Viruses-Basel最新文献_第10页

Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels. 整合基于序列和结构的相似性度量来划分多个病毒分类水平。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050642

Igor C Dos Santos, Rebecca di Stephano de Souza, Igor Tolstoy, Liliane S Oliveira, Arthur Gruber

{"title":"Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels.","authors":"Igor C Dos Santos, Rebecca di Stephano de Souza, Igor Tolstoy, Liliane S Oliveira, Arthur Gruber","doi":"10.3390/v17050642","DOIUrl":"10.3390/v17050642","url":null,"abstract":"Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, overcoming limitations inherent in sequence-based methods. In this work, we introduce MPACT (Multimetric Pairwise Comparison Tool), an integrated tool that utilizes both sequence- and structure-based metrics. The program incorporates five metrics: sequence identity, similarity, maximum likelihood distance, TM-score, and 3Di-character similarity. MPACT generates heatmaps and distance trees to visualize viral relationships across multiple levels, enabling users to substantiate viral taxa demarcation. Taxa delineation can be achieved by specifying appropriate score cutoffs for each metric, facilitating the definition of viral groups, and storing their corresponding sequence data. By analyzing diverse viral datasets spanning various levels of divergence, we demonstrate MPACT's capability to reveal viral relationships, even among distantly related taxa. This tool provides a comprehensive approach to assist viral classification, exceeding the current methods by integrating multiple metrics and uncovering deeper evolutionary connections.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162765","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

Transcriptomic and Proteomic Profiling of Rabbit Kidney Cells Infected with Equine Herpesvirus 8. 马疱疹病毒8感染兔肾细胞的转录组学和蛋白质组学分析

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050647

Yanfei Ji, Dandan Xu, Wenxuan Si, Yu Zhang, Muhammad Zahoor Khan, Xia Zhao, Wenqiang Liu

{"title":"Transcriptomic and Proteomic Profiling of Rabbit Kidney Cells Infected with Equine Herpesvirus 8.","authors":"Yanfei Ji, Dandan Xu, Wenxuan Si, Yu Zhang, Muhammad Zahoor Khan, Xia Zhao, Wenqiang Liu","doi":"10.3390/v17050647","DOIUrl":"10.3390/v17050647","url":null,"abstract":"The present study investigated the host cell response to EHV-8 infection in rabbit kidney (RK-13) cells through transcriptomic and proteomic approaches. At 24 h post-infection, a total of 2118 differentially expressed genes (DEGs) were identified, with 1338 upregulated and 780 downregulated. At 48 h, 7388 DEGs were detected, with 4342 upregulated and 3046 downregulated genes. Proteomic analysis revealed 932 differentially expressed proteins (DEPs) at 24 h (364 upregulated and 568 downregulated) and 3866 DEPs at 48 h (2285 upregulated and 1581 downregulated). Of these, 237 upregulated and 336 downregulated proteins were common across both time points. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the majority of DEGs and DEPs were enriched in key inflammation-related pathways, notably the TNF and NF-κB signaling pathways. Validation of the transcriptomic and proteomic data was performed using RT-PCR and parallel reaction monitoring (PRM), respectively, and confirmed consistent trends for TNFR1, NF-κB p65, and MAP3K8, as reported in the transcriptomic and proteomic screening. These findings suggest that EHV-8 infection may modulate host immune responses by activating the TNF signaling pathway. However, given that RK-13 cells may not fully replicate viral-host interactions in equine species, further in vivo studies in horses and donkeys are required to provide a more comprehensive understanding of the viral pathogenesis in these animals.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163253","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

PKM2 Facilitates Classical Swine Fever Virus Replication by Enhancing NS5B Polymerase Function. PKM2通过增强NS5B聚合酶功能促进猪瘟病毒复制。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050648

