Journal of Virology最新文献

{"title":"Distinct region-specific neutralization profiles of contemporary HIV-1 clade C against best-in-class broadly neutralizing antibodies.","authors":"Jyoti Sutar, Priyanka Jayal, Ranajoy Mullick, Sangeeta Chaudhary, Prajakta Kamble, Shilpa Bhowmick, Snehal Kaginkar, Varsha Padwal, Pratik Devadiga, Namrata Neman, Dale Kitchin, Haajira Kaldine, Nonhlanhla N Mkhize, Bongiwe Ndlovu, Kamini Gounder, Sohini Mukherjee, Shweta Shrivas, Neha Sharma, Chaman Prasad, Sonia Tewatia, Nainika Parihar, Naresh Kumar, Nandini Kasarpalkar, Balwant Singh, Shobha Mohapatra, Mohammad Aquil, C Vishal Kumar, Thongadi Ramesh Dinesha, Aylur Kailasom Srikrishnan, Jayanthi Shastri, Sachee Agrawal, Sushma Gaikwad, Sayantani Mondal, Bhaswati Bandyopadhyay, Subhasish Kamal Guha, Dipesh Kale, Debasis Biswas, Dhanashree Patil, Ramesh S Paranjape, Satyajit Mukhopadhyay, Hema, Ritika Das, Anand Kondapi, Vikrant Bhor, Suprit Deshpande, Devin Sok, Thumbi Ndung'u, Penny L Moore, Kailapuri Gangatharan Murugavel, Vainav Patel, Jayanta Bhattacharya","doi":"10.1128/jvi.00008-25","DOIUrl":"https://doi.org/10.1128/jvi.00008-25","url":null,"abstract":"<p><p>While broadly neutralizing antibodies (bnAbs) have been clinically shown to prevent HIV-1 acquisition, their relative effectiveness against regionally relevant HIV-1 forms is not clear. In the present study, we examined the extent of neutralization susceptibility of contemporary HIV-1 Indian clade C at a population level along with a head-to-head comparison with that from South Africa against a panel of clinically relevant best-in-class bnAbs. Env-pseudotyped viruses encoding HIV-1 India clade C <i>env</i> were found to be best neutralized by the V3 glycan-directed bnAbs (10-1074 and BG18) and select CD4 binding site (CD4bs)-directed bnAbs (VRC07, N6, and 1-18); however, they demonstrated significant resistance to V1/V2 apex-directed bnAbs. Interestingly, the magnitude of the neutralization sensitivity differed between contemporary India and South Africa clade C. Neutralization resistance to key bnAbs was observed to be associated with differences in residues on Env that form bnAb contact sites, gp120 loop lengths, and potential N-linked glycans. Notably, the second generation CD4bs bnAbs (VRC07, N6, 1-18) showed neutralization of VRC01- and 3BNC117-resistant viruses but with two- to sevenfold reduced potency compared to the VRC01-sensitive counterparts, likely due to the enrichment of resistance-associated residues observed in loop D. Predictive analysis indicated that the combination of BG18, N6, and PGDM1400 can provide over 95% neutralization coverage of contemporary India clade C at 1 µg/mL (IC80), an observation distinct from that observed with Africa clade C. Our study clearly highlights that both the complementarity of bnAb classes and the regionally relevant HIV-1 forms are important in achieving clinical effectiveness.IMPORTANCEWhile the development of vaccines to prevent HIV infection remains a global priority, their potential effectiveness is limited by the extraordinarily diversified circulating forms of HIV-1. The prospect of best-in-class broadly neutralizing antibodies (bnAbs) as a potential prevention option has been demonstrated in several studies, including the phase 2b Antibody-Mediated Prevention trials; however, to be broadly applicable, bnAbs will need to overcome the substantial variability of HIV <i>env</i> circulating globally, beyond the regions where efficacy trials are conducted. The present study highlights that the region-specific contemporary HIV-1 clade C viruses not only vary in their degree of susceptibility to the best-in-class clinically relevant bnAbs, but also are evolving at a population level to become increasingly resistant to the best-in-class bnAbs. Overall, the outcome of this study highlights the need for periodic assessment of sequence and neutralization profiles of the circulating regionally relevant HIV-1 forms toward prioritizing the bnAb combination suitable for effective intervention.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0000825"},"PeriodicalIF":4.