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Genetic determinants of HIV-1 subtype C Nef-mediated SERINC3 down-regulation.
IF 4 3区 医学
Virology Journal Pub Date : 2025-04-08 DOI: 10.1186/s12985-025-02705-x
Nikeisha Samlall, Tarylee Reddy, Nasreen Ismail, Mark A Brockman, Zabrina L Brumme, Thumbi Ndung'u, Jaclyn K Mann
{"title":"Genetic determinants of HIV-1 subtype C Nef-mediated SERINC3 down-regulation.","authors":"Nikeisha Samlall, Tarylee Reddy, Nasreen Ismail, Mark A Brockman, Zabrina L Brumme, Thumbi Ndung'u, Jaclyn K Mann","doi":"10.1186/s12985-025-02705-x","DOIUrl":"https://doi.org/10.1186/s12985-025-02705-x","url":null,"abstract":"<p><strong>Background: </strong>Nef-mediated down-regulation of the host restriction factors SERINC3 and SERINC5 significantly enhances HIV-1 infectivity. Natural Nef polymorphisms that affect SERINC3 down-regulation are not as well-characterised as those that affect SERINC5 down-regulation, particularly in HIV-1 subtype C infection. We therefore aimed to identify genetic determinants of SERINC3 down-regulation by subtype C Nef. In addition, we investigated the role of SERINC3 down-regulation activity in disease progression and its contribution to overall Nef function, using Nef fitness model-derived E values as a proxy for overall Nef function in vivo.</p><p><strong>Methods: </strong>SERINC3 down-regulation activity of 107 participant-derived Nef clones was measured using a flow cytometry-based assay in a T cell line. The relationship between SERINC3 down-regulation activity and viral load set point or rate of CD4 + T cell decline during untreated HIV infection was analysed by linear regression. Quantile regression was used to assess the contribution of SERINC3 down-regulation activity to overall Nef function. Individual Nef amino acids associated with a significantly altered SERINC3 down-regulation activity were identified using codon-by-codon Mann Whitney U tests.</p><p><strong>Results: </strong>SERINC3 down-regulation activity was not a significant predictor of viral load set point nor rate of CD4 + T cell decline. SERINC3 down-regulation activity was a significant predictor of estimated Nef fitness (E values) in univariate analysis (p < 0.0001) and remained significant in multivariate analyses adjusting for other Nef functions that were measured for the same Nef clones (p < 0.02). A total of 30 amino acids were identified to be associated with differential Nef-mediated ability to down-regulate SERINC3 (p < 0.05 and q < 0.3), with 63% of these residues being in the N-terminal domain.</p><p><strong>Conclusion: </strong>Although SERINC3 down-regulation did not associate significantly with markers of HIV disease progression, our results nevertheless suggest that SERINC3 down-regulation contributes significantly to overall Nef function and fitness. The identification of Nef amino acids associated with differential SERINC3 down-regulation ability may be useful for rational design of therapeutics and vaccines targeting the Nef region.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"94"},"PeriodicalIF":4.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Co-29, a 5-cyano-2-thiacetyl aromatic pyrimidinone, as a potential inhibitor targeting the RdRp of norovirus.
IF 4 3区 医学
Virology Journal Pub Date : 2025-04-04 DOI: 10.1186/s12985-025-02687-w
Xianglan Liu, Jiaming Hu, Jiarui Wu, Yiru Tian, Jinbo Wang, Chunyan Wu, Qingfeng Chen, Leonard Krall, Yanping He, Qun Lu
{"title":"Identification of Co-29, a 5-cyano-2-thiacetyl aromatic pyrimidinone, as a potential inhibitor targeting the RdRp of norovirus.","authors":"Xianglan Liu, Jiaming Hu, Jiarui Wu, Yiru Tian, Jinbo Wang, Chunyan Wu, Qingfeng Chen, Leonard Krall, Yanping He, Qun Lu","doi":"10.1186/s12985-025-02687-w","DOIUrl":"10.1186/s12985-025-02687-w","url":null,"abstract":"<p><strong>Background: </strong>Human norovirus (HNV) is the predominant pathogen causing outbreaks of acute gastroenteritis globally. Despite significant efforts to combat norovirus infections, there is currently no FDA approved vaccine or antiviral drug available. Consequently, the development of effective antiviral agents is of critical importance.</p><p><strong>Methods and results: </strong>In this study, a series of 41 5-cyano-2-thiacetyl aromatic pyrimidinone compounds were designed and synthesized. A cell viability-based screening for anti-murine norovirus (MNV) compounds was conducted, revealing that compound 29 (hereafter used as Co-29) exhibited antiviral activity against MNV. Co-29 demonstrated effective inhibition of MNV<sup>CW3</sup> RNA replication, exhibiting an EC<sub>50</sub> of 58.22 μM. An RdRp enzyme activity assay indicated that Co-29 directly inhibits RdRp activity to both MNV and HNV. Molecular docking studies suggested that Co-29 interacts with the palm region of RdRp via hydrogen bonding with specific residues, which are conserved in RdRps across MNV and HNV norovirus variants.</p><p><strong>Conclusions: </strong>In conclusion, our study suggests that the newly synthesized Co-29 may serve as a potential antiviral candidate or lead compound for future studies.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"93"},"PeriodicalIF":4.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11969896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation, molecular identification, and phylogenetic analysis of infectious bronchitis virus from commercial chicken farms in Mekele and Bishoftu, Ethiopia, 2023-2024.