Mengzhao Song, Shanchuan Liu, Yan Luo, Tiantian Ji, Yanming Zhang, Wen Deng

{"title":"PKM2 Facilitates Classical Swine Fever Virus Replication by Enhancing NS5B Polymerase Function.","authors":"Mengzhao Song, Shanchuan Liu, Yan Luo, Tiantian Ji, Yanming Zhang, Wen Deng","doi":"10.3390/v17050648","DOIUrl":"10.3390/v17050648","url":null,"abstract":"Host metabolic reprogramming is a critical strategy employed by many viruses to support their replication, and the key metabolic enzyme plays important roles in virus infection. This study investigates the role of pyruvate kinase M2 (PKM2), a glycolytic enzyme with non-canonical functions, in the replication of classical swine fever virus (CSFV). Using PK-15 cells and piglet models, we demonstrate that CSFV infection upregulates PKM2 expression both in vitro and in vivo, creating a proviral environment. knockdown of PKM2 by siRNA reduced CSFV proliferation, while PKM2 overexpression significantly increased virus propagation, which was evaluated by viral protein synthesis, genome replication, and progeny virion production. A direct interaction between PKM2 and CSFV NS5B protein was identified by co-immunoprecipitation and GST-pulldown assays, and PKM2 affected NS5B polymerase activity in a dual-luciferase reporter assay, with PKM2 depletion reducing RdRp function by 50%. Temporal analysis of the first viral replication cycle confirmed PKM2-dependent enhancement of CSFV RNA synthesis. These findings establish PKM2 as a proviral host factor that directly binds NS5B to potentiate RdRp activity, thereby bridging metabolic adaptation and viral genome replication. This study provides new evidence of a glycolytic enzyme physically interacting and enhancing viral polymerase function, offering new information about CSFV-host interaction.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163534","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

Individuals Infected with SARS-CoV-2 Prior to COVID-19 Vaccination Maintain Vaccine-Induced RBD-Specific Antibody Levels and Viral Neutralization Activity for One Year. 在接种COVID-19疫苗之前感染SARS-CoV-2的个体可维持疫苗诱导的rbd特异性抗体水平和病毒中和活性一年。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050640

Christina S Mcconney, Devin Kenney, Christina S Ennis, Erika L Smith-Mahoney, Maria Jose Ayuso, Jiabao Zhong, Florian Douam, Manish Sagar, Jennifer E Snyder-Cappione

{"title":"Individuals Infected with SARS-CoV-2 Prior to COVID-19 Vaccination Maintain Vaccine-Induced RBD-Specific Antibody Levels and Viral Neutralization Activity for One Year.","authors":"Christina S Mcconney, Devin Kenney, Christina S Ennis, Erika L Smith-Mahoney, Maria Jose Ayuso, Jiabao Zhong, Florian Douam, Manish Sagar, Jennifer E Snyder-Cappione","doi":"10.3390/v17050640","DOIUrl":"10.3390/v17050640","url":null,"abstract":"The effectiveness of multiple COVID-19 vaccinations in individuals with a history of SARS-CoV-2 infection remains unclear; specifically, elucidation of the durability of anti-viral antibody responses could provide important insights for epidemiological applications. We utilized the BU ELISA protocol to measure the circulating SARS-CoV-2 receptor-binding domain (RBD) and nucleocapsid (N) specific IgG and IgA antibody levels in a cohort of individuals infected with SARS-CoV-2 in the spring of 2020, with the sample collection spanning six months to two years post-symptom onset. Further, we interrogated the neutralization activity of these samples against the ancestral SARS-CoV-2 (WA-1) and Delta and Omicron (BA.1) variants. Consistent with previous studies, we found a more rapid waning of anti-N compared to anti-RBD antibodies in months prior to the first vaccinations. Vaccine-induced antibody responses in individuals previously infected with SARS-CoV-2 were elevated and sustained for more than one year post-vaccination. Similarly, neutralization activity against WA-1, Delta, and Omicron increased and remained higher than pre-vaccination levels for one year after the first COVID-19 vaccine dose. Collectively, these results indicate that infection followed by vaccination yields robust antibody responses against SARS-CoV-2 that endure for one year. These results suggest that an annual booster would stably boost anti-SARS-CoV-2 antibody responses, preventing infection and disease.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162681","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

