Virology Journal最新文献

{"title":"The value of promoter methylation of fibroblast factor 21 (FGF21) in predicting the course of chronic hepatitis B and the occurrence of oxidative stress.","authors":"Xue Li, Pei Liu, Zhaohui Wang, Xuefei Wei, Shuai Gao, YuChen Fan, Huihui Liu, Kai Wang","doi":"10.1186/s12985-024-02605-6","DOIUrl":"https://doi.org/10.1186/s12985-024-02605-6","url":null,"abstract":"<p><strong>Background: </strong>Oxidative stress plays a crucial role in the pathogenesis of HBV. This study aimed to investigate the value of fibroblast growth factor 21 (FGF21) promoter methylation in the occurrence and development of chronic hepatitis B (CHB) oxidative stress.</p><p><strong>Methods: </strong>A total of 241 participants including 221 patients with CHB and 20 healthy controls (HCs) were recruited. Methylation level of FGF21 promoter in peripheral blood mononuclear cells was quantitatively determined. Enzyme-linked immunosorbent assay was used to assess oxidative stress in CHB patients.</p><p><strong>Results: </strong>Our study shows that the FGF21 methylation level was significantly lower in HBeAg-positive CHB patients compared to HBeAg-negative CHB patients and HCs (P < 0.0001). The oxidative stress of HBeAg-positive CHB patients was more severe. Further correlation analysis showed that there was a significant correlation between the methylation level of FGF21 promoter and the occurrence of oxidative stress in CHB patients. In addition, assessment based on FGF21 promoter methylation level proved effective for predicting oxidative stress occurrence and disease progression among CHB patients.</p><p><strong>Conclusion: </strong>FGF21 promoter methylation level is an important marker for predicting oxidative stress and disease progression in patients with CHB.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"332"},"PeriodicalIF":4.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878156","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}

{"title":"A predictive model for functional cure in chronic HBV patients treated with pegylated interferon alpha: a comparative study of multiple algorithms based on clinical data.","authors":"Ya-Mei Ye, Yong Lin, Fang Sun, Wen-Yan Yang, Lina Zhou, Chun Lin, Chen Pan","doi":"10.1186/s12985-024-02599-1","DOIUrl":"https://doi.org/10.1186/s12985-024-02599-1","url":null,"abstract":"<p><strong>Background: </strong>A multivariate predictive model was constructed using baseline and 12-week clinical data to evaluate the rate of clearance of hepatitis B surface antigen (HBsAg) at the 48-week mark in patients diagnosed with chronic hepatitis B who are receiving treatment with pegylated interferon α (PEG-INFα).</p><p><strong>Methods: </strong>The study cohort comprised CHB patients who received pegylated interferon treatment at Mengchao Hepatobiliary Hospital, Fujian Medical University, between January 2019 and April 2024. Predictor variables were identified (LASSO), followed by multivariate analysis and logistic regression analysis. Subsequently, predictive models were developed via logistic regression, random forest (RF), gradient boosting decision tree (GBDT), extreme gradient boosting (XGBoost), and support vector machine (SVM) algorithms. The efficacy of these models was assessed through various performance metrics, including the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and F1 score.</p><p><strong>Results: </strong>This study included a total of 224 individuals diagnosed with chronic hepatitis B. The variables baseline log₂(HBsAg), gender, age, neutrophil count at week 12, HBsAg decline rate at week 12, and HBcAb at week 12 were closely associated with functional cure and were included in the predictive model. In the validation term, the logistic regression model had an AUC of 0.858, which was better than that of the other machine learning models (AUC = 0.858,F1 = 0.753). Consequently, this model was selected for the development of the predictive tool.</p><p><strong>Conclusions: </strong>The combined use of the baseline log₂(HBsAg) value, HBsAg decline rate at week 12, gender, neutrophil count at week 12, and age can serve as a foundational predicting model for anticipating the clearance of HBsAg in individuals with chronic hepatitis B who are receiving PEG-INFα therapy.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"333"},"PeriodicalIF":4.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878149","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}