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rubella virus mutations that confer resistance to inactivation at low pH.","authors":"Pratyush Kumar Das, Margaret Kielian","doi":"10.1128/jvi.00255-25","DOIUrl":"https://doi.org/10.1128/jvi.00255-25","url":null,"abstract":"","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0025525"},"PeriodicalIF":4.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Drosophila melanogaster</i> Toll-9 elicits antiviral immunity against Drosophila C virus.","authors":"Manish Chauhan, Peter E Martinak, Benjamin M Hollenberg, Alan G Goodman","doi":"10.1128/jvi.02214-24","DOIUrl":"https://doi.org/10.1128/jvi.02214-24","url":null,"abstract":"<p><p>The Toll pathway plays a pivotal role in innate immune responses against pathogens. The evolutionarily conserved pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), play a crucial role in recognition of pathogen-associated molecular patterns (PAMPs). The <i>Drosophila</i> genome encodes nine Toll receptors that are orthologous to mammalian TLRs. While mammalian TLRs directly recognize PAMPs, most <i>Drosophila</i> Tolls recognize the proteolytically cleaved ligand Spätzle to activate downstream signaling cascades. In this study, we demonstrated that Toll-9 is crucial for antiviral immunity against Drosophila C virus (DCV), a natural pathogen of <i>Drosophila</i>. A transposable element insertion in the <i>Toll-9</i> gene renders the flies more susceptible to DCV. The stable expression of Toll-9 in <i>Drosophila</i> S2 cells results in increased <i>Dicer2</i> induction and reduced AKT phosphorylation, collectively establishing an antiviral state that inhibits DCV replication. Toll-9 localizes to endosomes, where it binds viral double-stranded RNA (dsRNA), highlighting its role in detecting viral replication intermediates. Together, these findings identify Toll-9 as a key player in antiviral immunity against DCV infection, acting through its ability to recognize dsRNA and drive <i>Dicer2</i> expression, along with other AKT-mediated antiviral responses.</p><p><strong>Importance: </strong>Insects rely on innate immunity and RNA interference (RNAi) to combat viral infections. Our study underscores the pivotal role of <i>Drosophila</i> Toll-9 in antiviral immunity, aligning with findings in <i>Bombyx mori</i>, where Toll-9 activation upregulates the RNAi component <i>Dicer2</i>. We demonstrate that <i>Drosophila</i> Toll-9 functions as a pattern recognition receptor (PRR) for double-stranded RNA (dsRNA) during Drosophila C virus (DCV) infection, akin to mammalian Toll-like receptors (TLRs). Toll-9 activation during DCV infection leads to the upregulation of <i>Dicer2</i> and <i>Argonaute2</i> and dephosphorylation of AKT. This study also reveals that Toll-9 localizes in endosomal compartments where it interacts with dsRNA. These insights enhance our understanding of <i>Drosophila</i> innate immune mechanisms, reflecting the evolutionary conservation of immune responses across diverse species and providing impetus for further research into the conserved roles of TLRs across the animal kingdom.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0221424"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A single amino acid mutation in VP1 of coxsackievirus A6 determining efficiency of VP0 cleavage and proliferation.","authors":"Yihao Sun, ShaSha Qian, Yaxin Du, Jiahui Wu, Hadireya Rehemutula, Shengli Meng, Zejun Wang, Jing Guo, Shuo Shen","doi":"10.1128/jvi.00128-25","DOIUrl":"https://doi.org/10.1128/jvi.00128-25","url":null,"abstract":"<p><p>Coxsackievirus A6 (CV-A6) has emerged as a major pathogen associated with hand, foot, and mouth disease (HFMD), capable of infecting both children and adults. However, currently, there is no effective vaccine to prevent HFMD caused by non-EV-A71 enteroviruses. In this study, a pair of CV-A6 strains was selected from a rhabdomyosarcoma (RD)-isolated and Vero-adapted stock with a difference of 7 nucleotides in their genomes, resulting in three amino acid mutations in the structural proteins. Distinct differences in propagation, virulence in cells, and plaque size were observed. A series of single-site mutants was constructed, and a single mutation in VP1-143 was mapped to associate with phenotype changes. The mutation from glycine to arginine at VP1-143 dramatically