IF 4 3区 医学
Virology Journal Pub Date : 2025-04-02 DOI: 10.1186/s12985-025-02639-4
Nigusu Berhanu, Eyob Hirpa, Hawa Mohammed, Abinet Legesse, Getaw Deresse, Eyob Assefa, Takele Tesgera, Mirtneh Akalu, Takele Abayneh, Berecha Bayissa, Liyuwork Tesfaw, Kenaw Birhanu, Esayas Gelaye
{"title":"Isolation, molecular identification, and phylogenetic analysis of infectious bronchitis virus from commercial chicken farms in Mekele and Bishoftu, Ethiopia, 2023-2024.","authors":"Nigusu Berhanu, Eyob Hirpa, Hawa Mohammed, Abinet Legesse, Getaw Deresse, Eyob Assefa, Takele Tesgera, Mirtneh Akalu, Takele Abayneh, Berecha Bayissa, Liyuwork Tesfaw, Kenaw Birhanu, Esayas Gelaye","doi":"10.1186/s12985-025-02639-4","DOIUrl":"10.1186/s12985-025-02639-4","url":null,"abstract":"<p><strong>Background: </strong>Avian infectious bronchitis (IB) is a highly contagious respiratory disease that affects the poultry industry globally. The disease is caused by avian infectious bronchitis virus (IBV), member of the genus Gammacoronavirus. In Ethiopia, IBV has been reported in both commercial and backyard chickens based on clinical observation. The objectives of this study were to isolate the virus, conduct molecular based identification, and phylogenetic analysis of the circulating IBV isolates.</p><p><strong>Methods and materials: </strong>A cross-sectional study was conducted between November 2023 and May 2024 in Mekele and Bishoftu, Ethiopia. A total of 49 clinical samples were collected, comprising 12 tissue samples and 39 pooled swab samples. Of these, 6 samples-specifically, 5 swab samples and 1 tissue sample-tested positive for infectious bronchitis virus (IBV) through virus-specific conventional RT-PCR and real-time PCR. Nested PCR was performed using serotype-specific primers. The purified PCR products, which targeted the spike glycoprotein S1 subunit gene and the 3' UTR of the IBV, were sequenced, followed by phylogenetic tree analysis.</p><p><strong>Results: </strong>The six positive samples propagated into specific pathogen free embryonated eggs and exhibited characteristic IBV lesions and mortality observed over five consecutive passages. IBV isolates from Bishoftu (n = 4) and Mekele (n = 2) were amplified using one-step RT-PCR to target 466 bp of the S1 subunit gene and 433 bp of the 3'UTR. A BLAST search on the S1 partial gene and 3'UTR sequences, nested PCR, and phylogenetic analysis revealed that the present IBV isolates are genetically similar to the Massachusetts serotype. The S1 gene sequences of the five IBV isolates were deposited in GenBank with accession numbers PQ389500 to PQ389504.</p><p><strong>Conclusions: </strong>This is the first detailed study on IB virus isolation, molecular detection, sequencing, and phylogenetic analysis in Ethiopia. The findings revealed that the outbreaks were caused by the IB virus, which created a serious health risk and economic losses in the chicken industry. To the author's knowledge, this is the first comprehensive study on the isolation and genetic analysis of IBV in Ethiopia. Further research on the economic impact of IBV in chicken production, farm biosecurity, serotyping of circulating IB virus, and vaccine development based on the local serotypes is recommended.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"90"},"PeriodicalIF":4.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization of the epidemiology, susceptibility genes and clinical features of viral infections among children with inborn immune errors: a retrospective study.