Human Microglia Models for NeuroHIV. 神经hiv的人类小胶质细胞模型。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050641

Priyanka Sarkar, Xu Wang, Wenhui Hu, Jian Zhu, Wen-Zhe Ho

引用次数: 0

Concurrent Circulation of Canine Distemper Virus (South America-4 Lineage) at the Wild-Domestic Canid Interface in Aburrá Valley, Colombia. 犬瘟热病毒（南美-4系）在哥伦比亚aburr<e:1>谷野生-家养犬科动物界面同时传播。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050649

Carolina Rios-Usuga, Melissa C Ortiz-Pineda, Sergio Daniel Aguirre-Catolico, Víctor H Quiroz, Julian Ruiz-Saenz

{"title":"Concurrent Circulation of Canine Distemper Virus (South America-4 Lineage) at the Wild-Domestic Canid Interface in Aburrá Valley, Colombia.","authors":"Carolina Rios-Usuga, Melissa C Ortiz-Pineda, Sergio Daniel Aguirre-Catolico, Víctor H Quiroz, Julian Ruiz-Saenz","doi":"10.3390/v17050649","DOIUrl":"10.3390/v17050649","url":null,"abstract":"Canine distemper virus (CDV) is the causative agent of a widespread infectious disease affecting both domestic and wild carnivores. Owing to its ability to cross species barriers and its high fatality rate in unvaccinated animals, CDV poses a significant conservation threat to endangered wildlife worldwide. To date, two distinct CDV lineages have been reported in Colombia, with cases documented separately in domestic dogs and wild peri-urban carnivores. This study aimed to detect and characterize the concurrent circulation of CDV in naturally infected domestic dogs and crab-eating foxes (Cerdocyon thous) from the same area in Colombia. Through molecular and phylogenetic analyses, we identified the South America/North America-4 lineage infecting both populations simultaneously. Our findings revealed high genetic variability, multiple virus reintroductions, and a close relationship with CDV strains previously detected in the United States. These results confirm the simultaneous circulation of CDV in the domestic and wildlife interface and underscore the urgent need for an integrated approach to CDV prevention and control involving both domestic and wildlife health interventions.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163191","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

Advancements and Perspectives in Nanotechnology and Nanomedicine. 纳米技术与纳米医学的进展与展望。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050638

Olga Morozova

引用次数: 0

Sequences and Structures of Viral Proteins Linked to the Genomes (VPg) of RNA Viruses. RNA病毒基因组（VPg）连接病毒蛋白的序列和结构。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050645

Catherine H Schein

{"title":"Sequences and Structures of Viral Proteins Linked to the Genomes (VPg) of RNA Viruses.","authors":"Catherine H Schein","doi":"10.3390/v17050645","DOIUrl":"10.3390/v17050645","url":null,"abstract":"In the mid-1970s, it was revealed that the 5' end of the RNA genome of poliovirus (PV) was covalently linked to a peptide called VPg (viral protein, genome-linked). Subsequently, VPgs have been found attached to many other viruses and even phages. This review summarizes the patterns of physicochemical properties that are conserved within the VPgs of plus-strand RNA viruses where short-peptide VPgs have been identified. Mutagenesis and structural data indicate the importance of a 5 aa conserved motif at the N-termini of picornaviral VPgs (around the tyrosine 3 residue, which forms a covalent bond to UMP and the RNA). Hidden Markov models have been used to find motifs and VPgs in additional genera of picornaviruses, as well as dicistroviruses in insects and comoviruses in plants. These latter VPgs are bound to the RNA termina through linkages to serine or threonine. The role of free VPg and VPgpU needs clarification, especially in light of multiple genome copies in many of the viruses. Lysine and other positively charged side chains are hallmarks of VPgs. These may contribute to interactions with the viral RNA, polymerase, membranes and cellular proteins. The larger protein VPgs from potyviruses and noroviruses/caliciviruses may also show some areas of similar properties to these small peptides.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163542","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

