Virology Journal最新文献

{"title":"Trends and hotspots in research of virus and gastrointestinal mucosal immunity: a bibliometric analysis of four decades.","authors":"Yu Cai, Jingqi Liu, Mingxia Zhang, Nianhong Qin, Mingfeng Liao, Feng Gao, Zhenfu Zhao, Ou Sha","doi":"10.1186/s12985-025-02929-x","DOIUrl":"10.1186/s12985-025-02929-x","url":null,"abstract":"<p><strong>Background: </strong>Over the past four decades, the relationship between viruses and gastrointestinal (GI) mucosal immunity has gained increasing attention due to frequent viral epidemics.</p><p><strong>Objective: </strong>This study explores current research trends and future directions in this field through bibliometric analysis.</p><p><strong>Methods: </strong>Literature from January 1, 1985, to December 31, 2024, was retrieved from the Web of Science Core Collection (WoSCC) on January 6, 2025. Analyses were conducted using VOSviewer, Citespace, and the Bibliometrix R package.</p><p><strong>Results: </strong>A total of 4,842 publications were identified, with an annual growth rate of 8.65%. The United States (USA) led with 1,866 articles (38.54%), followed by China (794, 16.4%). The University of California was the leading institution (n = 605). Dandekar S was the most productive author (46 publications, H-index = 26). Major co-citation clusters focused on \"HIV infection,\" \"Infected macaque,\" and \"CoV-2 infection.\" Mattapallil JJ et al. (2005) had the strongest citation burst (burst = 47.09). \"HIV\" appeared the most frequently among keywords (n = 640), followed by \"mucosal immunity\" (n = 340) and \"vaccine\" (n = 184). Keyword and citation burst analyses revealed longstanding focus on the pathogenesis of human immunodeficiency virus (HIV) and antiretroviral therapy (ART), influenza, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human papillomavirus (HPV)-related disease prevention and early diagnosis, the role of the gut microbiome in antiviral defense, and the pathogenesis and prognostic prevention of inflammatory bowel disease (IBD).</p><p><strong>Conclusion: </strong>This bibliometric analysis provides insights into research trends and emerging hotspots in the field of viruses and GI mucosal immunity, aiding researchers in identifying key areas for future investigation.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"302"},"PeriodicalIF":4.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145178818","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}

{"title":"Prevalence, dynamic change and spatial distribution of HIV-1 CRF119_0107 from 2019 to 2024 in Nanjing, China: a genomic and spatial epidemiological analysis.","authors":"Yuanyuan Xu, Hongjie Shi, Xin Li, Tingyi Jiang, Mengkai Qiao, Dandan Xu, Rong Wu, Xin Yuan, Jingwen Wang, Xiajie Zhou, Zhengping Zhu","doi":"10.1186/s12985-025-02932-2","DOIUrl":"10.1186/s12985-025-02932-2","url":null,"abstract":"<p><strong>Background: </strong>Since its initial detection among men who have sex with men (MSM) in Nanjing, CRF119_0107 has rapidly emerged as the third most prevalent HIV-1 subtype. To elucidate its transmission dynamic, spatial characteristics, and the prevalence of transmitted drug resistance (TDR), we conducted a joint genomic and spatial epidemiological analysis.</p><p><strong>Methods: </strong>HIV-infected individuals diagnosed from 2109 to 2024 who were identified as CRF119_0107 and didn't undergo antiretroviral therapy (ART) were included in the study. The HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR. A molecular transmission network was constructed using HIV-TRACE, and spatial analysis was performed in ArcGIS. Multivariate logistic regression was employed to analyze factors associated with clustering. Transmission links of the network were visualized in intensity matrices and spatial transmission graph.</p><p><strong>Results: </strong>The 138 CRF119_0107 individuals predominantly consisted of unmarried, college-educated MSM. A notably high TDR prevalence of 15.9% was observed, with 15.2% (21/138) resistance to non-nucleoside reverse transcriptase inhibitor (NNRTI). At the genetic distance threshold of 0.005 substitutions/site, 78 sequences formed 11 transmission clusters, with a clustering rate of 56.6%. The transmission network analysis identified a drug-resistant cluster containing 19 drug-resistant individuals, all harboring K103N/KN mutation. Four large MSM-dominated clusters were identified, including two high-growth clusters expanding at over 2 nodes per year between 2022 and 2024. Multivariate logistic regression analysis revealed that individuals with high initial CD4 counts and TDR individuals had significantly higher clustering rate compared to those with CD4 counts < 200 cells/µL and without TDR. Spatial analysis revealed no significant autocorrelation in clustering rate at the district-level (Moran's I=-0.121, P = 0.774). Intensity matrices revealed extensive inter-district transmission across all 12 districts, with this transmission accounting for 83.8% of total transmissions. The spatial transmission graph showed that the strength of the connections between districts varied, and strong inter-district transmission linkages were also observed between geographically non-adjacent districts.</p><p><strong>Conclusions: </strong>Real-time surveillance and rapid response mechanisms should prioritize high-growth or drug-resistant transmission clusters. Cross-district coordination and joint interventions should be strengthened in districts with intensive transmission linkages. Our interdisciplinary approach offers an evidence-based framework for curbing dissemination of CRF119_0107.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"306"},"PeriodicalIF":4.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145178853","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}

