope mapping showed some major differences in our isolates NA gene. Present study was one of the rare comprehensive studies conducted in Shiraz/Iran on IBV resistant associated variants to NAIs. We reported 11.7% mutation in NA active site and some probable NAIs resistant mutations. Epitope mapping confirmed major changes in NA gene which needs broader studies to confirm.

Domestic cat hepadnavirus (DCH) (Orthohepadnavirus felisdomestici) is an emerging virus related to the hepatitis B virus (HBV) already reported in many countries. The molecular prevalence of DCH varies widely in the regions investigated so far. In the present work, we reported the presence of DCH in Brazil. Sixty cat serum samples tested by DCH presence using PCR and 1.67% (1/60) were positive, similar to the low positive molecular rates reported in United States and Japan. The DCH full-length genome was classified in genotype B, which is uncommon since this genotype was only reported once in Japan. The DCH-positive sample was obtained in a stray cat female apparently healthy, presenting ALT, AST, and ALKP normal values, and negative for FIV and FeLV. Due the low positivity rate detected, some factors as alteration in hepatic enzymes and FIV/FeLV infection could not be evaluated. Other works are necessary to statistically validate these observations in Brazil.

Klebsiella pneumoniae is an important gram-negative opportunistic pathogen that causes a variety of infectious diseases. As K. pneumoniae are becoming increasingly resistant to antibiotics, the use of bacteriophages may offer a non-antibiotic-based approach to treat these infections. In the present study, five lytic bacteriophages, 2044307w, k2044hw, k2044ew, k2044302 and 2146hw specific to K. pneumoniae were isolated from hospital sewage and characterized. They belong to group A of the KP32viruses based on transmission electron microscopy (TEM) and genome analysis. These bacteriophages have an extremely narrow host spectrum. The phenotypic characteristics of the phages were determined using lysis assay, pH, and temperature stability tests. This contributes to expanding our understanding of K. pneumoniae phages.

Human immunodeficiency virus type 1 (HIV-1) is characterized by its extremely high level of genetic diversity. The spread of different subtypes in the same population often leads to the emergence of circulating recombinant forms (CRFs) and unique recombinant forms (URFs). At present, the main recombinant subtypes of HIV-1 in China originate from CRF07_BC, CRF01_AE, CRF55_01B and subtype B. Here, we obtained the nearly full-length genomes (NFLGs) from eight HIV-1 infected patients in Guangdong Province, which shared highly similar recombinant patterns, involving two CRF01_AE, one CRF07_BC and two subtype B segments. The eight NFLG sequences own four similar breakpoints as follows: 1220 nucleotide (nt), 2243 nt, 2673 nt, and 5820 nt according to the HXB2 reference sequence, and they therefore were assigned as CRF162_cpx. This is the first complex CRF derived from CRF01_AE, CRF07_BC and subtype B in China. The Bayesian inference of the segments showed that HIV-1 CRF162_cpx was inferred to have approximately originated around 2010-2015. The emergence of CRF162_cpx indicates that the HIV diversity in southeast China constantly accumulates and evolves. Thus, intensive surveillance of HIV-1 molecular epidemiology should be reinforced.

Long noncoding RNAs (lncRNAs) are involved in the host antiviral response, but how host lncRNAs interact with viral proteins remains unclear. The NS1 protein of avian influenza viruses can affect the interferon-dependent expression of several host lncRNAs, but the exact mechanism is unknown. To further investigate the molecular mechanism and functions of NS1 proteins and host lncRNAs, we performed RNA-immunoprecipitation sequencing assays on A549 cells transfected with the H5N1-NS1 gene. We identified multiple sets of host lncRNAs that interact with NS1. The results of the RNA pulldown assay indicated that PIK3CD-AS2 can directly interact with NS1 in vitro. Immunofluorescence confocal microscopy showed that these proteins were colocalized in the nucleus. Further studies revealed that PIK3CD-AS2 can also inhibit the transcription of NS1, which in turn affects the translation of the NS1 protein. PIK3CD-AS2 overexpression regulates NS1 protein-induced cell cycle arrest and initiates apoptosis. We hope this work will help elucidate the molecular mechanisms associated with NS1 proteins in the study of viral infections to promote the development of potential treatments for patients infected with avian influenza A viruses.