Tissue-Specific Transcriptomic Responses to Avian Reovirus Inoculation in Ovo. 禽呼肠孤病毒接种蛋的组织特异性转录组反应。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050646

Zubair Khalid, Shahna Fathima, Ruediger Hauck

{"title":"Tissue-Specific Transcriptomic Responses to Avian Reovirus Inoculation in Ovo.","authors":"Zubair Khalid, Shahna Fathima, Ruediger Hauck","doi":"10.3390/v17050646","DOIUrl":"10.3390/v17050646","url":null,"abstract":"Avian reovirus (ARV) infections significantly impact the global poultry industry, but host responses across infection models remain poorly characterized. Using specific-pathogen-free chicken embryos, this study examined tissue-specific transcriptomic changes following in ovo inoculation with two doses of ARV S1133 at embryonic day 18. Quantitative PCR confirmed dose- and time-dependent viral replication, with the liver exhibiting the highest viral load at 24 h post-inoculation (hpi), whereas the kidneys, intestines, and bursa were only positive at 48 hpi with the higher viral dose. Transcriptomic profiling revealed the intestines mounted an extensive gene expression response, implicating early immune activation. Liver samples demonstrated strong upregulation of antiviral pathways, including interferon signaling and viral replication inhibition, while kidneys and intestines were enriched for coagulation and wound healing pathways. The bursae exhibited minimal immunity-related responses, suggesting insufficient maturation. Functional analyses confirmed tissue-specific immune and metabolic adaptations to infection. These findings indicate that ARV replication efficiency and host molecular responses are dose-, tissue-, and time-dependent. Notably, intestinal responses suggest preemptive immune engagement, while hepatic antiviral mechanisms may play a critical role in restricting viral spread. This study establishes foundational knowledge of host molecular responses to ARV in late-stage embryos, with implications for in ovo vaccination and early immunity.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163204","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

High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic. 高通量测序揭示了捷克共和国苹果病毒组多样性和新病毒。

IF 3.8 3区医学

Viruses-Basel Pub Date : 2025-04-29 DOI: 10.3390/v17050650

Karima Ben Mansour, Igor Koloniuk, Jana Brožová, Marcela Komínková, Jaroslava Přibylová, Tatiana Sarkisova, Jiří Sedlák, Josef Špak, Petr Komínek

{"title":"High-Throughput Sequencing Reveals Apple Virome Diversity and Novel Viruses in the Czech Republic.","authors":"Karima Ben Mansour, Igor Koloniuk, Jana Brožová, Marcela Komínková, Jaroslava Přibylová, Tatiana Sarkisova, Jiří Sedlák, Josef Špak, Petr Komínek","doi":"10.3390/v17050650","DOIUrl":"10.3390/v17050650","url":null,"abstract":"Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. Additionally, two novel viruses, ARWV1 and ARWV2 were identified for the first time in the Czech Republic. Phylogenetic analyses showed low genetic variability among ARWV2 isolates, suggesting a possible recent introduction or limited diversification. In contrast, ARWV1 isolates displayed distinct clustering in the coat protein coding region, separating symptomatic and asymptomatic samples, indicating a potential involvement of genetic determinants in symptom expression. Mixed infections were prevalent, with multiple molecular variants of ACLSV, ASPV, and AGCaV detected within individual samples, along with co-infections involving viruses from different families. Recombination analysis identified frequent recombination events in ACLSV and ASPV, often involving non-apple parental sequences, suggesting their potential for cross-host infections. Additionally, an interspecific recombination event was detected in an almond ApMV isolate, with PNRSV as a minor parent. These findings highlight the impact of agricultural practices on viral evolution and host adaptation. This study demonstrates the utility of HTS as a powerful tool for uncovering viral diversity, recombination events, and evolutionary dynamics.","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":"17 5","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163435","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