IF 4 3区 医学
Virology Journal Pub Date : 2025-04-02 DOI: 10.1186/s12985-025-02697-8
Haiqiao Zhang, Wenjie Wang, Qinhua Zhou, Jia Hou, Wenjing Ying, Xiaoying Hui, Jinqiao Sun, Lipin Liu, Luyao Liu, Chenhao Wang, Hai Zhang, Bijun Sun, Xiaochuan Wang
{"title":"Characterization of the epidemiology, susceptibility genes and clinical features of viral infections among children with inborn immune errors: a retrospective study.","authors":"Haiqiao Zhang, Wenjie Wang, Qinhua Zhou, Jia Hou, Wenjing Ying, Xiaoying Hui, Jinqiao Sun, Lipin Liu, Luyao Liu, Chenhao Wang, Hai Zhang, Bijun Sun, Xiaochuan Wang","doi":"10.1186/s12985-025-02697-8","DOIUrl":"10.1186/s12985-025-02697-8","url":null,"abstract":"<p><strong>Background: </strong>Although viral infections are one of the common clinical manifestations in patients with inborn errors of immunity (IEIs), little is known about the epidemiology, susceptibility genes, and clinical status of viral infections in patients with IEIs.</p><p><strong>Methods: </strong>The demographic information, clinical diagnoses, and laboratory findings of 931 IEI patients who underwent viral testing from January 2016 to December 2022 were collected and analyzed.</p><p><strong>Results: </strong>In total, 47.15% (439/931) patients with IEI tested positive for at least one virus during hospitalization. There were a total of 640 viral infections during the study period, mainly from EBV 131 (20.47%), HRV 102(15.94%), CMV 100(15.63%), and RV 84(13.13%). CMV and RV infections were more common in the combined immunodeficiencies (IEI_I) group during the infant stage, whereas EBV infection was more common in the immune dysregulation (IEI_IV) group during the preschool stage. Mutations in SH2D1A (57.14%), PIK3CD (56.41%) and LRBA (50%) make individuals susceptible to EBV infection; mutations in WAS (30%) make individuals susceptible to CMV infection; and mutations in IL2RG (56.52%) and RAG1 (37.5%) make individuals susceptible to RV infection. Joinpoint analysis revealed trends in viral positivity in different years.</p><p><strong>Conclusion: </strong>These data suggest that it is possible to target the prevention, treatment, and management of IEI patients who are infected with a virus by accounting for the age at infection, type of IEI, and mutant genes, but special attention needs to be paid to viral infections in IEI_I and IEI_IV patients during the infant stage.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"91"},"PeriodicalIF":4.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and characterization of a novel reovirus strain isolated fromgrass carp (Ctenopharyngodon idella).
IF 4 3区 医学
Virology Journal Pub Date : 2025-04-02 DOI: 10.1186/s12985-025-02716-8
Weiguang Kong, Guangyi Ding, Qiushi Zhang, Xinjie Yuan, Yuchao Zhu, Liyuan Ma, Chang Cai, Yong Shi, Qianqian Zhang, Zhen Xu
{"title":"Identification and characterization of a novel reovirus strain isolated fromgrass carp (Ctenopharyngodon idella).","authors":"Weiguang Kong, Guangyi Ding, Qiushi Zhang, Xinjie Yuan, Yuchao Zhu, Liyuan Ma, Chang Cai, Yong Shi, Qianqian Zhang, Zhen Xu","doi":"10.1186/s12985-025-02716-8","DOIUrl":"10.1186/s12985-025-02716-8","url":null,"abstract":"<p><strong>Background: </strong>Grass carp (Ctenopharyngodon idella) hemorrhagic disease (GCHD) is a devastating disease that leads to substantial economic losses in the freshwater aquaculture industry.</p><p><strong>Results: </strong>In this study, we investigated an outbreak of GCHD in large-scale grass carp and identified GCRV-II infection. Notably, hematoxylin and eosin (H&E) staining showed severe histopathological changes in the spleen, head kidney, gill, and gut. Furthermore, we sequenced the entire genome of the viral isolate, and multiple sequence alignment and phylogenetic tree analysis indicated that it represents a novel strain of GCRV-II, provisionally named GCRV-YX246. Finally, artificial infection experiments confirmed the strong virulence, high mortality, and severe pathological damage caused by GCRV-YX246, as demonstrated through artificial infection.</p><p><strong>Conclusions: </strong>A novel reovirus from large-scale grass carp cultured in China was identified. The discovery of this novel GCRV-II strain enhances our understanding of GCRV-II biology and provides valuable insights for developing more effective prevention strategies for GCHD.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"92"},"PeriodicalIF":4.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.