{"title":"Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis.","authors":"Serena Messali, Marta Giovanetti, Alessandro Rondina, Marta Bertelli, Melissa Duheric, Francesca Caccuri, Massimo Ciccozzi, Arnaldo Caruso","doi":"10.1186/s12985-024-02609-2","DOIUrl":"https://doi.org/10.1186/s12985-024-02609-2","url":null,"abstract":"<p><strong>Background: </strong>Since the beginning of the pandemic, contact tracing has been one of the most relevant issues to understand SARS-CoV-2 transmission dynamics and, in this context, the analysis of quasispecies may turn out to be a useful tool for outbreak investigations. Analysis of the intra-host single nucleotide variants (iSNVs) found in the nsp2, ORF3, and ORF7 genes of SARS-CoV-2 was conducted in order to correctly identify virus transmission chain among patients hospitalized in Brescia Civic Hospital.</p><p><strong>Methods: </strong>During the period between August and October 2023, 13 nasopharyngeal specimens, collected from patients admitted to Brescia Civic Hospital, were tested for SARS-CoV-2 positivity and molecularly characterized. Firstly, a phylogenetic analysis was performed to evaluate if they were epidemiologically linked and, then, the Beta-binomial method was used to estimate the transmission bottleneck size (Nb) and quantify the number of viral particles transmitted from one individual (donor) to another (recipient).</p><p><strong>Results: </strong>According to the molecular characterization of specimens, we identified two transmission clusters in the cardiology unit: the first cluster concerned patients tested positive for the HV.1/EG.5.1.6 lineage, while the second cluster concerned patients tested positive for the FL.10.1 lineage. Moreover, evaluating the bottleneck size, we were able to solve SARS-CoV-2 transmission chain among infected patients.</p><p><strong>Conclusion: </strong>Our method shows that it is possible to conduct a tracing study using a genomic approach based on iSNVs analysis.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"331"},"PeriodicalIF":4.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872835","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}

{"title":"Targeting SARS-CoV-2 main protease: a comprehensive approach using advanced virtual screening, molecular dynamics, and in vitro validation.","authors":"Smbat Gevorgyan, Hamlet Khachatryan, Anastasiya Shavina, Sajjad Gharaghani, Hovakim Zakaryan","doi":"10.1186/s12985-024-02607-4","DOIUrl":"https://doi.org/10.1186/s12985-024-02607-4","url":null,"abstract":"<p><p>The COVID-19 pandemic, driven by the SARS-CoV-2 virus, necessitates the development of effective therapeutics. The main protease of the virus, Mpro, is a key target due to its crucial role in viral replication. Our study presents a novel approach combining ligand-based pharmacophore modeling with structure-based advanced virtual screening to identify potential inhibitors of Mpro. We screened around 200 million compounds using this integrated methodology, resulting in a shortlist of promising compounds. These were further scrutinized through molecular dynamics simulations, revealing their interaction dynamics with Mpro. Subsequent in vitro assays using the Mpro enzyme identified two compounds exhibiting significant micromolar inhibitory activity. These findings provide valuable scaffolds for the development of advanced therapeutics targeting Mpro. The comprehensive nature of our approach, spanning computational predictions to experimental validations, offers a robust pathway for rapid and efficient identification of potential drug candidates against COVID-19.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"330"},"PeriodicalIF":4.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872637","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}

{"title":"Calceolarioside B inhibits SARS-CoV-2 Omicron BA.2 variant cell entry and modulates immune response.","authors":"Xiao-Bin Lin, Yu-Zhi Yao, Qi-Rong Wen, Fu-Bin Liu, Yuan-Xuan Cai, Rui-Hong Chen, Jin Han","doi":"10.1186/s12985-024-02566-w","DOIUrl":"https://doi.org/10.1186/s12985-024-02566-w","url":null,"abstract":"<p><p>This study evaluated the inhibitory effects of calceolarioside B, extracted from the traditional Chinese herb Mutong (Akebia quinata Thumb), on the SARS-CoV-2 Omicron BA.2 variant. Molecular docking and molecular dynamics simulations predicted the binding sites and interactions between calceolarioside B and the Omicron BA.2 spike (S) protein. Biolayer interferometry (BLI) and immunofluorescence assays validated its high-affinity binding. Pseudovirus entry assays assessed the inhibitory effects of calceolarioside B on viral entry into host cells, while enzyme-linked immunosorbent assay (ELISA) measured inflammatory cytokine levels. Flow cytometry was used to analyze its effects on macrophage phenotype switching. Results demonstrated that calceolarioside B could bind to the Omicron BA.2 S protein with high affinity, and significantly inhibited viral entry into host cells by interfering with the binding of angiotensin-converting enzyme 2 (ACE2) receptor and S protein. Additionally, calceolarioside B reduced IL(interleukin)-6 expression levels and promoted the switch of macrophages from the pro-inflammatory M1 phenotype to the anti-inflammatory M2 phenotype. These findings suggest that calceolarioside B possesses antiviral and immunomodulatory effects, making it a potential dual-function inhibitor for the treatment of COVID-19.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"329"},"PeriodicalIF":4.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872629","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}