Phylogenetic analysis based on whole-genome sequences is the gold standard for monkeypox virus (MPXV) phylogeny. However, genomic epidemiology capability and capacity are lacking or limited in resource poor countries of sub-Saharan Africa. Therefore, these make real-time genome surveillance of MPXV virtually impossible. We hypothesized that phylogenetic analysis based on single, conserved genes will produce phylogenetic tree topology consistent with MPXV whole-genome phylogeny, thus serving as a reliable proxy to phylogenomic analysis. In this study, we analyzed 62 conserved MPXV genes and showed that Bayesian phylogenetic analysis based on five genes (OPG 066/E4L, OPG068/E6R, OPG079/I3L, OPG145/A18R, and OPG150/A23R) generated phylogenetic trees with 72.2-96.3% topology similarity index to the reference phylogenomic tree topology. Our results showed that phylogenetic analysis of the identified five genes singly or in combination can serve as surrogate for whole-genome phylogenetic analysis, and thus obviates the need for whole-genome sequencing and phylogenomic analysis in regions where genomic epidemiology competence and capacity are lacking or unavailable. This study is relevant to evolution and genome surveillance of MPXV in resource limited countries.

Hepatitis B virus (HBV) infection remains a significant global health challenge, with chronic HBV leading to severe liver diseases, including cirrhosis and hepatocellular carcinoma. Current treatments often fail to eradicate the virus, highlighting the need for innovative therapeutic strategies. The CRISPR/Cas9 system has emerged as a dynamic tool for precise genome editing and presents a promising approach to targeting and eliminating HBV infection. This review provides a comprehensive overview of the advances, challenges, and delivery strategies associated with CRISPR/Cas9-based therapies for HBV. We begin by elucidating the mechanism of the CRISPR/Cas9 system and then explore HBV pathogenesis, focusing on the role of covalently closed circular DNA (cccDNA) and integrated HBV DNA in maintaining chronic infection. CRISPR/Cas9 can disrupt these key viral reservoirs, which are critical for persistent HBV replication and associated liver damage. The application of CRISPR/Cas9 in HBV treatment faces significant challenges, such as off-target effects, delivery efficiency, and immune responses. These challenges are addressed by examining current approaches to enhance the specificity, safety, and efficacy of CRISPR/Cas9. A future perspective on the development and clinical translation of CRISPR/Cas9 therapies for HBV is provided, emphasizing the requirement for further research to improve delivery methods and ensure durable safety and effectiveness. This review underscores the transformative potential of CRISPR/Cas9 in combating HBV and sets the stage for future breakthroughs in the field.

Messenger ribonucleic acid (mRNA) was discovered in 1961 as an intermediary for transferring genetic information from DNA to ribosomes for protein synthesis. The COVID-19 pandemic brought worldwide attention to mRNA vaccines. The emergency use authorization of two COVID-19 mRNA vaccines, BNT162b2 and mRNA-1273, were major achievements in the history of vaccine development. Lipid nanoparticles (LNPs), one of the most superior non-viral delivery vectors available, have made many exciting advances in clinical translation as part of the COVID-19 vaccine and therefore has the potential to accelerate the clinical translation of many gene drugs. In addition, due to these small size, biocompatibility and excellent biodegradability, LNPs can efficiently deliver nucleic acids into cells, which is particularly important for current mRNA therapeutic regimens. LNPs are composed cationic or pH-dependent ionizable lipid bilayer, polyethylene glycol (PEG), phospholipids, and cholesterol, represents an advanced system for the delivery of mRNA vaccines. Furthermore, optimization of these four components constituting the LNPs have demonstrated enhanced vaccine efficacy and diminished adverse effects. The incorporation of biodegradable lipids enhance the biocompatibility of LNPs, thereby improving its potential as an efficacious therapeutic approach for a wide range of challenging and intricate diseases, encompassing infectious diseases, liver disorders, cancer, cardiovascular diseases, cerebrovascular conditions, among others. Consequently, this review aims to furnish the scientific community with the most up-to-date information regarding mRNA vaccines and LNP delivery systems.