{"title":"Rodents as potential reservoirs for toroviruses.","authors":"Jaime Buigues, Adrià Viñals, Raquel Martínez-Recio, Juan S Monrós, Rafael Sanjuán, José M Cuevas","doi":"10.1186/s12985-025-02933-1","DOIUrl":"10.1186/s12985-025-02933-1","url":null,"abstract":"<p><strong>Background: </strong>Emerging zoonotic viruses pose a significant threat to global health. The order Nidovirales includes diverse viruses, such as coronaviruses, which are well known for their zoonotic potential. Toroviruses are a less-studied genus within Nidovirales primarily associated with gastrointestinal diseases in ungulates, although some evidence suggests their presence in humans.</p><p><strong>Methods: </strong>We set out to describe full-length genomes of potentially emerging viruses by collecting feces from dozens of small mammals, mainly rodents, captured in different regions of Spain. Viral reads were obtained by high-throughput Illumina sequencing and analyzed phylogenetically.</p><p><strong>Results: </strong>In this study, we report the discovery of a novel torovirus from a fecal sample of a dormouse (Eliomys quercinus) in Spain, which we named Dormouse torovirus (DToV). This represents the first complete genome of a rodent-associated torovirus. The 28,555-nucleotide genome encodes the six characteristic torovirus open reading frames, but these exhibit low amino acid sequence identity (44.3-86.3%) compared to other toroviruses, indicating that DToV likely represents a new viral species. Moreover, the basal phylogenetic position of DToV suggests that rodents may represent a reservoir for this viral genus.</p><p><strong>Conclusions: </strong>Our findings expand the known torovirus host range, underscore their potential for cross-species transmission, and highlight the importance of continued surveillance of wildlife viruses.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"305"},"PeriodicalIF":4.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145178793","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}

{"title":"Bacteriophage T4 propagation in E.coli exposed to severe substrate limitation.","authors":"Ana Lisac, Aleš Podgornik","doi":"10.1186/s12985-025-02934-0","DOIUrl":"10.1186/s12985-025-02934-0","url":null,"abstract":"<p><p>Understanding bacteriophage propagation on bacteria in different physiological conditions is imperative for predicting phage therapy efficacy on various bacterial infections, especially chronic ones. We investigated phage T4 propagation on bacteria E.coli grown in a chemostat at very low dilution rates extending down to 0.027 h^-1 and bacteria exposed to nutrient deprivation. An increase in adsorption constant and latent period with dilution rate D decrease and burst size being proportional to dilution rate (D) was confirmed, consistent with previously published results, extending validity of previous findings. Additional bacterial exposure to starvation, either through nutrient cessation or transferring bacteria into SM buffer, sustained phage propagation during first hours of starvation and diminished to formation of a single phage per infected cell after 24 h. Nutrient deprivation effects were investigated on fast growing bacteria and bacteria in a death phase. While no phage generation was observed within bacteria in death phase, fast growing bacteria transferred into SM buffer generated a single phage within 48 h without lysis, indicating that bacterial exposure to nutrient depleted conditions triggers a so called \"scavenger response\" whose intensity depends on starvation exposure time.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"304"},"PeriodicalIF":4.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145178858","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}