IF 4 3区 医学
Virology Journal Pub Date : 2025-03-28 DOI: 10.1186/s12985-025-02708-8
Gabriel Montenegro de Campos, Luan Gaspar Clemente, Alex Ranieri Jerônimo Lima, Eleonora Cella, Vagner Fonseca, João Paulo Bianchi Ximenez, Milton Yutaka Nishiyama, Enéas de Carvalho, Sandra Coccuzzo Sampaio, Marta Giovanetti, Maria Carolina Elias, Svetoslav Nanev Slavov
{"title":"Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.","authors":"Gabriel Montenegro de Campos, Luan Gaspar Clemente, Alex Ranieri Jerônimo Lima, Eleonora Cella, Vagner Fonseca, João Paulo Bianchi Ximenez, Milton Yutaka Nishiyama, Enéas de Carvalho, Sandra Coccuzzo Sampaio, Marta Giovanetti, Maria Carolina Elias, Svetoslav Nanev Slavov","doi":"10.1186/s12985-025-02708-8","DOIUrl":"10.1186/s12985-025-02708-8","url":null,"abstract":"<p><strong>Background: </strong>Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.</p><p><strong>Methods: </strong>In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.</p><p><strong>Results: </strong>Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.</p><p><strong>Conclusion: </strong>Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"88"},"PeriodicalIF":4.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of aberrant interferon-stimulated gene associated host responses potentially linked to poor prognosis in COVID-19 during the Omicron wave.
IF 4 3区 医学
Virology Journal Pub Date : 2025-03-28 DOI: 10.1186/s12985-025-02696-9
Zhan Li, Min Peng, Linlin Cheng, ZiRan Wang, Ziyan Wu, Futai Feng, Xinxin Feng, Siyu Wang, Ye Guo, Yongzhe Li
{"title":"Identification of aberrant interferon-stimulated gene associated host responses potentially linked to poor prognosis in COVID-19 during the Omicron wave.","authors":"Zhan Li, Min Peng, Linlin Cheng, ZiRan Wang, Ziyan Wu, Futai Feng, Xinxin Feng, Siyu Wang, Ye Guo, Yongzhe Li","doi":"10.1186/s12985-025-02696-9","DOIUrl":"https://doi.org/10.1186/s12985-025-02696-9","url":null,"abstract":"<p><strong>Background: </strong>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron has demonstrated decreased pathogenicity, yet a few individuals suffer severe pneumonia from coronavirus disease 2019 (COVID-19) infection; the underlying mechanisms are unknown.</p><p><strong>Methods: </strong>The present work investigated the role of Interferon-stimulated genes (ISGs) in the occurrence and progression of severe Omicron infection. The expression and dynamic changes of ISGs were assessed using quantitative real-time polymerase chain reaction (qRT-PCR), and the anti-ISG15 autoantibody in infected patients was detected by ELISA. Moreover, we evaluated the correlation of ISGs with disease severity and outcomes by comparing expression of ISGs among each group.</p><p><strong>Results: </strong>Decreased expression of several ISGs such as IFI6 are potentially linked to increased severity or poor outcomes of Omicron infection. Longitudinal data also demonstrates that the dynamic variation of IFI6 in the Omicron infection phase may be linked to the prognosis of the disease. The increase of anti-ISG15 autoantibody potentially links to the disease progression and poor outcome of patients with high level of ISG15 expression.</p><p><strong>Conclusions: </strong>These findings define aberrant Interferon-stimulated gene associated host responses and reveal potential mechanisms and therapeutic targets for Omicron or other viral infection.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"89"},"PeriodicalIF":4.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation, characterization, and genomic analysis of three novel Herelleviridae family lytic bacteriophages against uropathogenic isolates of Staphylococcus saprophyticus.