increased infectivity but decreased virulence, growth rate, and plaque size. Furthermore, the experiments using both purified whole virus and full particle (FP) demonstrated that glycine-to-arginine mutation increased VP0 cleavage efficiency because of decreased VP0/VP2 ratio. The decrease in VP0 cleavage efficiency led to the accumulation of non-infectious provirion. The efficiency of virus transmission between cells determined the rates of viral RNA (vRNA) and protein synthesis and was related to fast-slow growth and virulence phenotypes. In addition, the data indicated that the mutation did not affect the encapsidation of the genomic RNA, and the ratio of empty and full particles was unchanged. The results are important for understanding the mechanism of VP0 cleavage regulation and are relevant to developing vaccines and therapeutic reagents against CV-A6 infection and diseases.</p><p><strong>Importance: </strong>CV-A6 is a major pathogen in the context of HFMD. The cost of treatment and hospitalization of children with HFMD may have a considerable financial impact on the families of patients. CV-A6 is a member of picornaviruses and forms infectious virion through maturation cleavage of VP0 into VP4 and VP2. Although it is well accepted that the autocatalytic process involves viral RNA, the detailed mechanism remains unclear. In this study, residues in VP1-143 were demonstrated to regulate the efficiency of VP0 cleavage and affect the ratio of provirion and virion. Glycine-to-arginine mutation was tolerant, not abolished, but affected the efficiency of VP0 cleavage. The results support a theory that residue mutations on a structural protein of a serotype/genotype within enteroviruses, not well-conserved across picornaviruses and far away from the VP0 cleavage site on the outside surface, regulate the efficiency of VP0 cleavage and render phenotypically different strains.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0012825"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ANP32 proteins from ticks and vertebrates are key host factors for replication of Bourbon virus across species.","authors":"Zhenyu Zhang, Ishmael D Aziati, Thomas Nipper, Adrianus C M Boon, Andrew Mehle","doi":"10.1128/jvi.00522-25","DOIUrl":"https://doi.org/10.1128/jvi.00522-25","url":null,"abstract":"<p><p>Bourbon virus (BRBV) is a tick-borne virus in the genus <i>Thogotovirus</i> in the <i>Orthomyxoviridae</i> family. BRBV was initially identified as the presumptive causative agent of a fatal human infection in 2014 and has since been identified in ticks in the Midwest, Northeast, and Southern United States, with occasional spillovers into humans. However, little is known about how virus-host interactions impact their large host range. Here, we show that BRBV polymerase activity in human cells is completely dependent on cellular ANP32 proteins. BRBV polymerase activity was completely lost in cells lacking ANP32A and ANP32B, resulting in failed infections. BRBV polymerase activity was restored in the presence of ANP32 proteins from diverse hosts. Dhori virus and Thogoto virus, other related <i>Thogotovirus</i> members, retained high activity in the absence of ANP32 proteins, showing reduced dependence on these host factors. Interaction studies revealed that the BRBV polymerase trimer binds human ANP32A or ANP32B. Genetic analysis revealed that tick vectors for BRBV encode a single <i>ANP32</i> locus corresponding to <i>ANP32A</i>. Tick <i>ANP32A</i> produces multiple protein variants through alternative splicing and start-site selection, all of which enhance polymerase activity for <i>Thogotoviruses</i>. Unexpectedly, the BRBV polymerase was highly sensitive to changes at the N-terminus of ANP32, while it was insensitive to changes in the body of ANP32 that restrict the activity of influenza virus polymerases. Thus, ANP32A is a deeply conserved pro-viral cofactor, and <i>Thogotoviruses</i> show remarkable plasticity utilizing ANP32 homologs from different hosts separated by almost 1 billion years of evolution.IMPORTANCEViral polymerases rely on cellular cofactors to support efficient transcription of viral genes and replication of the viral genome. The RNA-dependent RNA polymerase of influenza