{"title":"Evolutionary dynamics of PRRS virus in Italian Pig farms: a retrospective study.","authors":"Giovanni Parisio, Giovanni Franzo, Ilaria Barbieri, Valentina Carta, Tomasz Stadejek, Sonia Manenti, Debora Campagna, Silvia Faccini, Greta Vignola, Giovanni L Alborali, Maria B Boniotti","doi":"10.1186/s12985-024-02569-7","DOIUrl":"https://doi.org/10.1186/s12985-024-02569-7","url":null,"abstract":"<p><p>Porcine Reproductive and Respiratory Syndrome (PRRS) causes huge economic losses to pig farms worldwide. Currently available vaccines do not always offer complete protection, due to the extreme variability of the virus. Therefore, good farming practices must be improved to prevent the disease from spreading across the pig production system. In this study, we inferred the dynamics of PRRSV population in Italy by applying bayesian methods on our ORF7 sequence dataset collected during a 15-years period. Random subsets from the overall dataset were built to reduce analysis runtime. Calculated evolutionary rate was consistent between subsets and with other findings on PRRSV and other RNA viruses (4-7 × 10^- 3 substitution/site/year) while Time to the Most Recent Common Ancestor was less consistent (from 1980 to 1990). Despite this, in all population dynamic reconstructions, a massive increase in size calculated in early 2000s lasting until around 2010 was inferred. This spike is followed by very heterogeneous dynamics with some differences between subsets, probably due to the random sampling. Geographical origin was inferred in Emilia-Romagna region despite Lombardy being the region with the highest number of farmed animals and farm size. These findings reflect the choices regarding farm management and biosecurity taken in the last two decades, and not strictly related to PRRS. Phylogeny and phylogeography are powerful tools to better understand microorganisms population dynamics and make appropriate choices for disease control.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"326"},"PeriodicalIF":4.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872631","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}

{"title":"The role of inflammatory gene polymorphisms in severe COVID-19: a review.","authors":"Jia Qi Yip, Adrian Oo, Yan Ling Ng, Kim Ling Chin, Kim-Kee Tan, Justin Jang Hann Chu, Sazaly AbuBakar, Nurhafiza Zainal","doi":"10.1186/s12985-024-02597-3","DOIUrl":"10.1186/s12985-024-02597-3","url":null,"abstract":"<p><p>The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has profoundly impacted global healthcare systems and spurred extensive research efforts over the past three years. One critical aspect of the disease is the intricate interplay between the virus and the host immune response, particularly the role of inflammatory gene expression in severe COVID-19. While numerous previous studies have explored the role of genetic polymorphisms in COVID-19, research specifically focusing on inflammatory genes and their associations with disease severity remains limited. This review explores the relationship between severe COVID-19 outcomes and genetic polymorphisms within key inflammatory genes. By investigating the impact of genetic variations on immune responses, which include cytokine production and downstream signalling pathways, we aim to provide a comprehensive overview of how genetic polymorphisms contribute to the variability in disease presentation. Through an in-depth analysis of existing literature, we shed light on potential therapeutic targets and personalized approaches that may enhance our understanding of disease pathogenesis and treatment strategies.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"327"},"PeriodicalIF":4.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872828","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}

{"title":"Identification and phylogenetic analysis of Jingmen tick virus in ticks and sheep from Henan Province, China.","authors":"Baicheng Xia, Zhenhua Li, Wenbing Zhu, Zhen Wu, Yuli Zhang, Yujing Zhu, Hengyi Sun, Guoyu Niu","doi":"10.1186/s12985-024-02587-5","DOIUrl":"https://doi.org/10.1186/s12985-024-02587-5","url":null,"abstract":"<p><p>Jingmen tick virus (JMTV) is a novel segmented Flavivirus that was first identified from Rhipicephalus microplus in the Jingmen region of Hubei Province, China, in 2010. Subsequently, it was detected in a variety of countries and regions around the world. Meanwhile, JMTV has been proved to be pathogenic to humans and animals and could cause viremia in animals. However, the pathogenic mechanism of JMTV and what role animals play in the viral cycle have not yet been elucidated. In this study, 38 sheep sera were collected from Xinyang region of Henan Province, China and 204 ticks attached to the sheep were collected. The qRT-PCR and nested PCR were used to confirm the presence of JMTV in serum and tick samples. The results showed that the positive rate of JMTV in serum and ticks was 13.16% (5/38) and 7.84% (16/204), respectively. Phylogenetic analysis showed that JMTV sequences in sheep and ticks shared a high degree of identity with each other, and JMTV was relatively conserved in evolution. These results enriched the evidence for the prevalence of JMTV in animals and further deepened our understanding of the mechanisms and routes of JMTV transmission.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"325"},"PeriodicalIF":4.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872649","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}