{"title":"HBx promotes podocyte-macrophage transdifferentiation by mediating NLRP3 expression in hepatitis B virus-associated glomerulonephritis.","authors":"Zhaotun He, Yanhua Zhu, Yuchao Niu, Haochen Guan, Yitong Yang","doi":"10.1186/s12985-025-02926-0","DOIUrl":"10.1186/s12985-025-02926-0","url":null,"abstract":"<p><strong>Background: </strong>Podocytes are identified as main injury targets in the pathogenesis of hepatitis B virus (HBV)-associated glomerulonephritis (HBV-GN). NLR family pyrin domain containing 3 (NLRP3) has a critical function in ​inducing podocyte injury across multiple renal pathologies. This study aimed to explore whether NLRP3 expression linked to podocyte injury participated in the pathogenic mechanism of HBV-GN.</p><p><strong>Methods: </strong>The expression of NLRP3, CD68, ‌intercellular cell adhesion molecule-1 (‌ICAM-1), and α-smooth muscle actin (α-SMA) was identified in HBV-GN renal biopsies. The correlations between renal NLRP3 expression and clinical parameters, as well as between HBV X (HBx) expression and inflammation and fibrosis markers, were analyzed. HBx-encoding plasmids were transferred into cultured human podocytes. The downstream targets of HBx determined by RNA-sequencing. The expression of NLRP3 and α-SMA was quantified by western blot analysis. The expression of CD68 was detected using immunofluorescence and flow cytometry. Inflammatory factor levels were examined via ELISA.</p><p><strong>Results: </strong>NLRP3 exhibited a remarkable increase in the podocytes of HBV-GN patients, and its expression showed a significant association with proteinuria levels. Furthermore, co-localization of NLRP3 and CD68 was observed within the podocytes of HBV-GN patients. In vitro, HBx markedly upregulated NLRP3 and induced podocyte-macrophage transdifferentiation (PMT) in human podocytes, thereby contributing to the inflammatory reaction and fibrosis. Further analysis indicated that the NLRP3 inhibitor tranilast (TR) attenuated HBx-induced PMT, inflammation and fibrosis.</p><p><strong>Conclusion: </strong>These findings indicate that HBx triggers NLRP3 upregulation in podocytes and activates PMT. Thereafter, podocytes may function as antigen-presenting cells (APCs), consequently stimulating immune cell activation and resulting in inflammation cascades and renal fibrosis associated with HBV-GN.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"301"},"PeriodicalIF":4.0,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151151","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}

{"title":"Enhancement of lentiviral vectors gene delivery against VEGFR2 expressing cells by co-display of the binding and fusogenic moieties: a two molecules targeting approach.","authors":"Roshanak Ahani, Mohammad Hossein Etemadzadeh, Nasir Mohajel, Mahdi Behdani, Reza Ahangari Cohan, Mohamad Reza Kalani, Navid Madani, Farzin Roohvand, Kayhan Azadmanesh","doi":"10.1186/s12985-025-02923-3","DOIUrl":"10.1186/s12985-025-02923-3","url":null,"abstract":"<p><strong>Background: </strong>Pseudotyped lentiviral vectors (LVs) were used in cancer therapy as gene delivery systems for inhibiting tumor angiogenesis by targeting cells overexpressing \"vascular endothelial growth factor receptor-2 (VEGFR2)\". Herein, we report that switching from chimeric sindbis virus glycoprotein (SVG) harboring VEGFR2-specific nanobody (VEGFR2-Nb) to Two-Molecules Targeting Approach (TMTA: independent co-display of binding and fusogenic moieties) highly enhanced the transduction efficiency (TE) of the targeted LVs.</p><p><strong>Methods: </strong>Several LVs co-displaying either the VEGFR2-Nb or the natural ligand (VEGF121) as targeting moiety, along with a de-targeted mutant form of SVG (as a binding deficient and fusion competent) fusogenic moiety were produced. LVs were constructed via various backbones and linkers (platelet-derived growth factor receptor \"PDGFR\" and CD28 as transmembrane domains, and HL and Fc as spacer domains).</p><p><strong>Results: </strong>Expression and incorporation of the VEGFR2-Nb and SVG onto lentiviral particles were confirmed by flowcytometry and Western blotting while their co-display was demonstrated by virus-capture ELISA and virus-cell binding assays. LVs co-enveloped with fusogen and either VEGFR2-Nb or VEGF121 showed higher TEs in VEGFR2-expressing cells (72% and 91%, respectively) over LVs pseudotyped with chimeric fusogen containing the same nanobody (30%). In silico analyses indicated a direct correlation for the TE and the distance between the nanobody and the lipid bilayer.</p><p><strong>Conclusion: </strong>Compared to the chimeric strategy, the two-molecule targeting approach of LVs, due to its flexible and modular nature provides higher TE and thus great potentials for targeted gene delivery.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"300"},"PeriodicalIF":4.0,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138803","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}