virus, an orthomyxovirus, requires the cellular ANP32A or ANP32B proteins for genome replication. However, little is known about whether ANP32 proteins are required by other orthomyxovirus family members, like the tick-borne thogotoviruses. We show that thogotoviruses use ANP32 proteins from diverse hosts to enhance polymerase activity, including that encoded by the single <i>ANP32A</i> gene found in ticks. However, thogotovirus polymerase showed varying levels of dependence on ANP32 proteins, with some polymerases functioning at near full activity even in the absence of ANP32 proteins. Thus, ANP32 proteins are deeply conserved viral cofactors, with each virus displaying distinct patterns of ANP32 usage and requirements for function.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0052225"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissection of the global responses of mandarin fish pyloric cecum to an acute ranavirus (MRV) infection reveals the formation of serositis and then ascites.","authors":"Wenfeng Zhang, Yong Li, Xiaosi Wu, Qianqian Sun, Yuting Fu, Shaoping Weng, Jianguo He, Chuanfu Dong","doi":"10.1128/jvi.02308-24","DOIUrl":"https://doi.org/10.1128/jvi.02308-24","url":null,"abstract":"<p><p>Mandarin fish ranavirus (MRV), a new member of the species <i>Ranavirus micropterus1</i>, sharing over 98% whole-genome nucleotide identity with the well-known largemouth bass virus (LMBV), is a distinct member of the genus <i>Ranavirus</i> within the family <i>Iridoviridae</i>. Our recent work showed that acute MRV infection predominantly affects the pyloric cecum, a critical visceral organ in mandarin fish, and was hypothesized to drive the characteristic external clinical sign of severe ascites. In this study, we reveal that acute MRV infection initially targets the serosal layer of the pyloric cecum of mandarin fish, leading to rapid progression into fibrinous serositis characterized by serosal hypertrophy, fibrosis, hyperemia, edema, and tissue adhesions. Using single-cell RNA sequencing, we dissect the cellular composition of epithelial, immune, and stromal populations, identifying significant enrichment of macrophages and granulocytes, alongside T and natural killer cells, as key mediators of acute cytokine and inflammatory responses. Then, robust experimental evidence demonstrates that MRV infects specific immune cell subsets of T and B cells and stromal cells of fibroblasts, myofibroblasts, endothelial cells, and pericytes, resulting in upregulation of genes and pathways associated with extracellular matrix (ECM) formation, collagen biosynthesis, and vascular remodeling in the hyperplastic serosal zone. Additionally, both host-derived type V collagens and MRV-encoded collagens are implicated in ECM formation in the hypertrophic serosa. Collectively, this study provides a comprehensive single-cell resolution analysis of the pyloric cecum's response to acute MRV infection and highlights virus-driven serositis as the underlying cause of severe ascites in mandarin fish.IMPORTANCEThe pyloric cecum is a vital digestive and immune organ in many bony fish species, including the mandarin fish, a carnivorous species with an exceptionally developed pyloric cecum comprising 207-326 ceca per individual. While MRV/LMBV infects various fish species, severe ascites is uniquely observed in infected mandarin fish. This study demonstrates that acute MRV infection induces fibrinous serositis in the pyloric cecum, characterized by hyperemia, edema, and hyperplasia, ultimately resulting in ascites and mortality. Leveraging single-cell RNA sequencing, we provide a detailed landscape of the cell types affected or involved in the inflammatory response, revealing their roles in the pathogenesis of serositis. These findings advance our understanding of MRV-induced pathology and its species-specific manifestations.