{"title":"Safety, pharmacokinetics, and antiviral efficacy of the novel capsid assembly modulator GST-HG141 in patients with chronic hepatitis B: a phase 1 trial with a randomized, placebo-controlled design.","authors":"Min Wu, Jiajia Mai, Hong Zhang, George Zhang, John Mao, Yanan Tang, Wenhao Yan, Wenqiang Wu, Jinlin Hou, Xieer Liang, Zhihong Liu, Yanhua Ding, Junqi Niu","doi":"10.1186/s12985-024-02584-8","DOIUrl":"https://doi.org/10.1186/s12985-024-02584-8","url":null,"abstract":"<p><p>In preclinical studies, GST-HG141, a novel hepatitis B virus (HBV) capsid assembly modulator displayed potent anti-HBV activity in vitro and strong efficacy in HBV animal models. A randomized, double-blind, ascending phase 1b trial assessed the pharmacokinetics, safety, and efficacy of GST-HG141 in chronic hepatitis B (CHB) individuals. Thirty treatment-naïve CHB patients were enrolled in three cohorts (25, 50, and 100 mg twice orally after meals daily) over 28 days, with 10 subjects per cohort (8:2 ratio for GST-HG141 and placebo). Dose-related safety and tolerability, pharmacokinetic profiles, and drug responses were evaluated. GST-HG141 exhibited a generally favorable safety profile across all doses with predominantly mild adverse reactions, including three cases of grade 1 transaminase elevations. Significant reductions in HBV DNA and pregenomic RNA (pgRNA) levels were observed across all doses of (25, 50, and 100 mg of GST-HG141, twice-daily) after 28 days of treatment. Pharmacokinetic analysis showed a consistent linear trend in GST-HG141 concentrations, with mean trough concentrations ranging from 75 to 240 ng/mL. These concentrations adequately covered the protein binding-adjusted EC50 (16.89 ng/mL) by factors of 4.4, 11.1, and 14.6 for doses of 25, 50, and 100 mg, respectively. Our study demonstrated GST-HG141's well-tolerated profile up to 100 mg over 4 weeks, alongside robust antiviral activity in CHB patients, supporting its progression into further clinical investigation for CHB management.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"328"},"PeriodicalIF":4.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872592","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}

{"title":"CRISPR/Cas12a and recombinase polymerase amplification-based rapid on-site nucleic acid detection of duck circovirus.","authors":"Qi-Zhang Liang, Wei Chen, Rong-Chang Liu, Qiu-Ling Fu, Guang-Hua Fu, Long-Fei Cheng, Hong-Mei Chen, Nan-Song Jiang, Ting Zhu, Yu Huang","doi":"10.1186/s12985-024-02577-7","DOIUrl":"https://doi.org/10.1186/s12985-024-02577-7","url":null,"abstract":"<p><strong>Background: </strong>Duck circovirus (DuCV) infections commonly induce immunosuppression and secondary infections in ducks, resulting in significant economic losses in the duck breeding industry. Currently, effective vaccines and treatments for DuCV have been lacking. Therefore, rapid, specific, and sensitive detection methods are crucial for preventing and controlling DuCV.</p><p><strong>Methods: </strong>A lateral flow strip (LFS) detection method was developed using recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a). The RPA-CRISPR/Cas12a-LFS targeted the DuCV replication protein (Rep) and was operated at 37 ℃ and allowed for visual interpretation without requiring sophisticated equipment.</p><p><strong>Results: </strong>The results revealed that the reaction time of RPA-CRISPR/Cas12a-LFS is only 45 min. This method achieved a low detection limit of 2.6 gene copies. Importantly, this method demonstrated high specificity and no cross-reactivity with six other avian viruses. In a study involving 97 waterfowl samples, the Rep RPA-CRISPR/Cas12a-LFS showed 100% consistency and agreement with real-time quantitative polymerase chain reaction.</p><p><strong>Conclusion: </strong>These findings underscored the potential of this user-friendly, rapid, sensitive, and accurate detection method for on-site DuCV detection.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"21 1","pages":"322"},"PeriodicalIF":4.0,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865252","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}