{"title":"Author's response to the letter \"From correlation to causation: unraveling the role of long non-coding RNAs in COVID-19 pathogenesis\".","authors":"Sara Fayazzadeh, Raheleh Heydari, Anna Meyfour","doi":"10.1186/s12985-025-02876-7","DOIUrl":"10.1186/s12985-025-02876-7","url":null,"abstract":"<p><p>A recent letter to the editor, from correlation to causation: unraveling the role of long non-coding RNAs in COVID-19 pathogenesis, provided recommendations and suggestions concerning our published paper, Long non-coding RNAs in Biomarking COVID-19: A Machine Learning-Based Approach (2024). The comments focused primarily on future directions. In this response, we clarify and emphasize the rationale underlying our original approach.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"299"},"PeriodicalIF":4.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971014","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}

{"title":"SDS-EDTA-treated chromatography paper strips for sampling and transportation of monkeypox virus, varicella zoster virus and herpes simplex 1 and 2 viruses.","authors":"Nikola Sklenovská, Mandy Bloemen, Graciela Andrei, Katrien Bruyninckx, Elke Wollants, Marc Van Ranst","doi":"10.1186/s12985-025-02920-6","DOIUrl":"10.1186/s12985-025-02920-6","url":null,"abstract":"<p><p>Mpox is a viral zoonotic disease characterized by flu-like symptoms followed by rash, which can be difficult to distinguish from other rash-presenting infections. Laboratory diagnosis is essential for confirming monkeypox virus (MPXV) infection; However, challenges in specimen transport and storage in endemic regions, especially in rural areas with limited infrastructure, hinder timely diagnosis. This study evaluates the use of SDS-EDTA-treated chromatography paper strips for testing different viral dilutions of MPXV, varicella-zoster virus (VZV), herpes simplex viruses 1 (HSV-1) and 2 (HSV-2) under different storage durations and temperatures. The results showed that all viral dilutions could be reliably detected even after 120 days at 37 °C. Notably, MPXV concentrations as low as 2 copies/µL were detected, highlighting the clinical relevance of these strips. This method could enhance mpox testing in resource-limited areas by overcoming logistical barriers, offering a cost-effective and reliable alternative for specimen collection, transport and storage in regions affected by mpox outbreaks.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"298"},"PeriodicalIF":4.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12403532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970800","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}

{"title":"Global trends and insights in interferon therapy for chronic hepatitis B: a bibliometric analysis.","authors":"Lei Duan, Yang Liu, Dingyu Wu, Ting Wen, Song Huang, Xiuyun Zhu, Guangyan Sun, Guohong Yang, Yinbao Hu, Shoucui Pu, Qiangwei Zeng, Qingyu Yang","doi":"10.1186/s12985-025-02922-4","DOIUrl":"10.1186/s12985-025-02922-4","url":null,"abstract":"","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"297"},"PeriodicalIF":4.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12400557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971019","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}

{"title":"Editorial Expression of Concern: Development of an in vitro cleavage assay system to examine vaccinia virus I7L cysteine proteinase activity.","authors":"Chelsea M Byrd, Dennis E Hruby","doi":"10.1186/s12985-025-02894-5","DOIUrl":"https://doi.org/10.1186/s12985-025-02894-5","url":null,"abstract":"","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"296"},"PeriodicalIF":4.0,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970987","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}