Virus Genes最新文献

{"title":"Characterization and genome analysis of Klebsiella phages with lytic activity against Klebsiella pneumoniae.","authors":"Shanzheng Bi, Hong Peng, Xiao Wei, Changjun Wang, Xiangna Zhao","doi":"10.1007/s11262-024-02123-1","DOIUrl":"https://doi.org/10.1007/s11262-024-02123-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment and application of a duplex fluorescent quantitative PCR assay for H9N2 subtype avian influenza virus and infectious bronchitis virus.","authors":"Wanting Zhou, Qiuyan Mao, Shuning Zhou, Tingting Li, Jie Tian, Xiaoqi Li, Shuo Liu, Cheng Peng, Zhibin Hu, Jinping Li, Guangyu Hou, Houhui Song, Wenming Jiang, Hualei Liu","doi":"10.1007/s11262-024-02121-3","DOIUrl":"https://doi.org/10.1007/s11262-024-02121-3","url":null,"abstract":"<p><p>The H9N2 subtype of avian influenza virus (AIV) and infectious bronchitis virus (IBV) are important avian viruses that cause respiratory symptoms in poultry, and can form mixed infections. In this study, primers and probes were designed based on the HA gene of H9N2 and the 5' noncoding region of IBV, respectively, and a fluorescent quantitative RT-PCR assay was established for simultaneous detection of these two pathogens. The reaction system and conditions were optimized. The method only detected AIV subtype H9N2 and IBV and no other viruses, confirming its high specificity. The assay detected 13.5 copies/μL and 1.66 copies/μL of H9N2 and IBV in clinical samples, respectively. The coefficients of variation for intra- and interassay repeatability were < 3%. The established method was used to analyze 254 clinical samples (oropharyngeal and cloacal swabs) from Hubei Province, China; 98.82% were positive for both pathogens. In summary, a duplex fluorescent quantitative RT-PCR method capable of simultaneously detecting AIV subtype H9N2 and IBV was established. It is specific, sensitive, and reproducible, and can be used for diagnosis of a variety of clinical samples. It provides a technological means for the rapid and simultaneous detection of both pathogens, and thus can facilitate clinical diagnosis and epidemiological investigations.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142636191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization, phylogeny and recombination of Rhynchosia yellow mosaic virus infecting Rhynchosia minima, a wild relative of pigeonpea (Cajanus cajan) from India.","authors":"Mohammad Akram, Naimuddin Kamaal, Deepender Kumar, Dibendu Datta, Aniruddha Kumar Agnihotri","doi":"10.1007/s11262-024-02120-4","DOIUrl":"https://doi.org/10.1007/s11262-024-02120-4","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic characterization of influenza B virus and oseltamivir resistance in pediatric patients with acute respiratory infections: a cross-sectional study.","authors":"Sheida Alizadeh, Fahime Edalat, Arash Letafati, Neda Pirbonyeh, Alireza Tabibzadeh, Leila Mousavizadeh, Afagh Moattari, Mohammad Hadi Karbalaie Niya","doi":"10.1007/s11262-024-02119-x","DOIUrl":"https://doi.org/10.1007/s11262-024-02119-x","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lumpy skin disease: a systematic review of mode of transmission, risk of emergence, and risk entry pathways.","authors":"Bhawanpreet Kaur, Sehajpal Singh Dhillon, Amarpreet Singh Pannu, C S Mukhopadhyay","doi":"10.1007/s11262-024-02117-z","DOIUrl":"https://doi.org/10.1007/s11262-024-02117-z","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The H5N1-NS1 protein affects the host cell cycle and apoptosis through interaction with the host lncRNA PIK3CD-AS2.","authors":"Man Zhang, Yingyue Zeng, Qingqing Liu, Feng Li, Jian Zhao, Zhikui Liu, Hongsheng Liu, Huawei Feng","doi":"10.1007/s11262-024-02118-y","DOIUrl":"https://doi.org/10.1007/s11262-024-02118-y","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling potential gene biomarkers for dengue infection through RNA sequencing.","authors":"Jeyanthi Suppiah, Saiful Safuan Md Sani, Safiah Sabrina Hassan, Nur Iman Fasohah Nadzar, Nurul 'Izzah Ibrahim, Ravindran Thayan, Rozainanee Mohd Zain","doi":"10.1007/s11262-024-02114-2","DOIUrl":"https://doi.org/10.1007/s11262-024-02114-2","url":null,"abstract":"<p><p>Dengue virus hijacks host cell mechanisms and immune responses in order to replicate efficiently. The interaction between the host and the virus affects the host's gene expression, which remains largely unexplored. This pilot study aimed to profile the host transcriptome as a potential strategy for identifying specific biomarkers for dengue prediction and detection. High-throughput RNA sequencing (RNA-seq) was employed to generate host transcriptome profiles in 16 dengue patients and 10 healthy controls. Differentially expressed genes (DEGs) were identified in patients with severe dengue and those with dengue with warning signs compared to healthy individuals. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the functions of upregulated and downregulated genes. Compared to healthy controls, 6466 genes were significantly differentially expressed (p < 0.05) in the dengue with warning signs group and 3082 genes in the severe dengue group, with over half being upregulated. The major KEGG pathways implicated included transport and catabolism (14.4%-16.3%), signal transduction (6.6%-7.3%), global and overview maps (6.7%-7.1%), viral diseases (4.6%-4.8%), and the immune system (4.4%-4.6%). Several genes exhibited consistent and significant upregulation across all dengue patients, regardless of severity: Interferon alpha inducible protein 27 (IFI27), Potassium Channel Tetramerization Domain Containing 14 (KCTD14), Syndecan 1 (SDC1), DCC netrin 1 receptor (DCC), Ubiquitin C-terminal hydrolase L1 (UCHL1), Marginal zone B and B1 cell-specific protein (MZB1), Nestin (NES), C-C motif chemokine ligand 2 (CCL2), TNF receptor superfamily member 17 (TNFSF17), and TNF receptor superfamily member 13B (TNFRSF13B). Further analysis revealed potential biomarkers for severe dengue prediction, including TNF superfamily member 15 (TNFSF15), Plasminogen Activator Inhibitor-2 (SERPINB2), motif chemokine ligand 7 (CCL7), aconitate decarboxylase 1 (ACOD1), Metallothionein 1G (MT1G), and Myosin Light Chain Kinase (MYLK2), which were expressed 3.5 times, 2.9 times, 2.3 times, 2.1 times, 1.7 times, and 1.4 times greater, respectively, than dengue patients exhibiting warning signs. The identification of these host biomarkers through RNA-sequencing holds promising implications and potential to augment existing dengue detection algorithms, contributing significantly to improved diagnostic and prognostic capabilities.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Domestic cat hepadnavirus genotype B is present in Southern Brazil.","authors":"Alaíse Tessmann, Juliana Sumienski, Alexandre Sita, Larissa Mallmann, Gabriela Espíndola Birlem, Nilson Júnior da Silva Nunes, Camila Gottlieb Lupion, Juliana Schaeffer Eckert, Meriane Demoliner, Juliana Schons Gularte, Paula Rodrigues de Almeida, Fernando Rosado Spilki, Matheus Nunes Weber","doi":"10.1007/s11262-024-02115-1","DOIUrl":"https://doi.org/10.1007/s11262-024-02115-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The isolation and serotyping of foot-and-mouth disease virus in Iran during 2019-2022.","authors":"Siamak Khoshnood, Seyed Mahmoud Azimi, Zahra Ziafati Kafi, Hamideh Najafi, Arash Ghalyanchilangeroudi","doi":"10.1007/s11262-024-02116-0","DOIUrl":"https://doi.org/10.1007/s11262-024-02116-0","url":null,"abstract":"<p><p>Foot-and-mouth disease (FMD) is a significant transboundary animal disease that has a considerable economic impact on livestock systems worldwide. In order to determine the presence and type of FMD virus in Iran, a total of 90 samples of vesicular fluid and epithelial tissue were collected from the tongues, tooth pads, and hooves of clinically suspect cattle on 40 vaccinated farms in 9 provinces of Iran. These samples were collected during four years, from January 2019 to December 2022, and the vaccine was a locally produced polyvalent inactivated vaccine. The collected samples were analyzed using ELISA and isolation methods to identify and characterize the FMD virus. The results of the ELISA tests revealed that 66.66% of the samples were positive for FMD, and the serotypes of the virus were determined. Considering ELISA reslut, 62% of the samples were assigned to serotype O, 33% to serotype A, and 5% to serotype Asia-1. Furthermore, 90% of the positive samples were inoculated onto monolayer cultures of pig kidneys (IB-RS2) for isolation and antigen detection by serotype-specific ELISA kit. The great majority of detected serotype O viruses were from Esfahan province, while the most detected serotype A and serotype Asia-1 viruses were from Qom and Tehran provinces, respectively. These findings indicate that the ELISA and isolation methods are suitable for identifying and typing FMD viruses. The vaccination program in Iran, which includes three serotypes (O, A, and Asia-1), appears to be effective in controlling the spread of the disease. However, the continued circulation of these serotypes in most provinces suggests that ongoing surveillance and vaccination efforts are necessary.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and epidemiological analysis of a putative novel hantavirus in Australian flying foxes.","authors":"Craig S Smith, Darren J Underwood, Anita Gordon, Michael J Pyne, Anna Smyth, Benjamin Genge, Luke Driver, David G Mayer, Jane Oakey","doi":"10.1007/s11262-024-02113-3","DOIUrl":"https://doi.org/10.1007/s11262-024-02113-3","url":null,"abstract":"<p><p>In July 2017, an investigation into the cause of neurological signs in a black flying fox (Pteropus alecto, family Pteropodidae) identified a putative novel hantavirus (Robina virus, ROBV, order Bunyavirales, family Hantaviridae, genus Mobatvirus) in its brain. Analysis of the evolutionary relationship between other hantaviruses using maximum-likelihood, a systematic Bayesian clustering approach, and a minimum spanning tree, all suggest that ROBV is most closely related to another Mobatvirus, Quezon virus, previously identified in the lung of a Philippine frugivorous bat (Rousettus amplexicaudatus, also family Pteropodidae). Subsequently, between March 2018 and October 2023, a total of 495 bats were opportunistically screened for ROBV with an experimental qRT-PCR. The total prevalence of ROBV RNA detected in Pteropus spp. was 4.2% (95% CI 2.8-6.4%). Binomial modelling identified that there was substantial evidence supporting an increase (P = 0.033) in the detection of ROBV RNA in bats in 2019 and 2020 suggesting of a possible transient epidemic. There was also moderate evidence to support the effect of season (P = 0.064), with peak detection in the cooler seasons, autumn, and winter, possibly driven by physiological and ecological factors similar to those already identified for other bat-borne viruses. This is Australia's first reported putative hantavirus and its identification could expand the southern known range of hantaviruses in Australasia.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}