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0230824"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143978020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage therapy: a promising approach for <i>Staphylococcus aureus</i> diabetic foot infections.","authors":"Lucile Plumet, Chloé Magnan, Denis Costechareyre, Albert Sotto, Jean-Philippe Lavigne, Virginie Molle","doi":"10.1128/jvi.00458-25","DOIUrl":"https://doi.org/10.1128/jvi.00458-25","url":null,"abstract":"<p><p>Diabetic foot infections (DFIs), predominantly caused by <i>Staphylococcus aureus</i>, pose a significant healthcare challenge with severe consequences, including amputation. Phage therapy, which utilizes bacteriophages to specifically target bacterial pathogens, has emerged as a promising alternative to conventional antibiotic treatments. This review evaluates the efficacy of phage therapy as a complementary treatment for DFIs caused by <i>S. aureus</i>, synthesizing evidence from preclinical and clinical studies while addressing the limitations and challenges associated with current research. The analysis highlights promising results from diabetic animal models, demonstrating effective bacterial load reduction and improved wound healing. Clinical case reports and series further underline significant improvements in infection management and ulcer healing, with no major adverse effects reported. Ongoing clinical trials are also discussed, offering insights into the study parameters evaluating phage therapy potential efficacy and safety for <i>S. aureus</i>-related DFIs. While the collected data highlight the potential of phage therapy as a valuable complement to traditional antibiotic treatments, particularly in managing antibiotic-resistant infections, further research is essential to address existing limitations, including gaps in long-term efficacy data and challenges in standardization. With continued investigation, phage therapy holds significant potential to alleviate the healthcare burden of DFIs and improve patient outcomes.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0045825"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endothelial cell-released mitochondrial DNA promotes B cell differentiation and virus replication during severe fever with thrombocytopenia syndrome virus infection.","authors":"Yun-Fa Zhang, Ning Cui, Tong Yang, Jin-Xia Wang, Jia-Hao Chen, Xin Yang, Yong-Xiang Wu, Li-Fen Hu, Xiao-Ai Zhang, Qing-Bin Lu, Xin Su, Hao Li, Wei Liu","doi":"10.1128/jvi.01323-24","DOIUrl":"https://doi.org/10.1128/jvi.01323-24","url":null,"abstract":"<p><p>Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease acquired through tick bites. We have previously demonstrated the correlation between SFTSV-induced mitochondrial dysfunction and inflammation induction, disease progression, and fatal outcome. In the current study, our clinical observation study establishes a strong correlation between elevated levels of circulating cell-free mtDNA and poor prognosis. <i>In vivo</i> studies further reveal endothelial cells as an important source responsible for releasing mtDNA into circulation, which promotes B cell activation, migration, and differentiation via Toll-like receptor 9 (TLR9). Notably, TLR9 activation enhances B-cell susceptibility to SFTSV infection. These findings suggest that mtDNA released by injured endothelial cells facilitates B cell differentiation and virus replication, emphasizing the significant role of mitochondrial damage within endothelial cells in contributing to the severity of SFTS outcomes.IMPORTANCESevere fever with thrombocytopenia syndrome (SFTS) is a new acute tick-borne infectious disease with a high fatality rate of 10%-50%. There is a strong correlation between SFTSV-induced mitochondrial dysfunction and inflammation induction, disease progression, and fatal outcome. Our research has revealed the crucial role of mtDNA in predicting the prognosis of SFTS and its impact on vascular endothelial injuries as well as B cell differentiation, two previously unexplored features of SFTSV infection. Moreover, mtDNA could activate the TLR9 signal to induce plasmablast differentiation in B cells and promote SFTSV infection. This study provides valuable mechanistic and clinical insights into the adverse outcomes associated with SFTSV infection.