IF 4 3区 医学
Virology Journal Pub Date : 2025-03-27 DOI: 10.1186/s12985-025-02710-0
Hesamaddin Shirzad-Aski, Mahsa Yazdi, Alireza Mohebbi, Maryam Rafiee, Abbas Soleimani-Delfan, Alijan Tabarraei, Ezzat Allah Ghaemi
{"title":"Isolation, characterization, and genomic analysis of three novel Herelleviridae family lytic bacteriophages against uropathogenic isolates of Staphylococcus saprophyticus.","authors":"Hesamaddin Shirzad-Aski, Mahsa Yazdi, Alireza Mohebbi, Maryam Rafiee, Abbas Soleimani-Delfan, Alijan Tabarraei, Ezzat Allah Ghaemi","doi":"10.1186/s12985-025-02710-0","DOIUrl":"10.1186/s12985-025-02710-0","url":null,"abstract":"<p><strong>Background: </strong>Staphylococcus saprophyticus (S. saprophyticus) is the second most prevalent etiological agent of urinary tract infections (UTIs) in young women. However, there is a paucity of data regarding its bacteriophage (phage). Therefore, this study was conducted to isolate and identify new lytic phages from municipal wastewater with the objective of increasing knowledge about phages and their genomes.</p><p><strong>Methods: </strong>A total of 11 clinical isolates of S. saprophyticus and 30 wastewater samples were used to isolate three lytic phages (vB_SsapH-Golestan-100, vB_SsapH-Golestan101-M, and vB_SsapH-Golestan-105-M). The morphology, behavioral characteristics, and complete DNA genomes of these phages were analyzed.</p><p><strong>Results: </strong>The microscopic images of the phages revealed that the sizes of their heads and tail lengths fell within the ranges of 90-111 nm and 234-266 nm, respectively. All phages exhibited high adsorption rates (99.5% in 15 min) and burst sizes (150-210 PFU per infected cell), with a potential for a narrow host range. Genomic analysis of Staphylococcus phages indicated a size of 136,433 base pairs (bp) with a guanine-cytosine (GC) content of 33.7% and 192 open reading frames (ORFs) for vB_SsapH-Golestan-100, 144,081 bp with a GC content of 29.6% and 205 ORFs for vB_SsapH-Golestan101-M, and 142,199 bp with a GC content of 30.6% and 203 ORFs for vB_SsapH-Golestan-105-M. A bioinformatics analysis indicated that all three phages belong to the Twortvirinae subfamily of Herelleviridae. Among the three phages, vB_SsapH-Golestan-100 exhibited the least similarity to previously known phages, with less than 21% similarity with its closest counterparts in genomic databases.</p><p><strong>Conclusions: </strong>This study identified new phages that have the ability to destroy a broad range of S. saprophyticus isolates and may potentially be classified as a new genus and species within the Herelleviridae family in future studies.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"87"},"PeriodicalIF":4.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Processing of genomic RNAs by Dicer in bat cells limits SARS-CoV-2 replication.
IF 4 3区 医学
Virology Journal Pub Date : 2025-03-25 DOI: 10.1186/s12985-025-02693-y
Iyanuoluwani J Owolabi, Shazeed-Ul Karim, Sweta Khanal, Sergio Valdivia, Christopher Frenzel, Fengwei Bai, Alex S Flynt
{"title":"Processing of genomic RNAs by Dicer in bat cells limits SARS-CoV-2 replication.","authors":"Iyanuoluwani J Owolabi, Shazeed-Ul Karim, Sweta Khanal, Sergio Valdivia, Christopher Frenzel, Fengwei Bai, Alex S Flynt","doi":"10.1186/s12985-025-02693-y","DOIUrl":"10.1186/s12985-025-02693-y","url":null,"abstract":"<p><p>Bats are reservoirs for numerous viruses that cause serious diseases in other animals and humans. Several mechanisms are proposed to contribute to the tolerance of bats to these pathogens. This study investigates the response of bat cells to double-stranded RNA generated by SARS-CoV-2 replication. Here, we found the involvement of Dicer in the processing of viral genomic RNAs during SARS-CoV-2 infection. Examining RNA sequencing of infected cells, small-interfering RNA (siRNA)-like fragments were found derived from viral RNAs. Depletion of Dicer showed a reduction in these RNAs and an increase in viral loads suggesting unlike other mammals, bats may use Dicer to limit viral replication. This prompted the exploration of key dsRNA sensors in bat cells. Our analysis showed significant upregulation of OAS1 and MX1 in response to dsRNA, while PKR levels remained low, suggesting alternative dsRNA-response mechanisms are present that eschew the common PKR-based system. These results further show how bats employ distinct strategies for antiviral defense that may contribute to tolerating viral infections. They suggest the involvement of Dicer in antiviral mechanisms in bats, a function not observed in other mammals. This highlights a mechanism for bat originating viruses to evolve features that in other animals could cause extreme antiviral responses such as is seen with SARS-CoV-2.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"86"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus.
IF 4 3区 医学
Virology Journal Pub Date : 2025-03-24 DOI: 10.1186/s12985-025-02699-6
Ali N Alhafufi, Samy Kasem, Fahad N Almajhdi, Hassan A Albaqshi, Fanan A Alaql, Ehab A Rihan, Ehab M Abd-Allah, Ameen A Alyousaf, Yahya K Aljasem, Najwa D Aljehani, Mohei A Haridy, Ahmed R Alhimaidi, Ahmed S Abdel-Moneim
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