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0132324"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clicking viruses-with chemistry toward mechanisms in infection.","authors":"Urs F Greber","doi":"10.1128/jvi.00471-25","DOIUrl":"https://doi.org/10.1128/jvi.00471-25","url":null,"abstract":"<p><p>Viruses subvert cells and evade host defense. They emerge unpredictably and threaten humans and livestock through their genetic and phenotypic diversity. Despite more than 100 years since the discovery of viruses, the molecular underpinnings of virus infections are incompletely understood. The introduction of new methodologies into the field, such as that of click chemistry some 10 years ago, keeps uncovering new facets of viruses. Click chemistry uses bio-orthogonal reactions on chemical probes and couples nucleic acids, proteins, and lipids with tractable labels, such as fluorophores for single-cell and single-molecule imaging, or biotin for biochemical profiling of infections. Its applications in single cells often achieve single-molecule resolution and provide important insights into the widely known phenomenon of cell-to-cell infection variability. This review describes click chemistry advances to unravel infection mechanisms of a select set of enveloped and nonenveloped DNA and RNA viruses, including adenovirus, herpesvirus, and human immunodeficiency virus. It highlights recent click chemistry breakthroughs with viral DNA, viral RNA, protein, as well as host-derived lipid functions in both live and chemically fixed cells. It discusses new insights on specific processes including virus entry, uncoating, transcription, replication, packaging, and assembly and provides a perspective for click chemistry to explore viral cell biology, infection variability, and genome organization in the particle.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0047125"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The NSP6-L260F substitution in SARS-CoV-2 BQ.1.1 and XBB.1.16 lineages compensates for the reduced viral polymerase activity caused by mutations in NSP13 and NSP14.","authors":"Yuri Furusawa, Kiyoko Iwatsuki-Horimoto, Seiya Yamayoshi, Yoshihiro Kawaoka","doi":"10.1128/jvi.00656-25","DOIUrl":"https://doi.org/10.1128/jvi.00656-25","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants emerged at the end of 2021, and their subvariants are still circulating worldwide. While changes in the S protein of these variants have been extensively studied, the roles of amino acid substitutions in non-structural proteins have not been fully revealed. In this study, we found that SARS-CoV-2 bearing the NSP6-L260F substitution emerged repeatedly when we generated several SARS-CoV-2 variants by reverse genetics or when we passaged SARS-CoV-2 isolated from clinical samples and that it was selected under cell culture conditions. Although this substitution has been detected in BQ.1.1 and XBB.1.16 that circulated in nature, its effect on viral properties is unclear. Here, we generated SARS-CoV-2 with or without the NSP6-L260F by reverse genetics and found that NSP6-L260F promotes virus replication <i>in vitro</i> and <i>in vivo</i> by increasing viral polymerase activity and enhancing virus pathogenicity in hamsters. We also identified disadvantageous substitutions, NSP13-M233I and NSP14-D222Y, that reduced BQ.1.1 and XBB.1.16 replication, respectively. These adverse effects were compensated for by NSP6-L260F. Our findings suggest the importance of NSP6-L260F for virus replication and pathogenicity and reveal part of the evolutionary process of Omicron variants.IMPORTANCEAlthough the properties of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants continue to change through the acquisition of various amino acid substitutions, the roles of the amino acid substitutions in the non-structural proteins have not been fully explored. In this study, we found that the NSP6-L260F substitution enhances viral polymerase activity and is important for viral replication and pathogenicity. In addition, we found that the NSP13-M233I substitution in the BQ.1.1 lineage and the NSP14-D222Y substitution in the XBB.1.16 lineage reduce viral polymerase activity, and this adverse effect is compensated for by the NSP6-L260F substitution. Our results provide insight into the evolutionary process of SARS-CoV-2.</p>","PeriodicalId":17583,"journal":{"name":"Journal of Virology","volume":" ","pages":"e0065625"},"PeriodicalIF":4.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}